Daily Papers

In this work, we introduce OmniGen2, a versatile and open-source generative model designed to provide a unified solution for diverse generation tasks, including text-to-image, image editing, and in-context generation. Unlike OmniGen v1, OmniGen2 features two distinct decoding pathways for text and image modalities, utilizing unshared parameters and a decoupled image tokenizer. This design enables OmniGen2 to build upon existing multimodal understanding models without the need to re-adapt VAE inputs, thereby preserving the original text generation capabilities. To facilitate the training of OmniGen2, we developed comprehensive data construction pipelines, encompassing image editing and in-context generation data. Additionally, we introduce a reflection mechanism tailored for image generation tasks and curate a dedicated reflection dataset based on OmniGen2. Despite its relatively modest parameter size, OmniGen2 achieves competitive results on multiple task benchmarks, including text-to-image and image editing. To further evaluate in-context generation, also referred to as subject-driven tasks, we introduce a new benchmark named OmniContext. OmniGen2 achieves state-of-the-art performance among open-source models in terms of consistency. We will release our models, training code, datasets, and data construction pipeline to support future research in this field. Project Page: https://vectorspacelab.github.io/OmniGen2; GitHub Link: https://github.com/VectorSpaceLab/OmniGen2

A critical component of a successful language generation pipeline is the decoding algorithm. However, the general principles that should guide the choice of decoding algorithm remain unclear. Previous works only compare decoding algorithms in narrow scenarios and their findings do not generalize across tasks. To better structure the discussion, we introduce a taxonomy that groups decoding strategies based on their implicit assumptions about how well the model's likelihood is aligned with the task-specific notion of utility. We argue that this taxonomy allows a broader view of the decoding problem and can lead to generalizable statements because it is grounded on the interplay between the decoding algorithms and the likelihood-utility misalignment. Specifically, by analyzing the correlation between the likelihood and the utility of predictions across a diverse set of tasks, we provide the first empirical evidence supporting the proposed taxonomy, and a set of principles to structure reasoning when choosing a decoding algorithm. Crucially, our analysis is the first one to relate likelihood-based decoding strategies with strategies that rely on external information such as value-guided methods and prompting, and covers the most diverse set of tasks up-to-date.

In enhancing the reasoning capabilities of large language models (LLMs), prior research primarily focuses on specific prompting techniques such as few-shot or zero-shot chain-of-thought (CoT) prompting. These methods, while effective, often involve manually intensive prompt engineering. Our study takes a novel approach by asking: Can LLMs reason effectively without prompting? Our findings reveal that, intriguingly, CoT reasoning paths can be elicited from pre-trained LLMs by simply altering the decoding process. Rather than conventional greedy decoding, we investigate the top-k alternative tokens, uncovering that CoT paths are frequently inherent in these sequences. This approach not only bypasses the confounders of prompting but also allows us to assess the LLMs' intrinsic reasoning abilities. Moreover, we observe that the presence of a CoT in the decoding path correlates with a higher confidence in the model's decoded answer. This confidence metric effectively differentiates between CoT and non-CoT paths. Extensive empirical studies on various reasoning benchmarks show that the proposed CoT-decoding substantially outperforms the standard greedy decoding.

Genetic pathways usually encode molecular mechanisms that can inform targeted interventions. It is often challenging for existing machine learning approaches to jointly model genetic pathways (higher-order features) and variants (atomic features), and present to clinicians interpretable models. In order to build more accurate and better interpretable machine learning models for genetic medicine, we introduce Pathway Augmented Nonnegative Tensor factorization for HighER-order feature learning (PANTHER). PANTHER selects informative genetic pathways that directly encode molecular mechanisms. We apply genetically motivated constrained tensor factorization to group pathways in a way that reflects molecular mechanism interactions. We then train a softmax classifier for disease types using the identified pathway groups. We evaluated PANTHER against multiple state-of-the-art constrained tensor/matrix factorization models, as well as group guided and Bayesian hierarchical models. PANTHER outperforms all state-of-the-art comparison models significantly (p<0.05). Our experiments on large scale Next Generation Sequencing (NGS) and whole-genome genotyping datasets also demonstrated wide applicability of PANTHER. We performed feature analysis in predicting disease types, which suggested insights and benefits of the identified pathway groups.

Inference-time optimization scales computation to derive deliberate reasoning steps for effective performance. While previous search-based strategies address the short-sightedness of auto-regressive generation, the vast search space leads to excessive exploration and insufficient exploitation. To strike an efficient balance to derive the optimal step, we frame the decoding strategy as foresight sampling, leveraging simulated future steps to obtain globally optimal step estimation. Built on it, we propose a novel decoding strategy, named phi-Decoding. To provide a precise and expressive estimation of step value, phi-Decoding approximates two distributions via foresight and clustering. Sampling from the joint distribution, the optimal steps can be selected for exploitation. To support adaptive computation allocation, we propose in-width and in-depth pruning strategies, featuring a light-weight solution to achieve inference efficiency. Extensive experiments across seven benchmarks show phi-Decoding outperforms strong baselines in both performance and efficiency. Additional analysis demonstrates its generalization across various LLMs and scalability across a wide range of computing budgets. The code will be released at https://github.com/xufangzhi/phi-Decoding, and the open-source PyPI package is coming soon.

Pathology diagnosis based on EEG signals and decoding brain activity holds immense importance in understanding neurological disorders. With the advancement of artificial intelligence methods and machine learning techniques, the potential for accurate data-driven diagnoses and effective treatments has grown significantly. However, applying machine learning algorithms to real-world datasets presents diverse challenges at multiple levels. The scarcity of labelled data, especially in low regime scenarios with limited availability of real patient cohorts due to high costs of recruitment, underscores the vital deployment of scaling and transfer learning techniques. In this study, we explore a real-world pathology classification task to highlight the effectiveness of data and model scaling and cross-dataset knowledge transfer. As such, we observe varying performance improvements through data scaling, indicating the need for careful evaluation and labelling. Additionally, we identify the challenges of possible negative transfer and emphasize the significance of some key components to overcome distribution shifts and potential spurious correlations and achieve positive transfer. We see improvement in the performance of the target model on the target (NMT) datasets by using the knowledge from the source dataset (TUAB) when a low amount of labelled data was available. Our findings indicate a small and generic model (e.g. ShallowNet) performs well on a single dataset, however, a larger model (e.g. TCN) performs better on transfer and learning from a larger and diverse dataset.

We propose to improve transformers of a specific modality with irrelevant data from other modalities, e.g., improve an ImageNet model with audio or point cloud datasets. We would like to highlight that the data samples of the target modality are irrelevant to the other modalities, which distinguishes our method from other works utilizing paired (e.g., CLIP) or interleaved data of different modalities. We propose a methodology named Multimodal Pathway - given a target modality and a transformer designed for it, we use an auxiliary transformer trained with data of another modality and construct pathways to connect components of the two models so that data of the target modality can be processed by both models. In this way, we utilize the universal sequence-to-sequence modeling abilities of transformers obtained from two modalities. As a concrete implementation, we use a modality-specific tokenizer and task-specific head as usual but utilize the transformer blocks of the auxiliary model via a proposed method named Cross-Modal Re-parameterization, which exploits the auxiliary weights without any inference costs. On the image, point cloud, video, and audio recognition tasks, we observe significant and consistent performance improvements with irrelevant data from other modalities. The code and models are available at https://github.com/AILab-CVC/M2PT.

To mitigate the high inference latency stemming from autoregressive decoding in Large Language Models (LLMs), Speculative Decoding has emerged as a novel decoding paradigm for LLM inference. In each decoding step, this method first efficiently drafts several future tokens and then verifies them in parallel. Unlike autoregressive decoding, Speculative Decoding facilitates the simultaneous decoding of multiple tokens per step, thereby accelerating inference. This paper presents a comprehensive overview and analysis of this promising decoding paradigm. We begin by providing a formal definition and formulation of Speculative Decoding. Then, we organize in-depth discussions on its key facets, including current leading techniques, the challenges faced, and potential future directions in this field. We aim for this work to serve as a catalyst for further research on Speculative Decoding, ultimately contributing to more efficient LLM inference.

In recent years, large-scale transformer decoders such as the GPT-x family of models have become increasingly popular. Studies examining the behavior of these models tend to focus only on the output of the language modeling head and avoid analysis of the internal states of the transformer decoder. In this study, we present a collection of methods to analyze the hidden states of GPT-2 and use the model's navigation of garden path sentences as a case study. To enable this, we compile the largest currently available dataset of garden path sentences. We show that Manhattan distances and cosine similarities provide more reliable insights compared to established surprisal methods that analyze next-token probabilities computed by a language modeling head. Using these methods, we find that negating tokens have minimal impacts on the model's representations for unambiguous forms of sentences with ambiguity solely over what the object of a verb is, but have a more substantial impact of representations for unambiguous sentences whose ambiguity would stem from the voice of a verb. Further, we find that analyzing the decoder model's hidden states reveals periods of ambiguity that might conclude in a garden path effect but happen not to, whereas surprisal analyses routinely miss this detail.

The end-to-end nature of neural machine translation (NMT) removes many ways of manually guiding the translation process that were available in older paradigms. Recent work, however, has introduced a new capability: lexically constrained or guided decoding, a modification to beam search that forces the inclusion of pre-specified words and phrases in the output. However, while theoretically sound, existing approaches have computational complexities that are either linear (Hokamp and Liu, 2017) or exponential (Anderson et al., 2017) in the number of constraints. We present a algorithm for lexically constrained decoding with a complexity of O(1) in the number of constraints. We demonstrate the algorithms remarkable ability to properly place these constraints, and use it to explore the shaky relationship between model and BLEU scores. Our implementation is available as part of Sockeye.

In recent years, many interpretability methods have been proposed to help interpret the internal states of Transformer-models, at different levels of precision and complexity. Here, to analyze encoder-decoder Transformers, we propose a simple, new method: DecoderLens. Inspired by the LogitLens (for decoder-only Transformers), this method involves allowing the decoder to cross-attend representations of intermediate encoder layers instead of using the final encoder output, as is normally done in encoder-decoder models. The method thus maps previously uninterpretable vector representations to human-interpretable sequences of words or symbols. We report results from the DecoderLens applied to models trained on question answering, logical reasoning, speech recognition and machine translation. The DecoderLens reveals several specific subtasks that are solved at low or intermediate layers, shedding new light on the information flow inside the encoder component of this important class of models.

Neural decoding, the process of understanding how brain activity corresponds to different stimuli, has been a primary objective in cognitive sciences. Over the past three decades, advancements in functional Magnetic Resonance Imaging and machine learning have greatly improved our ability to map visual stimuli to brain activity, especially in the visual cortex. Concurrently, research has expanded into decoding more complex processes like language and memory across the whole brain, utilizing techniques to handle greater variability and improve signal accuracy. We argue that "seeing" involves more than just mapping visual stimuli onto the visual cortex; it engages the entire brain, as various emotions and cognitive states can emerge from observing different scenes. In this paper, we develop algorithms to enhance our understanding of visual processes by incorporating whole-brain activation maps while individuals are exposed to visual stimuli. We utilize large-scale fMRI encoders and Image generative models pre-trained on large public datasets, which are then fine-tuned through Image-fMRI contrastive learning. Our models hence can decode visual experience across the entire cerebral cortex, surpassing the traditional confines of the visual cortex. We first compare our method with state-of-the-art approaches to decoding visual processing and show improved predictive semantic accuracy by 43%. A network ablation analysis suggests that beyond the visual cortex, the default mode network contributes most to decoding stimuli, in line with the proposed role of this network in sense-making and semantic processing. Additionally, we implemented zero-shot imagination decoding on an extra validation dataset, achieving a p-value of 0.0206 for mapping the reconstructed images and ground-truth text stimuli, which substantiates the model's capability to capture semantic meanings across various scenarios.

Information flows by routes inside the network via mechanisms implemented in the model. These routes can be represented as graphs where nodes correspond to token representations and edges to operations inside the network. We automatically build these graphs in a top-down manner, for each prediction leaving only the most important nodes and edges. In contrast to the existing workflows relying on activation patching, we do this through attribution: this allows us to efficiently uncover existing circuits with just a single forward pass. Additionally, the applicability of our method is far beyond patching: we do not need a human to carefully design prediction templates, and we can extract information flow routes for any prediction (not just the ones among the allowed templates). As a result, we can talk about model behavior in general, for specific types of predictions, or different domains. We experiment with Llama 2 and show that the role of some attention heads is overall important, e.g. previous token heads and subword merging heads. Next, we find similarities in Llama 2 behavior when handling tokens of the same part of speech. Finally, we show that some model components can be specialized on domains such as coding or multilingual texts.

Decoding methods play an indispensable role in converting language models from next-token predictors into practical task solvers. Prior research on decoding methods, primarily focusing on task-specific models, may not extend to the current era of general-purpose large language models (LLMs). Moreover, the recent influx of decoding strategies has further complicated this landscape. This paper provides a comprehensive and multifaceted analysis of various decoding methods within the context of LLMs, evaluating their performance, robustness to hyperparameter changes, and decoding speeds across a wide range of tasks, models, and deployment environments. Our findings reveal that decoding method performance is notably task-dependent and influenced by factors such as alignment, model size, and quantization. Intriguingly, sensitivity analysis exposes that certain methods achieve superior performance at the cost of extensive hyperparameter tuning, highlighting the trade-off between attaining optimal results and the practicality of implementation in varying contexts.

Every day, the human brain processes an immense volume of visual information, relying on intricate neural mechanisms to perceive and interpret these stimuli. Recent breakthroughs in functional magnetic resonance imaging (fMRI) have enabled scientists to extract visual information from human brain activity patterns. In this study, we present an innovative method for decoding brain activity into meaningful images and captions, with a specific focus on brain captioning due to its enhanced flexibility as compared to brain decoding into images. Our approach takes advantage of cutting-edge image captioning models and incorporates a unique image reconstruction pipeline that utilizes latent diffusion models and depth estimation. We utilized the Natural Scenes Dataset, a comprehensive fMRI dataset from eight subjects who viewed images from the COCO dataset. We employed the Generative Image-to-text Transformer (GIT) as our backbone for captioning and propose a new image reconstruction pipeline based on latent diffusion models. The method involves training regularized linear regression models between brain activity and extracted features. Additionally, we incorporated depth maps from the ControlNet model to further guide the reconstruction process. We evaluate our methods using quantitative metrics for both generated captions and images. Our brain captioning approach outperforms existing methods, while our image reconstruction pipeline generates plausible images with improved spatial relationships. In conclusion, we demonstrate significant progress in brain decoding, showcasing the enormous potential of integrating vision and language to better understand human cognition. Our approach provides a flexible platform for future research, with potential applications in various fields, including neural art, style transfer, and portable devices.

Drug discovery is a complex and time-intensive process that requires identifying and validating new therapeutic candidates. Computational approaches using large-scale biomedical knowledge graphs (KGs) offer a promising solution to accelerate this process. However, extracting meaningful insights from large-scale KGs remains challenging due to the complexity of graph traversal. Existing subgraph-based methods are tailored to graph neural networks (GNNs), making them incompatible with other models, such as large language models (LLMs). We introduce K-Paths, a retrieval framework that extracts structured, diverse, and biologically meaningful paths from KGs. Integrating these paths enables LLMs and GNNs to effectively predict unobserved drug-drug and drug-disease interactions. Unlike traditional path-ranking approaches, K-Paths retrieves and transforms paths into a structured format that LLMs can directly process, facilitating explainable reasoning. K-Paths employs a diversity-aware adaptation of Yen's algorithm to retrieve the K shortest loopless paths between entities in an interaction query, prioritizing biologically relevant and diverse relationships. Our experiments on benchmark datasets show that K-Paths improves the zero-shot performance of Llama 8.1B's F1-score by 12.45 points on drug repurposing and 13.42 points on interaction severity prediction. We also show that Llama 70B achieves F1-score gains of 6.18 and 8.46 points, respectively. K-Paths also improves the supervised training efficiency of EmerGNN, a state-of-the-art GNN, by reducing KG size by 90% while maintaining strong predictive performance. Beyond its scalability and efficiency, K-Paths uniquely bridges the gap between KGs and LLMs, providing explainable rationales for predicted interactions. These capabilities show that K-Paths is a valuable tool for efficient data-driven drug discovery.

A central goal for mechanistic interpretability has been to identify the right units of analysis in large language models (LLMs) that causally explain their outputs. While early work focused on individual neurons, evidence that neurons often encode multiple concepts has motivated a shift toward analyzing directions in activation space. A key question is how to find directions that capture interpretable features in an unsupervised manner. Current methods rely on dictionary learning with sparse autoencoders (SAEs), commonly trained over residual stream activations to learn directions from scratch. However, SAEs often struggle in causal evaluations and lack intrinsic interpretability, as their learning is not explicitly tied to the computations of the model. Here, we tackle these limitations by directly decomposing MLP activations with semi-nonnegative matrix factorization (SNMF), such that the learned features are (a) sparse linear combinations of co-activated neurons, and (b) mapped to their activating inputs, making them directly interpretable. Experiments on Llama 3.1, Gemma 2 and GPT-2 show that SNMF derived features outperform SAEs and a strong supervised baseline (difference-in-means) on causal steering, while aligning with human-interpretable concepts. Further analysis reveals that specific neuron combinations are reused across semantically-related features, exposing a hierarchical structure in the MLP's activation space. Together, these results position SNMF as a simple and effective tool for identifying interpretable features and dissecting concept representations in LLMs.

Autoregressive decoding limits the efficiency of transformers for Machine Translation (MT). The community proposed specific network architectures and learning-based methods to solve this issue, which are expensive and require changes to the MT model, trading inference speed at the cost of the translation quality. In this paper, we propose to address the problem from the point of view of decoding algorithms, as a less explored but rather compelling direction. We propose to reframe the standard greedy autoregressive decoding of MT with a parallel formulation leveraging Jacobi and Gauss-Seidel fixed-point iteration methods for fast inference. This formulation allows to speed up existing models without training or modifications while retaining translation quality. We present three parallel decoding algorithms and test them on different languages and models showing how the parallelization introduces a speedup up to 38% w.r.t. the standard autoregressive decoding and nearly 2x when scaling the method on parallel resources. Finally, we introduce a decoding dependency graph visualizer (DDGviz) that let us see how the model has learned the conditional dependence between tokens and inspect the decoding procedure.

Despite the progress in machine translation quality estimation and evaluation in the last years, decoding in neural machine translation (NMT) is mostly oblivious to this and centers around finding the most probable translation according to the model (MAP decoding), approximated with beam search. In this paper, we bring together these two lines of research and propose quality-aware decoding for NMT, by leveraging recent breakthroughs in reference-free and reference-based MT evaluation through various inference methods like N-best reranking and minimum Bayes risk decoding. We perform an extensive comparison of various possible candidate generation and ranking methods across four datasets and two model classes and find that quality-aware decoding consistently outperforms MAP-based decoding according both to state-of-the-art automatic metrics (COMET and BLEURT) and to human assessments. Our code is available at https://github.com/deep-spin/qaware-decode.

Recent studies have revealed a number of pathologies of neural machine translation (NMT) systems. Hypotheses explaining these mostly suggest there is something fundamentally wrong with NMT as a model or its training algorithm, maximum likelihood estimation (MLE). Most of this evidence was gathered using maximum a posteriori (MAP) decoding, a decision rule aimed at identifying the highest-scoring translation, i.e. the mode. We argue that the evidence corroborates the inadequacy of MAP decoding more than casts doubt on the model and its training algorithm. In this work, we show that translation distributions do reproduce various statistics of the data well, but that beam search strays from such statistics. We show that some of the known pathologies and biases of NMT are due to MAP decoding and not to NMT's statistical assumptions nor MLE. In particular, we show that the most likely translations under the model accumulate so little probability mass that the mode can be considered essentially arbitrary. We therefore advocate for the use of decision rules that take into account the translation distribution holistically. We show that an approximation to minimum Bayes risk decoding gives competitive results confirming that NMT models do capture important aspects of translation well in expectation.

Large language model (LLM) decoding involves generating a sequence of tokens based on a given context, where each token is predicted one at a time using the model's learned probabilities. The typical autoregressive decoding method requires a separate forward pass through the model for each token generated, which is computationally inefficient and poses challenges for deploying LLMs in latency-sensitive scenarios. The main limitations of current decoding methods stem from their inefficiencies and resource demands. Existing approaches either necessitate fine-tuning smaller models, which is resource-intensive, or rely on fixed retrieval schemes to construct drafts for the next tokens, which lack adaptability and fail to generalize across different models and contexts. To address these issues, we introduce a novel methodology called ADED, which accelerates LLM decoding without requiring fine-tuning. Our approach involves an adaptive draft-verification process that evolves over time to improve efficiency. We utilize a tri-gram matrix-based LLM representation to dynamically approximate the output distribution of the LLM, allowing the model to adjust to changing token probabilities during the decoding process. Additionally, we implement a draft construction mechanism that effectively balances exploration and exploitation, ensuring that the drafts generated are both diverse and close to the true output distribution of the LLM. The importance of this design lies in its ability to optimize the draft distribution adaptively, leading to faster and more accurate decoding. Through extensive experiments on various benchmark datasets and LLM architectures, we demonstrate that ADED significantly accelerates the decoding process while maintaining high accuracy, making it suitable for deployment in a wide range of practical applications.

Efficient inference in large language models (LLMs) has become a critical focus as their scale and complexity grow. Traditional autoregressive decoding, while effective, suffers from computational inefficiencies due to its sequential token generation process. Speculative decoding addresses this bottleneck by introducing a two-stage framework: drafting and verification. A smaller, efficient model generates a preliminary draft, which is then refined by a larger, more sophisticated model. This paper provides a comprehensive survey of speculative decoding methods, categorizing them into draft-centric and model-centric approaches. We discuss key ideas associated with each method, highlighting their potential for scaling LLM inference. This survey aims to guide future research in optimizing speculative decoding and its integration into real-world LLM applications.

Given a prefix (context), open-ended generation aims to decode texts that are coherent, which do not abruptly drift from previous topics, and informative, which do not suffer from undesired repetitions. In this paper, we propose Look-back, an improved decoding algorithm that leverages the Kullback-Leibler divergence to track the distribution distance between current and historical decoding steps. Thus Look-back can automatically predict potential repetitive phrase and topic drift, and remove tokens that may cause the failure modes, restricting the next token probability distribution within a plausible distance to the history. We perform decoding experiments on document continuation and story generation, and demonstrate that Look-back is able to generate more fluent and coherent text, outperforming other strong decoding methods significantly in both automatic and human evaluations.

Decoding language from brain activity is a long-awaited goal in both healthcare and neuroscience. Major milestones have recently been reached thanks to intracranial devices: subject-specific pipelines trained on invasive brain responses to basic language tasks now start to efficiently decode interpretable features (e.g. letters, words, spectrograms). However, scaling this approach to natural speech and non-invasive brain recordings remains a major challenge. Here, we propose a single end-to-end architecture trained with contrastive learning across a large cohort of individuals to predict self-supervised representations of natural speech. We evaluate our model on four public datasets, encompassing 169 volunteers recorded with magneto- or electro-encephalography (M/EEG), while they listened to natural speech. The results show that our model can identify, from 3s of MEG signals, the corresponding speech segment with up to 72.5% top-10 accuracy out of 1,594 distinct segments (and 44% top-1 accuracy), and up to 19.1% out of 2,604 segments for EEG recordings -- hence allowing the decoding of phrases absent from the training set. Model comparison and ablation analyses show that these performances directly benefit from our original design choices, namely the use of (i) a contrastive objective, (ii) pretrained representations of speech and (iii) a common convolutional architecture simultaneously trained across several participants. Together, these results delineate a promising path to decode natural language processing in real time from non-invasive recordings of brain activity.

The recent development of chain-of-thought (CoT) decoding has enabled large language models (LLMs) to generate explicit logical reasoning paths for complex problem-solving. However, research indicates that these paths are not always deliberate and optimal. The tree-of-thought (ToT) method employs tree-searching to extensively explore the reasoning space and find better reasoning paths that CoT decoding might overlook. This deliberation, however, comes at the cost of significantly increased inference complexity. In this work, we demonstrate that fine-tuning LLMs leveraging the search tree constructed by ToT allows CoT to achieve similar or better performance, thereby avoiding the substantial inference burden. This is achieved through Chain of Preference Optimization (CPO), where LLMs are fine-tuned to align each step of the CoT reasoning paths with those of ToT using the inherent preference information in the tree-search process. Extensive experimental results show that CPO significantly improves LLM performance in solving a variety of complex problems, including question answering, fact verification, and arithmetic reasoning, demonstrating its effectiveness. Our code is available at https://github.com/sail-sg/CPO.

Conditional neural text generation models generate high-quality outputs, but often concentrate around a mode when what we really want is a diverse set of options. We present a search algorithm to construct lattices encoding a massive number of generation options. First, we restructure decoding as a best-first search, which explores the space differently than beam search and improves efficiency by avoiding pruning paths. Second, we revisit the idea of hypothesis recombination: we can identify pairs of similar generation candidates during search and merge them as an approximation. On both summarization and machine translation, we show that our algorithm encodes thousands of diverse options that remain grammatical and high-quality into one lattice. This algorithm provides a foundation for building downstream generation applications on top of massive-scale diverse outputs.

Traditional approaches to semantic parsing (SP) work by training individual models for each available parallel dataset of text-meaning pairs. In this paper, we explore the idea of polyglot semantic translation, or learning semantic parsing models that are trained on multiple datasets and natural languages. In particular, we focus on translating text to code signature representations using the software component datasets of Richardson and Kuhn (2017a,b). The advantage of such models is that they can be used for parsing a wide variety of input natural languages and output programming languages, or mixed input languages, using a single unified model. To facilitate modeling of this type, we develop a novel graph-based decoding framework that achieves state-of-the-art performance on the above datasets, and apply this method to two other benchmark SP tasks.

Methods for knowledge editing and unlearning in large language models seek to edit or remove undesirable knowledge or capabilities without compromising general language modeling performance. This work investigates how mechanistic interpretability -- which, in part, aims to identify model components (circuits) associated to specific interpretable mechanisms that make up a model capability -- can improve the precision and effectiveness of editing and unlearning. We find a stark difference in unlearning and edit robustness when training components localized by different methods. We highlight an important distinction between methods that localize components based primarily on preserving outputs, and those finding high level mechanisms with predictable intermediate states. In particular, localizing edits/unlearning to components associated with the lookup-table mechanism for factual recall 1) leads to more robust edits/unlearning across different input/output formats, and 2) resists attempts to relearn the unwanted information, while also reducing unintended side effects compared to baselines, on both a sports facts dataset and the CounterFact dataset across multiple models. We also find that certain localized edits disrupt the latent knowledge in the model more than any other baselines, making unlearning more robust to various attacks.

Hallucinations in large language models are a widespread problem, yet the mechanisms behind whether models will hallucinate are poorly understood, limiting our ability to solve this problem. Using sparse autoencoders as an interpretability tool, we discover that a key part of these mechanisms is entity recognition, where the model detects if an entity is one it can recall facts about. Sparse autoencoders uncover meaningful directions in the representation space, these detect whether the model recognizes an entity, e.g. detecting it doesn't know about an athlete or a movie. This suggests that models can have self-knowledge: internal representations about their own capabilities. These directions are causally relevant: capable of steering the model to refuse to answer questions about known entities, or to hallucinate attributes of unknown entities when it would otherwise refuse. We demonstrate that despite the sparse autoencoders being trained on the base model, these directions have a causal effect on the chat model's refusal behavior, suggesting that chat finetuning has repurposed this existing mechanism. Furthermore, we provide an initial exploration into the mechanistic role of these directions in the model, finding that they disrupt the attention of downstream heads that typically move entity attributes to the final token.

Large Language Models (LLMs) are increasingly required to generate text that is both factually accurate and diverse across various open-ended applications. However, current stochastic decoding methods struggle to balance such objectives. We introduce Dynamic Focus Decoding (DFD), a novel plug-and-play stochastic approach that resolves this trade-off without requiring additional data, knowledge, or models. DFD adaptively adjusts the decoding focus based on distributional differences across layers, leveraging the modular and hierarchical nature of factual knowledge within LLMs. This dynamic adjustment improves factuality in knowledge-intensive decoding steps and promotes diversity in less knowledge-reliant steps. DFD can be easily integrated with existing decoding methods, enhancing both factuality and diversity with minimal computational overhead. Extensive experiments across seven datasets demonstrate that DFD significantly improves performance, providing a scalable and efficient solution for open-ended text generation.

While large language models have demonstrated exceptional performance across a wide range of tasks, they remain susceptible to hallucinations -- generating plausible yet factually incorrect contents. Existing methods to mitigating such risk often rely on sampling multiple full-length generations, which introduces significant response latency and becomes ineffective when the model consistently produces hallucinated outputs with high confidence. To address these limitations, we introduce Monitoring Decoding (MD), a novel framework that dynamically monitors the generation process and selectively applies in-process interventions, focusing on revising crucial tokens responsible for hallucinations. Instead of waiting until completion of multiple full-length generations, we identify hallucination-prone tokens during generation using a monitor function, and further refine these tokens through a tree-based decoding strategy. This approach ensures an enhanced factual accuracy and coherence in the generated output while maintaining efficiency. Experimental results demonstrate that MD consistently outperforms self-consistency-based approaches in both effectiveness and efficiency, achieving higher factual accuracy while significantly reducing computational overhead.

Transformers exhibit impressive capabilities but are often regarded as black boxes due to challenges in understanding the complex nonlinear relationships between features. Interpreting machine learning models is of paramount importance to mitigate risks, and mechanistic interpretability is in particular of current interest as it opens up a window for guiding manual modifications and reverse-engineering solutions. In this work, we introduce contextual decomposition for transformers (CD-T), extending a prior work on CD for RNNs and CNNs, to address mechanistic interpretation computationally efficiently. CD-T is a flexible interpretation method for transformers. It can capture contributions of combinations of input features or source internal components (e.g. attention heads, feed-forward networks) to (1) final predictions or (2) the output of any target internal component. Using CD-T, we propose a novel algorithm for circuit discovery. On a real-world pathology report classification task: we show CD-T distills a more faithful circuit of attention heads with improved computational efficiency (speed up 2x) than a prior benchmark, path patching. As a versatile interpretation method, CD-T also exhibits exceptional capabilities for local interpretations. CD-T is shown to reliably find words and phrases of contrasting sentiment/topic on SST-2 and AGNews datasets. Through human experiments, we demonstrate CD-T enables users to identify the more accurate of two models and to better trust a model's outputs compared to alternative interpretation methods such as SHAP and LIME.

Transformer models underpin many recent advances in practical machine learning applications, yet understanding their internal behavior continues to elude researchers. Given the size and complexity of these models, forming a comprehensive picture of their inner workings remains a significant challenge. To this end, we set out to understand small transformer models in a more tractable setting: that of solving mazes. In this work, we focus on the abstractions formed by these models and find evidence for the consistent emergence of structured internal representations of maze topology and valid paths. We demonstrate this by showing that the residual stream of only a single token can be linearly decoded to faithfully reconstruct the entire maze. We also find that the learned embeddings of individual tokens have spatial structure. Furthermore, we take steps towards deciphering the circuity of path-following by identifying attention heads (dubbed adjacency heads), which are implicated in finding valid subsequent tokens.

Deciphering visual content from functional Magnetic Resonance Imaging (fMRI) helps illuminate the human vision system. However, the scarcity of fMRI data and noise hamper brain decoding model performance. Previous approaches primarily employ subject-specific models, sensitive to training sample size. In this paper, we explore a straightforward but overlooked solution to address data scarcity. We propose shallow subject-specific adapters to map cross-subject fMRI data into unified representations. Subsequently, a shared deeper decoding model decodes cross-subject features into the target feature space. During training, we leverage both visual and textual supervision for multi-modal brain decoding. Our model integrates a high-level perception decoding pipeline and a pixel-wise reconstruction pipeline guided by high-level perceptions, simulating bottom-up and top-down processes in neuroscience. Empirical experiments demonstrate robust neural representation learning across subjects for both pipelines. Moreover, merging high-level and low-level information improves both low-level and high-level reconstruction metrics. Additionally, we successfully transfer learned general knowledge to new subjects by training new adapters with limited training data. Compared to previous state-of-the-art methods, notably pre-training-based methods (Mind-Vis and fMRI-PTE), our approach achieves comparable or superior results across diverse tasks, showing promise as an alternative method for cross-subject fMRI data pre-training. Our code and pre-trained weights will be publicly released at https://github.com/YulongBonjour/See_Through_Their_Minds.

Autoregressive transformer language models (LMs) possess strong syntactic abilities, often successfully handling phenomena from agreement to NPI licensing. However, the features they use to incrementally process language inputs are not well understood. In this paper, we fill this gap by studying the mechanisms underlying garden path sentence processing in LMs. We ask: (1) Do LMs use syntactic features or shallow heuristics to perform incremental sentence processing? (2) Do LMs represent only one potential interpretation, or multiple? and (3) Do LMs reanalyze or repair their initial incorrect representations? To address these questions, we use sparse autoencoders to identify interpretable features that determine which continuation - and thus which reading - of a garden path sentence the LM prefers. We find that while many important features relate to syntactic structure, some reflect syntactically irrelevant heuristics. Moreover, while most active features correspond to one reading of the sentence, some features correspond to the other, suggesting that LMs assign weight to both possibilities simultaneously. Finally, LMs do not re-use features from garden path sentence processing to answer follow-up questions.

Ever since neural models were adopted in data-to-text language generation, they have invariably been reliant on extrinsic components to improve their semantic accuracy, because the models normally do not exhibit the ability to generate text that reliably mentions all of the information provided in the input. In this paper, we propose a novel decoding method that extracts interpretable information from encoder-decoder models' cross-attention, and uses it to infer which attributes are mentioned in the generated text, which is subsequently used to rescore beam hypotheses. Using this decoding method with T5 and BART, we show on three datasets its ability to dramatically reduce semantic errors in the generated outputs, while maintaining their state-of-the-art quality.

Language models trained on large amounts of data require careful tuning to be safely deployed in real world. We revisit the guided decoding paradigm, where the goal is to augment the logits of the base language model using the scores from a task-specific reward model. We propose a simple but efficient parameterization of the autoregressive reward model enabling fast and effective guided decoding. On detoxification and sentiment control tasks, we show that our efficient parameterization performs on par with RAD, a strong but less efficient guided decoding approach.

We propose controlled decoding (CD), a novel off-policy reinforcement learning method to control the autoregressive generation from language models towards high reward outcomes. CD solves an off-policy reinforcement learning problem through a value function for the reward, which we call a prefix scorer. The prefix scorer is used at inference time to steer the generation towards higher reward outcomes. We show that the prefix scorer may be trained on (possibly) off-policy data to predict the expected reward when decoding is continued from a partially decoded response. We empirically demonstrate that CD is effective as a control mechanism on Reddit conversations corpus. We also show that the modularity of the design of CD makes it possible to control for multiple rewards, effectively solving a multi-objective reinforcement learning problem with no additional complexity. Finally, we show that CD can be applied in a novel blockwise fashion at inference-time, again without the need for any training-time changes, essentially bridging the gap between the popular best-of-K strategy and token-level reinforcement learning. This makes CD a promising approach for alignment of language models.

Mechanistic interpretability seeks to understand the internal mechanisms of machine learning models, where localization -- identifying the important model components -- is a key step. Activation patching, also known as causal tracing or interchange intervention, is a standard technique for this task (Vig et al., 2020), but the literature contains many variants with little consensus on the choice of hyperparameters or methodology. In this work, we systematically examine the impact of methodological details in activation patching, including evaluation metrics and corruption methods. In several settings of localization and circuit discovery in language models, we find that varying these hyperparameters could lead to disparate interpretability results. Backed by empirical observations, we give conceptual arguments for why certain metrics or methods may be preferred. Finally, we provide recommendations for the best practices of activation patching going forwards.

We present the Pathways Autoregressive Text-to-Image (Parti) model, which generates high-fidelity photorealistic images and supports content-rich synthesis involving complex compositions and world knowledge. Parti treats text-to-image generation as a sequence-to-sequence modeling problem, akin to machine translation, with sequences of image tokens as the target outputs rather than text tokens in another language. This strategy can naturally tap into the rich body of prior work on large language models, which have seen continued advances in capabilities and performance through scaling data and model sizes. Our approach is simple: First, Parti uses a Transformer-based image tokenizer, ViT-VQGAN, to encode images as sequences of discrete tokens. Second, we achieve consistent quality improvements by scaling the encoder-decoder Transformer model up to 20B parameters, with a new state-of-the-art zero-shot FID score of 7.23 and finetuned FID score of 3.22 on MS-COCO. Our detailed analysis on Localized Narratives as well as PartiPrompts (P2), a new holistic benchmark of over 1600 English prompts, demonstrate the effectiveness of Parti across a wide variety of categories and difficulty aspects. We also explore and highlight limitations of our models in order to define and exemplify key areas of focus for further improvements. See https://parti.research.google/ for high-resolution images.

Mechanistic interpretability aims to understand model behaviors in terms of specific, interpretable features, often hypothesized to manifest as low-dimensional subspaces of activations. Specifically, recent studies have explored subspace interventions (such as activation patching) as a way to simultaneously manipulate model behavior and attribute the features behind it to given subspaces. In this work, we demonstrate that these two aims diverge, potentially leading to an illusory sense of interpretability. Counterintuitively, even if a subspace intervention makes the model's output behave as if the value of a feature was changed, this effect may be achieved by activating a dormant parallel pathway leveraging another subspace that is causally disconnected from model outputs. We demonstrate this phenomenon in a distilled mathematical example, in two real-world domains (the indirect object identification task and factual recall), and present evidence for its prevalence in practice. In the context of factual recall, we further show a link to rank-1 fact editing, providing a mechanistic explanation for previous work observing an inconsistency between fact editing performance and fact localization. However, this does not imply that activation patching of subspaces is intrinsically unfit for interpretability. To contextualize our findings, we also show what a success case looks like in a task (indirect object identification) where prior manual circuit analysis informs an understanding of the location of a feature. We explore the additional evidence needed to argue that a patched subspace is faithful.

The rapid progress of research aimed at interpreting the inner workings of advanced language models has highlighted a need for contextualizing the insights gained from years of work in this area. This primer provides a concise technical introduction to the current techniques used to interpret the inner workings of Transformer-based language models, focusing on the generative decoder-only architecture. We conclude by presenting a comprehensive overview of the known internal mechanisms implemented by these models, uncovering connections across popular approaches and active research directions in this area.

Brain decoding, a pivotal field in neuroscience, aims to reconstruct stimuli from acquired brain signals, primarily utilizing functional magnetic resonance imaging (fMRI). Currently, brain decoding is confined to a per-subject-per-model paradigm, limiting its applicability to the same individual for whom the decoding model is trained. This constraint stems from three key challenges: 1) the inherent variability in input dimensions across subjects due to differences in brain size; 2) the unique intrinsic neural patterns, influencing how different individuals perceive and process sensory information; 3) limited data availability for new subjects in real-world scenarios hampers the performance of decoding models. In this paper, we present a novel approach, MindBridge, that achieves cross-subject brain decoding by employing only one model. Our proposed framework establishes a generic paradigm capable of addressing these challenges by introducing biological-inspired aggregation function and novel cyclic fMRI reconstruction mechanism for subject-invariant representation learning. Notably, by cycle reconstruction of fMRI, MindBridge can enable novel fMRI synthesis, which also can serve as pseudo data augmentation. Within the framework, we also devise a novel reset-tuning method for adapting a pretrained model to a new subject. Experimental results demonstrate MindBridge's ability to reconstruct images for multiple subjects, which is competitive with dedicated subject-specific models. Furthermore, with limited data for a new subject, we achieve a high level of decoding accuracy, surpassing that of subject-specific models. This advancement in cross-subject brain decoding suggests promising directions for wider applications in neuroscience and indicates potential for more efficient utilization of limited fMRI data in real-world scenarios. Project page: https://littlepure2333.github.io/MindBridge

This technical report describes the design and training of novel speculative decoding draft models, for accelerating the inference speeds of large language models in a production environment. By conditioning draft predictions on both context vectors and sampled tokens, we can train our speculators to efficiently predict high-quality n-grams, which the base model then accepts or rejects. This allows us to effectively predict multiple tokens per inference forward pass, accelerating wall-clock inference speeds of highly optimized base model implementations by a factor of 2-3x. We explore these initial results and describe next steps for further improvements.

Transformers use the dense self-attention mechanism which gives a lot of flexibility for long-range connectivity. Over multiple layers of a deep transformer, the number of possible connectivity patterns increases exponentially. However, very few of these contribute to the performance of the network, and even fewer are essential. We hypothesize that there are sparsely connected sub-networks within a transformer, called information pathways which can be trained independently. However, the dynamic (i.e., input-dependent) nature of these pathways makes it difficult to prune dense self-attention during training. But the overall distribution of these pathways is often predictable. We take advantage of this fact to propose Stochastically Subsampled self-Attention (SSA) - a general-purpose training strategy for transformers that can reduce both the memory and computational cost of self-attention by 4 to 8 times during training while also serving as a regularization method - improving generalization over dense training. We show that an ensemble of sub-models can be formed from the subsampled pathways within a network, which can achieve better performance than its densely attended counterpart. We perform experiments on a variety of NLP, computer vision and graph learning tasks in both generative and discriminative settings to provide empirical evidence for our claims and show the effectiveness of the proposed method.

Stepwise inference protocols, such as scratchpads and chain-of-thought, help language models solve complex problems by decomposing them into a sequence of simpler subproblems. Despite the significant gain in performance achieved via these protocols, the underlying mechanisms of stepwise inference have remained elusive. To address this, we propose to study autoregressive Transformer models on a synthetic task that embodies the multi-step nature of problems where stepwise inference is generally most useful. Specifically, we define a graph navigation problem wherein a model is tasked with traversing a path from a start to a goal node on the graph. Despite is simplicity, we find we can empirically reproduce and analyze several phenomena observed at scale: (i) the stepwise inference reasoning gap, the cause of which we find in the structure of the training data; (ii) a diversity-accuracy tradeoff in model generations as sampling temperature varies; (iii) a simplicity bias in the model's output; and (iv) compositional generalization and a primacy bias with in-context exemplars. Overall, our work introduces a grounded, synthetic framework for studying stepwise inference and offers mechanistic hypotheses that can lay the foundation for a deeper understanding of this phenomenon.

Despite superior reasoning prowess demonstrated by Large Language Models (LLMs) with Chain-of-Thought (CoT) prompting, a lack of understanding prevails around the internal mechanisms of the models that facilitate CoT generation. This work investigates the neural sub-structures within LLMs that manifest CoT reasoning from a mechanistic point of view. From an analysis of LLaMA-2 7B applied to multistep reasoning over fictional ontologies, we demonstrate that LLMs deploy multiple parallel pathways of answer generation for step-by-step reasoning. These parallel pathways provide sequential answers from the input question context as well as the generated CoT. We observe a striking functional rift in the middle layers of the LLM. Token representations in the initial half remain strongly biased towards the pretraining prior, with the in-context taking over abruptly in the later half. This internal phase shift manifests in different functional components: attention heads that write the answer token predominantly appear in the later half, attention heads that move information along ontological relationships appear exclusively in the initial half, and so on. To the best of our knowledge, this is the first attempt towards mechanistic investigation of CoT reasoning in LLMs.

We present a conditional text generation framework that posits sentential expressions of possible causes and effects. This framework depends on two novel resources we develop in the course of this work: a very large-scale collection of English sentences expressing causal patterns CausalBank; and a refinement over previous work on constructing large lexical causal knowledge graphs Cause Effect Graph. Further, we extend prior work in lexically-constrained decoding to support disjunctive positive constraints. Human assessment confirms that our approach gives high-quality and diverse outputs. Finally, we use CausalBank to perform continued training of an encoder supporting a recent state-of-the-art model for causal reasoning, leading to a 3-point improvement on the COPA challenge set, with no change in model architecture.

We introduce Reward-Guided Speculative Decoding (RSD), a novel framework aimed at improving the efficiency of inference in large language models (LLMs). RSD synergistically combines a lightweight draft model with a more powerful target model, incorporating a controlled bias to prioritize high-reward outputs, in contrast to existing speculative decoding methods that enforce strict unbiasedness. RSD employs a process reward model to evaluate intermediate decoding steps and dynamically decide whether to invoke the target model, optimizing the trade-off between computational cost and output quality. We theoretically demonstrate that a threshold-based mixture strategy achieves an optimal balance between resource utilization and performance. Extensive evaluations on challenging reasoning benchmarks, including Olympiad-level tasks, show that RSD delivers significant efficiency gains against decoding with the target model only (up to 4.4x fewer FLOPs), while achieving significant better accuracy than parallel decoding method on average (up to +3.5). These results highlight RSD as a robust and cost-effective approach for deploying LLMs in resource-intensive scenarios.

Large language models (LLMs) exhibit strong reasoning abilities, often attributed to few-shot or zero-shot chain-of-thought (CoT) prompting. While effective, these methods require labor-intensive prompt engineering, raising the question of whether reasoning can be induced without reliance on explicit prompts. In this work, we unlock the reasoning capabilities of LLMs without explicit prompting. Inspired by zero-shot CoT and CoT-decoding, we propose a novel decoding strategy that systematically nudges LLMs to continue reasoning, thereby preventing immature reasoning processes. Specifically, we monitor the model's generation and inject a designated phrase whenever it is likely to conclude its response prematurely, before completing the reasoning process. Our experimental evaluations on diverse reasoning benchmarks demonstrate that our proposed strategy substantially improves LLM reasoning capabilities, highlighting the potential of decoding-based interventions as an alternative to traditional prompting techniques.

Recent advances with large language models (LLM) illustrate their diverse capabilities. We propose a novel algorithm, staged speculative decoding, to accelerate LLM inference in small-batch, on-device scenarios. We address the low arithmetic intensity of small-batch inference by improving upon previous work in speculative decoding. First, we restructure the speculative batch as a tree, which reduces generation costs and increases the expected tokens per batch. Second, we add a second stage of speculative decoding. Taken together, we reduce single-batch decoding latency by 3.16x with a 762M parameter GPT-2-L model while perfectly preserving output quality.

Recently, Large Vision-Language Models (LVLMs) have demonstrated impressive capabilities in multi-modal context comprehension. However, they still suffer from hallucination problems referring to generating inconsistent outputs with the image content. To mitigate hallucinations, previous studies mainly focus on retraining LVLMs with custom datasets. Although effective, they inherently come with additional computational costs. In this paper, we propose a training-free framework, MVP, that aims to reduce hallucinations by making the most of the innate capabilities of the LVLMs via Multi-View Multi-Path Reasoning. Specifically, we first devise a multi-view information-seeking strategy to thoroughly perceive the comprehensive information in the image, which enriches the general global information captured by the original vision encoder in LVLMs. Furthermore, during the answer decoding, we observe that the occurrence of hallucinations has a strong correlation with the certainty of the answer tokens. Thus, we propose multi-path reasoning for each information view to quantify and aggregate the certainty scores for each potential answer among multiple decoding paths and finally decide the output answer. By fully grasping the information in the image and carefully considering the certainty of the potential answers when decoding, our MVP can effectively reduce hallucinations in LVLMs.The extensive experiments verify that our proposed MVP significantly mitigates the hallucination problem across four well-known LVLMs. The source code is available at: https://github.com/GasolSun36/MVP.

Text generation with beam search has proven successful in a wide range of applications. The commonly-used implementation of beam decoding follows a first come, first served heuristic: it keeps a set of already completed sequences over time steps and stops when the size of this set reaches the beam size. We introduce a patience factor, a simple modification to this decoding algorithm, that generalizes the stopping criterion and provides flexibility to the depth of search. Extensive empirical results demonstrate that the patience factor improves decoding performance of strong pretrained models on news text summarization and machine translation over diverse language pairs, with a negligible inference slowdown. Our approach only modifies one line of code and can be thus readily incorporated in any implementation.

Speculative decoding (SD) accelerates large language model inference by using a smaller draft model to predict multiple tokens, which are then verified in parallel by the larger target model. However, the limited capacity of the draft model often necessitates tree-based sampling to improve prediction accuracy, where multiple candidates are generated at each step. We identify a key limitation in this approach: the candidates at the same step are derived from the same representation, limiting diversity and reducing overall effectiveness. To address this, we propose Jakiro, leveraging Mixture of Experts (MoE), where independent experts generate diverse predictions, effectively decoupling correlations among candidates. Furthermore, we introduce a hybrid inference strategy, combining autoregressive decoding for initial tokens with parallel decoding for subsequent stages, and enhance the latter with contrastive mechanism in features to improve accuracy. Our method significantly boosts prediction accuracy and achieves higher inference speedups. Extensive experiments across diverse models validate the effectiveness and robustness of our approach, establishing a new SOTA in speculative decoding. Our codes are available at https://github.com/haiduo/Jakiro.

Large language models have demonstrated exceptional capability in natural language understanding and generation. However, their generation speed is limited by the inherently sequential nature of their decoding process, posing challenges for real-time applications. This paper introduces Lexical Unit Decoding (LUD), a novel decoding methodology implemented in a data-driven manner, accelerating the decoding process without sacrificing output quality. The core of our approach is the observation that a pre-trained language model can confidently predict multiple contiguous tokens, forming the basis for a lexical unit, in which these contiguous tokens could be decoded in parallel. Extensive experiments validate that our method substantially reduces decoding time while maintaining generation quality, i.e., 33\% speed up on natural language generation with no quality loss, and 30\% speed up on code generation with a negligible quality loss of 3\%. Distinctively, LUD requires no auxiliary models and does not require changes to existing architectures. It can also be integrated with other decoding acceleration methods, thus achieving an even more pronounced inference efficiency boost. We posit that the foundational principles of LUD could define a new decoding paradigm for future language models, enhancing their applicability for a broader spectrum of applications. All codes are be publicly available at https://github.com/tjunlp-lab/Lexical-Unit-Decoding-LUD-. Keywords: Parallel Decoding, Lexical Unit Decoding, Large Language Model

Chain-of-thought (CoT) decoding enables language models to improve reasoning performance at the cost of high generation latency in decoding. Recent proposals have explored variants of contemplation tokens, a term we introduce that refers to special tokens used during inference to allow for extra computation. Prior work has considered fixed-length sequences drawn from a discrete set of embeddings as contemplation tokens. Here we propose Compressed Chain-of-Thought (CCoT), a framework to generate contentful and continuous contemplation tokens of variable sequence length. The generated contemplation tokens are compressed representations of explicit reasoning chains, and our method can be applied to off-the-shelf decoder language models. Through experiments, we illustrate how CCoT enables additional reasoning over dense contentful representations to achieve corresponding improvements in accuracy. Moreover, the reasoning improvements can be adaptively modified on demand by controlling the number of contemplation tokens generated.

Query-focused summarization (QFS) aims to provide a summary of a single document/multi documents that can satisfy the information needs of a given query. It is useful for various real-world applications, such as abstractive snippet generation or more recent retrieval augmented generation (RAG). A prototypical QFS pipeline consists of a retriever (sparse or dense retrieval) and a generator (usually a large language model). However, applying large language models (LLM) potentially leads to hallucinations, especially when the evidence contradicts the prior belief of LLMs. There has been growing interest in developing new decoding methods to improve generation quality and reduce hallucination. In this work, we conduct a large-scale reproducibility study on one recently proposed decoding method -- Context-aware Decoding (CAD). In addition to replicating CAD's experiments on news summarization datasets, we include experiments on QFS datasets, and conduct more rigorous analysis on computational complexity and hyperparameter sensitivity. Experiments with eight different language models show that performance-wise, CAD improves QFS quality by (1) reducing factuality errors/hallucinations while (2) mostly retaining the match of lexical patterns, measured by ROUGE scores, while also at a cost of increased inference-time FLOPs and reduced decoding speed. The code implementation based on Huggingface Library is made available https://github.com/zhichaoxu-shufe/context-aware-decoding-qfs

Speculative Decoding is a widely used technique to speed up inference for Large Language Models (LLMs) without sacrificing quality. When performing inference, speculative decoding uses a smaller draft model to generate speculative tokens and then uses the target LLM to verify those draft tokens. The speedup provided by speculative decoding heavily depends on the choice of the draft model. In this work, we perform a detailed study comprising over 350 experiments with LLaMA-65B and OPT-66B using speculative decoding and delineate the factors that affect the performance gain provided by speculative decoding. Our experiments indicate that the performance of speculative decoding depends heavily on the latency of the draft model, and the draft model's capability in language modeling does not correlate strongly with its performance in speculative decoding. Based on these insights we explore a new design space for draft models and design hardware-efficient draft models for speculative decoding. Our newly designed draft model for LLaMA-65B can provide 60% higher throughput than existing draft models and can generalize further to the LLaMA-2 model family and supervised fine-tuned models.

Large language models (LLMs) demonstrate great performance in text generation. However, LLMs are still suffering from hallucinations. In this work, we propose an inference-time method, Self-Highlighted Hesitation (SH2), to help LLMs decode more truthfully. SH2 is based on a simple fact rooted in information theory that for an LLM, the tokens predicted with lower probabilities are prone to be more informative than others. Our analysis shows that the tokens assigned with lower probabilities by an LLM are more likely to be closely related to factual information, such as nouns, proper nouns, and adjectives. Therefore, we propose to ''highlight'' the factual information by selecting the tokens with the lowest probabilities and concatenating them to the original context, thus forcing the model to repeatedly read and hesitate on these tokens before generation. During decoding, we also adopt contrastive decoding to emphasize the difference in the output probabilities brought by the hesitation. Experimental results demonstrate that our SH2, requiring no additional data or models, can effectively help LLMs elicit factual knowledge and distinguish hallucinated contexts. Significant and consistent improvements are achieved by SH2 for LLaMA-7b and LLaMA2-7b on multiple hallucination tasks.

Decoding non-invasive brain recordings is pivotal for advancing our understanding of human cognition but faces challenges due to individual differences and complex neural signal representations. Traditional methods often require customized models and extensive trials, lacking interpretability in visual reconstruction tasks. Our framework integrates 3D brain structures with visual semantics using a Vision Transformer 3D. This unified feature extractor efficiently aligns fMRI features with multiple levels of visual embeddings, eliminating the need for subject-specific models and allowing extraction from single-trial data. The extractor consolidates multi-level visual features into one network, simplifying integration with Large Language Models (LLMs). Additionally, we have enhanced the fMRI dataset with diverse fMRI-image-related textual data to support multimodal large model development. Integrating with LLMs enhances decoding capabilities, enabling tasks such as brain captioning, complex reasoning, concept localization, and visual reconstruction. Our approach demonstrates superior performance across these tasks, precisely identifying language-based concepts within brain signals, enhancing interpretability, and providing deeper insights into neural processes. These advances significantly broaden the applicability of non-invasive brain decoding in neuroscience and human-computer interaction, setting the stage for advanced brain-computer interfaces and cognitive models.

Chain-of-thought (CoT) reasoning enables large language models (LLMs) to move beyond fast System-1 responses and engage in deliberative System-2 reasoning. However, this comes at the cost of significant inefficiency due to verbose intermediate output. Recent latent-space reasoning methods improve efficiency by operating on hidden states without decoding into language, yet they treat all steps uniformly, failing to distinguish critical deductions from auxiliary steps and resulting in suboptimal use of computational resources. In this paper, we propose System-1.5 Reasoning, an adaptive reasoning framework that dynamically allocates computation across reasoning steps through shortcut paths in latent space. Specifically, System-1.5 Reasoning introduces two types of dynamic shortcuts. The model depth shortcut (DS) adaptively reasons along the vertical depth by early exiting non-critical tokens through lightweight adapter branches, while allowing critical tokens to continue through deeper Transformer layers. The step shortcut (SS) reuses hidden states across the decoding steps to skip trivial steps and reason horizontally in latent space. Training System-1.5 Reasoning involves a two-stage self-distillation process: first distilling natural language CoT into latent-space continuous thought, and then distilling full-path System-2 latent reasoning into adaptive shortcut paths (System-1.5 Reasoning). Experiments on reasoning tasks demonstrate the superior performance of our method. For example, on GSM8K, System-1.5 Reasoning achieves reasoning performance comparable to traditional CoT fine-tuning methods while accelerating inference by over 20x and reducing token generation by 92.31% on average.

Advancements in DNA sequencing technologies have significantly improved our ability to decode genomic sequences. However, the prediction and interpretation of these sequences remain challenging due to the intricate nature of genetic material. Large language models (LLMs) have introduced new opportunities for biological sequence analysis. Recent developments in genomic language models have underscored the potential of LLMs in deciphering DNA sequences. Nonetheless, existing models often face limitations in robustness and application scope, primarily due to constraints in model structure and training data scale. To address these limitations, we present GENERator, a generative genomic foundation model featuring a context length of 98k base pairs (bp) and 1.2B parameters. Trained on an expansive dataset comprising 386B bp of eukaryotic DNA, the GENERator demonstrates state-of-the-art performance across both established and newly proposed benchmarks. The model adheres to the central dogma of molecular biology, accurately generating protein-coding sequences that translate into proteins structurally analogous to known families. It also shows significant promise in sequence optimization, particularly through the prompt-responsive generation of promoter sequences with specific activity profiles. These capabilities position the GENERator as a pivotal tool for genomic research and biotechnological advancement, enhancing our ability to interpret and predict complex biological systems and enabling precise genomic interventions.

While exploring visual scenes, humans' scanpaths are driven by their underlying attention processes. Understanding visual scanpaths is essential for various applications. Traditional scanpath models predict the where and when of gaze shifts without providing explanations, creating a gap in understanding the rationale behind fixations. To bridge this gap, we introduce GazeXplain, a novel study of visual scanpath prediction and explanation. This involves annotating natural-language explanations for fixations across eye-tracking datasets and proposing a general model with an attention-language decoder that jointly predicts scanpaths and generates explanations. It integrates a unique semantic alignment mechanism to enhance the consistency between fixations and explanations, alongside a cross-dataset co-training approach for generalization. These novelties present a comprehensive and adaptable solution for explainable human visual scanpath prediction. Extensive experiments on diverse eye-tracking datasets demonstrate the effectiveness of GazeXplain in both scanpath prediction and explanation, offering valuable insights into human visual attention and cognitive processes.

Speculative decoding is a relatively new decoding framework that leverages small and efficient draft models to reduce the latency of LLMs. In this study, we introduce GliDe and CaPE, two low-hassle modifications to vanilla speculative decoding to further improve the decoding speed of a frozen LLM. Specifically, GliDe is a modified draft model architecture that reuses the cached keys and values from the target LLM, while CaPE is a proposal expansion method that uses the draft model's confidence scores to help select additional candidate tokens for verification. Extensive experiments on different benchmarks demonstrate that our proposed GliDe draft model significantly reduces the expected decoding latency. Additional evaluation using walltime reveals that GliDe can accelerate Vicuna models up to 2.17x and further extend the improvement to 2.61x with CaPE. We will release our code, data, and the trained draft models.

Multimodal Large Language Models (MLLMs) frequently exhibit hallucination phenomena, but the underlying reasons remain poorly understood. In this paper, we present an empirical analysis and find that, although MLLMs incorrectly generate the objects in the final output, they are actually able to recognize visual objects in the preceding layers. We speculate that this may be due to the strong knowledge priors of the language model suppressing the visual information, leading to hallucinations. Motivated by this, we propose a novel dynamic correction decoding method for MLLMs (DeCo), which adaptively selects the appropriate preceding layers and proportionally integrates knowledge into the final layer to adjust the output logits. Note that DeCo is model agnostic and can be seamlessly incorporated with various classic decoding strategies and applied to different MLLMs. We evaluate DeCo on widely-used benchmarks, demonstrating that it can reduce hallucination rates by a large margin compared to baselines, highlighting its potential to mitigate hallucinations. Code is available at https://github.com/zjunlp/DeCo.

The most common training pipeline for large language models includes pretraining, finetuning and aligning phases, with their respective resulting models, such as the pretrained model and the finetuned model. Finetuned and aligned models show improved abilities of instruction following and safe generation, however their abilities to stay factual about the world are impacted by the finetuning process. Furthermore, the common practice of using sampling during generation also increases chances of hallucination. In this work, we introduce a collaborative decoding framework to harness the high factuality within pretrained models through the concept of critical tokens. We first design a critical token classifier to decide which model to use for the next token, and subsequently generates the next token using different decoding strategies. Experiments with different models and datasets show that our decoding framework is able to reduce model hallucination significantly, showcasing the importance of the collaborative decoding framework.

Large Language Models (LLMs) typically have billions of parameters and are thus often difficult to interpret in their operation. Such black-box models can pose a significant risk to safety when trusted to make important decisions. The lack of interpretability of LLMs is more related to their sheer size, rather than the complexity of their individual components. The TARS method for knowledge removal (Davies et al 2024) provides strong evidence for the hypothesis that that linear layer weights which act directly on the residual stream may have high correlation with different concepts encoded in the residual stream. Building upon this, we attempt to decode neuron weights directly into token probabilities through the final projection layer of the model (the LM-head). Firstly, we show that with Llama 3.1 8B we can utilise the LM-head to decode specialised feature neurons that respond strongly to certain concepts, with examples such as "dog" and "California". This is then confirmed by demonstrating that these neurons can be clamped to affect the probability of the concept in the output. This extends to the fine-tuned assistant Llama 3.1 8B instruct model, where we find that over 75% of neurons in the up-projection layers have the same top associated token compared to the pretrained model. Finally, we demonstrate that clamping the "dog" neuron leads the instruct model to always discuss dogs when asked about its favourite animal. Through our method, it is possible to map the entirety of Llama 3.1 8B's up-projection neurons in less than 15 minutes with no parallelization.

Speculative decoding (SD) is a promising method for accelerating the decoding process of Large Language Models (LLMs). The efficiency of SD primarily hinges on the consistency between the draft model and the verify model. However, existing drafting approaches typically require additional modules to be trained, which can be challenging to implement and ensure compatibility across various LLMs. In this paper, we propose CLaSp, an in-context layer-skipping strategy for self-speculative decoding. Unlike prior methods, CLaSp does not require additional drafting modules or extra training. Instead, it employs a plug-and-play mechanism by skipping intermediate layers of the verify model to construct a compressed draft model. Specifically, we develop a dynamic programming algorithm that optimizes the layer-skipping process by leveraging the complete hidden states from the last verification stage as an objective. This enables CLaSp to dynamically adjust its layer-skipping strategy after each verification stage, without relying on pre-optimized sets of skipped layers. Experimental results across diverse downstream tasks demonstrate that CLaSp achieves a speedup of 1.3x ~ 1.7x on LLaMA3 series models without altering the original distribution of the generated text.

The complex nature of big biological systems pushed some scientists to classify its understanding under the inconceivable missions. Different leveled challenges complicated this task, one of is the prediction of a protein's function. In recent years, significant progress has been made in this field through the development of various machine learning approaches. However, most existing methods formulate the task as a multi-classification problem, i.e assigning predefined labels to proteins. In this work, we propose a novel approach, Prot2Text, which predicts a protein function's in a free text style, moving beyond the conventional binary or categorical classifications. By combining Graph Neural Networks(GNNs) and Large Language Models(LLMs), in an encoder-decoder framework, our model effectively integrates diverse data types including proteins' sequences, structures, and textual annotations. This multimodal approach allows for a holistic representation of proteins' functions, enabling the generation of detailed and accurate descriptions. To evaluate our model, we extracted a multimodal protein dataset from SwissProt, and demonstrate empirically the effectiveness of Prot2Text. These results highlight the transformative impact of multimodal models, specifically the fusion of GNNs and LLMs, empowering researchers with powerful tools for more accurate prediction of proteins' functions. The code, the models and a demo will be publicly released.

The rapid growth in the parameters of large language models (LLMs) has made inference latency a fundamental bottleneck, limiting broader application of LLMs. Speculative decoding represents a lossless approach to accelerate inference through a guess-and-verify paradigm, leveraging the parallel capabilities of modern hardware. Some speculative decoding methods rely on additional structures to guess draft tokens, such as small models or parameter-efficient architectures, which need extra training before use. Alternatively, retrieval-based train-free techniques build libraries from pre-existing corpora or by n-gram generation. However, they face challenges like large storage requirements, time-consuming retrieval, and limited adaptability. Observing that candidate tokens generated during the decoding process are likely to reoccur in future sequences, we propose Token Recycling. This approach stores candidate tokens in an adjacency matrix and employs a breadth-first search (BFS)-like algorithm on the matrix to construct a draft tree. The tree is then validated through tree attention. New candidate tokens from the decoding process are then used to update the matrix. Token Recycling requires \textless2MB of additional storage and achieves approximately 2x speedup across all sizes of LLMs. It significantly outperforms existing train-free methods by 30\% and even a training method by 25\%. It can be directly applied to any existing LLMs and tasks without the need for adaptation.

In a conversation or a dialogue process, attention and intention play intrinsic roles. This paper proposes a neural network based approach that models the attention and intention processes. It essentially consists of three recurrent networks. The encoder network is a word-level model representing source side sentences. The intention network is a recurrent network that models the dynamics of the intention process. The decoder network is a recurrent network produces responses to the input from the source side. It is a language model that is dependent on the intention and has an attention mechanism to attend to particular source side words, when predicting a symbol in the response. The model is trained end-to-end without labeling data. Experiments show that this model generates natural responses to user inputs.

In this paper, we introduce an improved approach of speculative decoding aimed at enhancing the efficiency of serving large language models. Our method capitalizes on the strengths of two established techniques: the classic two-model speculative decoding approach, and the more recent single-model approach, Medusa. Drawing inspiration from Medusa, our approach adopts a single-model strategy for speculative decoding. However, our method distinguishes itself by employing a single, lightweight draft head with a recurrent dependency design, akin in essence to the small, draft model uses in classic speculative decoding, but without the complexities of the full transformer architecture. And because of the recurrent dependency, we can use beam search to swiftly filter out undesired candidates with the draft head. The outcome is a method that combines the simplicity of single-model design and avoids the need to create a data-dependent tree attention structure only for inference in Medusa. We empirically demonstrate the effectiveness of the proposed method on several popular open source language models, along with a comprehensive analysis of the trade-offs involved in adopting this approach.

Large reasoning models (LRMs) achieve strong reasoning performance by emitting long chains of thought. Yet, these verbose traces slow down inference and often drift into unnecessary detail, known as the overthinking phenomenon. To better understand LRMs' behavior, we systematically analyze the token-level misalignment between reasoning and non-reasoning models. While it is expected that their primary difference lies in the stylistic "thinking cues", LRMs uniquely exhibit two pivotal, previously under-explored phenomena: a Global Misalignment Rebound, where their divergence from non-reasoning models persists or even grows as response length increases, and more critically, a Local Misalignment Diminish, where the misalignment concentrates at the "thinking cues" each sentence starts with but rapidly declines in the remaining of the sentence. Motivated by the Local Misalignment Diminish, we propose FoReaL-Decoding, a collaborative fast-slow thinking decoding method for cost-quality trade-off. In FoReaL-Decoding, a Leading model leads the first few tokens for each sentence, and then a weaker draft model completes the following tokens to the end of each sentence. FoReaL-Decoding adopts a stochastic gate to smoothly interpolate between the small and the large model. On four popular math-reasoning benchmarks (AIME24, GPQA-Diamond, MATH500, AMC23), FoReaL-Decoding reduces theoretical FLOPs by 30 to 50% and trims CoT length by up to 40%, while preserving 86 to 100% of model performance. These results establish FoReaL-Decoding as a simple, plug-and-play route to controllable cost-quality trade-offs in reasoning-centric tasks.

Autoregressive language models (LMs) generate one token at a time, yet human reasoning operates over higher-level abstractions - sentences, propositions, and concepts. This contrast raises a central question- Can LMs likewise learn to reason over structured semantic units rather than raw token sequences? In this work, we investigate whether pretrained LMs can be lifted into such abstract reasoning spaces by building on their learned representations. We present a framework that adapts a pretrained token-level LM to operate in sentence space by autoregressively predicting continuous embeddings of next sentences. We explore two embedding paradigms inspired by classical representation learning: 1) semantic embeddings, learned via autoencoding to preserve surface meaning; and 2) contextual embeddings, trained via next-sentence prediction to encode anticipatory structure. We evaluate both under two inference regimes: Discretized, which decodes each predicted embedding into text before re-encoding; and Continuous, which reasons entirely in embedding space for improved efficiency. Across four domains - mathematics, logic, commonsense, and planning - contextual embeddings under continuous inference show competitive performance with Chain-of-Thought (CoT) while reducing inference-time FLOPs on average by half. We also present early signs of scalability and modular adaptation. Finally, to visualize latent trajectories, we introduce SentenceLens, a diagnostic tool that decodes intermediate model states into interpretable sentences. Together, our results indicate that pretrained LMs can effectively transition to abstract, structured reasoning within latent embedding spaces.

Interpretability research aims to bridge the gap between empirical success and our scientific understanding of the inner workings of large language models (LLMs). However, most existing research focuses on analyzing a single mechanism, such as how models copy or recall factual knowledge. In this work, we propose a formulation of competition of mechanisms, which focuses on the interplay of multiple mechanisms instead of individual mechanisms and traces how one of them becomes dominant in the final prediction. We uncover how and where mechanisms compete within LLMs using two interpretability methods: logit inspection and attention modification. Our findings show traces of the mechanisms and their competition across various model components and reveal attention positions that effectively control the strength of certain mechanisms. Code: https://github.com/francescortu/comp-mech. Data: https://huggingface.co/datasets/francescortu/comp-mech.

Individual neurons participate in the representation of multiple high-level concepts. To what extent can different interpretability methods successfully disentangle these roles? To help address this question, we introduce RAVEL (Resolving Attribute-Value Entanglements in Language Models), a dataset that enables tightly controlled, quantitative comparisons between a variety of existing interpretability methods. We use the resulting conceptual framework to define the new method of Multi-task Distributed Alignment Search (MDAS), which allows us to find distributed representations satisfying multiple causal criteria. With Llama2-7B as the target language model, MDAS achieves state-of-the-art results on RAVEL, demonstrating the importance of going beyond neuron-level analyses to identify features distributed across activations. We release our benchmark at https://github.com/explanare/ravel.

Multi-hop question answering (MHQA) requires a model to retrieve and integrate information from multiple passages to answer a complex question. Recent systems leverage the power of large language models and integrate evidence retrieval with reasoning prompts (e.g., chain-of-thought reasoning) for the MHQA task. However, the complexities in the question types (bridge v.s. comparison questions) and the reasoning types (sequential v.s. parallel reasonings) require more novel and fine-grained prompting methods to enhance the performance of MHQA under the zero-shot setting. In this paper, we propose STOC-TOT, a stochastic tree-of-thought reasoning prompting method with constrained decoding for MHQA and conduct a detailed comparison with other reasoning prompts on different question types and reasoning types. Specifically, we construct a tree-like reasoning structure by prompting the model to break down the original question into smaller sub-questions to form different reasoning paths. In addition, we prompt the model to provide a probability estimation for each reasoning path at each reasoning step. At answer time, we conduct constrained decoding on the model to generate more grounded answers and reduce hallucination. Experiments comparing STOC-TOT with two MHQA datasets and five large language models showed that our framework outperforms other reasoning prompts by a significant margin.

In this work, we propose FastCoT, a model-agnostic framework based on parallel decoding without any further training of an auxiliary model or modification to the LLM itself. FastCoT uses a size-varying context window whose size changes with position to conduct parallel decoding and auto-regressive decoding simultaneously, thus fully utilizing GPU computation resources. In FastCoT, the parallel decoding part provides the LLM with a quick glance of the future composed of approximate tokens, which could lead to faster answers compared to regular autoregressive decoding used by causal transformers. We also provide an implementation of parallel decoding within LLM, which supports KV-cache generation and batch processing. Through extensive experiments, we demonstrate that FastCoT saves inference time by nearly 20% with only a negligible performance drop compared to the regular approach. Additionally, we show that the context window size exhibits considerable robustness for different tasks.

Recent works have suggested that In-Context Learning (ICL) operates in dual modes, i.e. task retrieval (remember learned patterns from pre-training) and task learning (inference-time ``learning'' from demonstrations). However, disentangling these the two modes remains a challenging goal. We introduce ICL CIPHERS, a class of task reformulations based on substitution ciphers borrowed from classic cryptography. In this approach, a subset of tokens in the in-context inputs are substituted with other (irrelevant) tokens, rendering English sentences less comprehensible to human eye. However, by design, there is a latent, fixed pattern to this substitution, making it reversible. This bijective (reversible) cipher ensures that the task remains a well-defined task in some abstract sense, despite the transformations. It is a curious question if LLMs can solve ICL CIPHERS with a BIJECTIVE mapping, which requires deciphering the latent cipher. We show that LLMs are better at solving ICL CIPHERS with BIJECTIVE mappings than the NON-BIJECTIVE (irreversible) baseline, providing a novel approach to quantify ``learning'' in ICL. While this gap is small, it is consistent across the board on four datasets and six models. Finally, we examine LLMs' internal representations and identify evidence in their ability to decode the ciphered inputs.

Endowing dialogue systems with personas is essential to deliver more human-like conversations. However, this problem is still far from well explored due to the difficulties of both embodying personalities in natural languages and the persona sparsity issue observed in most dialogue corpora. This paper proposes a pre-training based personalized dialogue model that can generate coherent responses using persona-sparse dialogue data. In this method, a pre-trained language model is used to initialize an encoder and decoder, and personal attribute embeddings are devised to model richer dialogue contexts by encoding speakers' personas together with dialogue histories. Further, to incorporate the target persona in the decoding process and to balance its contribution, an attention routing structure is devised in the decoder to merge features extracted from the target persona and dialogue contexts using dynamically predicted weights. Our model can utilize persona-sparse dialogues in a unified manner during the training process, and can also control the amount of persona-related features to exhibit during the inference process. Both automatic and manual evaluation demonstrates that the proposed model outperforms state-of-the-art methods for generating more coherent and persona consistent responses with persona-sparse data.

We present a novel approach for the prediction of anticancer compound sensitivity by means of multi-modal attention-based neural networks (PaccMann). In our approach, we integrate three key pillars of drug sensitivity, namely, the molecular structure of compounds, transcriptomic profiles of cancer cells as well as prior knowledge about interactions among proteins within cells. Our models ingest a drug-cell pair consisting of SMILES encoding of a compound and the gene expression profile of a cancer cell and predicts an IC50 sensitivity value. Gene expression profiles are encoded using an attention-based encoding mechanism that assigns high weights to the most informative genes. We present and study three encoders for SMILES string of compounds: 1) bidirectional recurrent 2) convolutional 3) attention-based encoders. We compare our devised models against a baseline model that ingests engineered fingerprints to represent the molecular structure. We demonstrate that using our attention-based encoders, we can surpass the baseline model. The use of attention-based encoders enhance interpretability and enable us to identify genes, bonds and atoms that were used by the network to make a prediction.

We introduce a hierarchical filtering procedure for generative models of sequences on trees, enabling control over the range of positional correlations in the data. Leveraging this controlled setting, we provide evidence that vanilla encoder-only transformer architectures can implement the optimal Belief Propagation algorithm on both root classification and masked language modeling tasks. Correlations at larger distances corresponding to increasing layers of the hierarchy are sequentially included as the network is trained. We analyze how the transformer layers succeed by focusing on attention maps from models trained with varying degrees of filtering. These attention maps show clear evidence for iterative hierarchical reconstruction of correlations, and we can relate these observations to a plausible implementation of the exact inference algorithm for the network sizes considered.

Multimodal Large Language Models (MLLMs) demonstrate robust zero-shot capabilities across diverse vision-language tasks after training on mega-scale datasets. However, dense prediction tasks, such as semantic segmentation and keypoint detection, pose significant challenges for MLLMs when represented solely as text outputs. Simultaneously, current MLLMs utilizing latent embeddings for visual task decoding generally demonstrate limited adaptability to both multi-task learning and multi-granularity scenarios. In this work, we present REF-VLM, an end-to-end framework for unified training of various visual decoding tasks. To address complex visual decoding scenarios, we introduce the Triplet-Based Referring Paradigm (TRP), which explicitly decouples three critical dimensions in visual decoding tasks through a triplet structure: concepts, decoding types, and targets. TRP employs symbolic delimiters to enforce structured representation learning, enhancing the parsability and interpretability of model outputs. Additionally, we construct Visual-Task Instruction Following Dataset (VTInstruct), a large-scale multi-task dataset containing over 100 million multimodal dialogue samples across 25 task types. Beyond text inputs and outputs, VT-Instruct incorporates various visual prompts such as point, box, scribble, and mask, and generates outputs composed of text and visual units like box, keypoint, depth and mask. The combination of different visual prompts and visual units generates a wide variety of task types, expanding the applicability of REF-VLM significantly. Both qualitative and quantitative experiments demonstrate that our REF-VLM outperforms other MLLMs across a variety of standard benchmarks. The code, dataset, and demo available at https://github.com/MacavityT/REF-VLM.

Advances in hardware and language model architecture have spurred a revolution in natural language generation. However, autoregressive models compute probability distributions over next-token choices, and sampling from these distributions, known as decoding, has received significantly less attention than other design choices. Existing decoding strategies are largely based on heuristics, resulting in methods that are hard to apply or improve in a principled manner. We develop the theory of decoding strategies for language models by expressing popular decoding algorithms as equilibrium states in the language of ergodic theory and stating the functions they optimize. Using this, we analyze the effect of the local normalization step of top-k, nucleus, and temperature sampling, used to make probabilities sum to one. We argue that local normalization distortion is a fundamental defect of decoding strategies and quantify the size of this distortion and its effect on mathematical proxies for the quality and diversity of generated text. Contrary to the prevailing explanation, we argue that the major cause of the under-performance of top-k sampling relative to nucleus sampling is local normalization distortion. This yields conclusions for the future design of decoding algorithms and the detection of machine-generated text.

Complex cell signaling systems -- governed by varying protein abundances and interactions -- generate diverse cell types across organs. These systems evolve under influences such as age, sex, diet, environmental exposures, and diseases, making them challenging to decode given the involvement of tens of thousands of genes and proteins. Recently, hundreds of millions of single-cell omics data have provided a robust foundation for understanding these signaling networks within various cell subpopulations and conditions. Inspired by the success of large foundation models (for example, large language models and large vision models) pre-trained on massive datasets, we introduce OmniCellTOSG, the first dataset of cell text-omic signaling graphs (TOSGs). Each TOSG represents the signaling network of an individual or meta-cell and is labeled with information such as organ, disease, sex, age, and cell subtype. OmniCellTOSG offers two key contributions. First, it introduces a novel graph model that integrates human-readable annotations -- such as biological functions, cellular locations, signaling pathways, related diseases, and drugs -- with quantitative gene and protein abundance data, enabling graph reasoning to decode cell signaling. This approach calls for new joint models combining large language models and graph neural networks. Second, the dataset is built from single-cell RNA sequencing data of approximately 120 million cells from diverse tissues and conditions (healthy and diseased) and is fully compatible with PyTorch. This facilitates the development of innovative cell signaling models that could transform research in life sciences, healthcare, and precision medicine. The OmniCellTOSG dataset is continuously expanding and will be updated regularly. The dataset and code are available at https://github.com/FuhaiLiAiLab/OmniCellTOSG.

Speculative decoding (SD), where an extra draft model is employed to provide multiple draft tokens first and then the original target model verifies these tokens in parallel, has shown great power for LLM inference acceleration. However, existing SD methods suffer from the mutual waiting problem, i.e., the target model gets stuck when the draft model is guessing tokens, and vice versa. This problem is directly incurred by the asynchronous execution of the draft model and the target model, and is exacerbated due to the fixed draft length in speculative decoding. To address these challenges, we propose a conceptually simple, flexible, and general framework to boost speculative decoding, namely Parallel spEculative decoding with Adaptive dRaft Length (PEARL). Specifically, PEARL proposes pre-verify to verify the first draft token in advance during the drafting phase, and post-verify to generate more draft tokens during the verification phase. PEARL parallels the drafting phase and the verification phase via applying the two strategies, and achieves adaptive draft length for different scenarios, which effectively alleviates the mutual waiting problem. Moreover, we theoretically demonstrate that the mean accepted tokens of PEARL is more than existing draft-then-verify works. Experiments on various text generation benchmarks demonstrate the effectiveness of our \name, leading to a superior speedup performance up to 3.79times and 1.52times, compared to auto-regressive decoding and vanilla speculative decoding, respectively.

To tackle the high inference latency exhibited by autoregressive language models, previous studies have proposed an early-exiting framework that allocates adaptive computation paths for each token based on the complexity of generating the subsequent token. However, we observed several shortcomings, including performance degradation caused by a state copying mechanism or numerous exit paths, and sensitivity to exit confidence thresholds. Consequently, we propose a Fast and Robust Early-Exiting (FREE) framework, which incorporates a shallow-deep module and a synchronized parallel decoding. Our framework enables faster inference by synchronizing the decoding process of the current token with previously stacked early-exited tokens. Furthermore, as parallel decoding allows us to observe predictions from both shallow and deep models, we present a novel adaptive threshold estimator that exploits a Beta mixture model to determine suitable confidence thresholds. We empirically demonstrated the superiority of our proposed framework on extensive generation tasks.

The drug development pipeline for a new compound can last 10-20 years and cost over 10 billion. Drug repurposing offers a more time- and cost-effective alternative. Computational approaches based on biomedical knowledge graph representations have recently yielded new drug repurposing hypotheses. In this study, we present a novel, disease-specific hypergraph representation learning technique to derive contextual embeddings of biological pathways of various lengths but that all start at any given drug and all end at the disease of interest. Further, we extend this method to multi-disease hypergraphs. To determine the repurposing potential of each of the 1,522 drugs, we derive drug-specific distributions of cosine similarity values and ultimately consider the median for ranking. Cosine similarity values are computed between (1) all biological pathways starting at the considered drug and ending at the disease of interest and (2) all biological pathways starting at drugs currently prescribed against that disease and ending at the disease of interest. We illustrate our approach with Alzheimer's disease (AD) and two of its risk factors: hypertension (HTN) and type 2 diabetes (T2D). We compare each drug's rank across four hypergraph settings (single- or multi-disease): AD only, AD + HTN, AD + T2D, and AD + HTN + T2D. Notably, our framework led to the identification of two promising drugs whose repurposing potential was significantly higher in hypergraphs combining two diseases: dapagliflozin (antidiabetic; moved up, from top 32% to top 7%, across all considered drugs) and debrisoquine (antihypertensive; moved up, from top 76% to top 23%). Our approach serves as a hypothesis generation tool, to be paired with a validation pipeline relying on laboratory experiments and semi-automated parsing of the biomedical literature.

To combat the memory bandwidth-bound nature of autoregressive LLM inference, previous research has proposed the speculative decoding framework. To perform speculative decoding, a small draft model proposes candidate continuations of the input sequence, that are then verified in parallel by the base model. One way to specify the draft model, as used in the recent Medusa decoding framework, is as a collection of light-weight heads, called draft heads, that operate on the base model's hidden states. To date, all existing draft heads have been sequentially independent, meaning that they speculate tokens in the candidate continuation independently of any preceding tokens in the candidate continuation. In this work, we propose Hydra heads, a sequentially dependent, drop-in replacement for standard draft heads that significantly improves speculation accuracy. Decoding with Hydra heads improves throughput compared to Medusa decoding with standard draft heads. We further explore the design space of Hydra head training objectives and architectures, and propose a carefully-tuned Hydra head recipe, which we call Hydra++, that improves decoding throughput by 1.31x and 2.71x compared to Medusa decoding and autoregressive decoding, respectively. Overall, Hydra heads are a simple intervention on standard draft heads that significantly improve the end-to-end speed of draft head based speculative decoding.

Despite their impressive capabilities, large language models (LLMs) are prone to hallucinations, i.e., generating content that deviates from facts seen during pretraining. We propose a simple decoding strategy for reducing hallucinations with pretrained LLMs that does not require conditioning on retrieved external knowledge nor additional fine-tuning. Our approach obtains the next-token distribution by contrasting the differences in logits obtained from projecting the later layers versus earlier layers to the vocabulary space, exploiting the fact that factual knowledge in an LLMs has generally been shown to be localized to particular transformer layers. We find that this Decoding by Contrasting Layers (DoLa) approach is able to better surface factual knowledge and reduce the generation of incorrect facts. DoLa consistently improves the truthfulness across multiple choices tasks and open-ended generation tasks, for example improving the performance of LLaMA family models on TruthfulQA by 12-17% absolute points, demonstrating its potential in making LLMs reliably generate truthful facts.

Mechanistic interpretability aims to understand the computational mechanisms underlying neural networks' capabilities in order to accomplish concrete scientific and engineering goals. Progress in this field thus promises to provide greater assurance over AI system behavior and shed light on exciting scientific questions about the nature of intelligence. Despite recent progress toward these goals, there are many open problems in the field that require solutions before many scientific and practical benefits can be realized: Our methods require both conceptual and practical improvements to reveal deeper insights; we must figure out how best to apply our methods in pursuit of specific goals; and the field must grapple with socio-technical challenges that influence and are influenced by our work. This forward-facing review discusses the current frontier of mechanistic interpretability and the open problems that the field may benefit from prioritizing.

Adapting medical Large Language Models to local languages can reduce barriers to accessing healthcare services, but data scarcity remains a significant challenge, particularly for low-resource languages. To address this, we first construct a high-quality medical dataset and conduct analysis to ensure its quality. In order to leverage the generalization capability of multilingual LLMs to efficiently scale to more resource-constrained languages, we explore the internal information flow of LLMs from a multilingual perspective using Mixture of Experts (MoE) modularity. Technically, we propose a novel MoE routing method that employs language-specific experts and cross-lingual routing. Inspired by circuit theory, our routing analysis revealed a Spread Out in the End information flow mechanism: while earlier layers concentrate cross-lingual information flow, the later layers exhibit language-specific divergence. This insight directly led to the development of the Post-MoE architecture, which applies sparse routing only in the later layers while maintaining dense others. Experimental results demonstrate that this approach enhances the generalization of multilingual models to other languages while preserving interpretability. Finally, to efficiently scale the model to 50 languages, we introduce the concept of language family experts, drawing on linguistic priors, which enables scaling the number of languages without adding additional parameters.

Pre-trained language models based on masked language modeling (MLM) objective excel in natural language understanding (NLU) tasks. While fine-tuned MLM-based encoders consistently outperform causal language modeling decoders of comparable size, a recent trend of scaling decoder models to multiple billion parameters resulted in large language models (LLMs), making them competitive with MLM-based encoders. Although scale amplifies their prowess in NLU tasks, LLMs fall short of SOTA results in information extraction (IE) tasks, many framed as sequence labeling (SL). However, whether this is an intrinsic limitation of LLMs or whether their SL performance can be improved remains unclear. To address this, we explore strategies to enhance the SL performance of "open" LLMs (Llama2 and Mistral) on IE tasks. We investigate bidirectional information flow within groups of decoder blocks, applying layer-wise removal or enforcement of the causal mask (CM) during LLM fine-tuning. This approach yields performance gains competitive with SOTA SL models, matching or outperforming the results of CM removal from all blocks. Our findings hold for diverse SL tasks, proving that "open" LLMs with layer-dependent CM removal outperform strong MLM-based encoders and instruction-tuned LLMs. However, we observe no effect from CM removal on a small scale when maintaining an equivalent model size, pre-training steps, and pre-training and fine-tuning data.

Language model detoxification aims to minimize the risk of generating offensive or harmful content in pretrained language models (PLMs) for safer deployment. Existing methods can be roughly categorized as finetuning-based and decoding-based. However, the former is often resource-intensive, while the latter relies on additional components and potentially compromises the generation fluency. In this paper, we propose a more lightweight approach that enables the PLM itself to achieve "self-detoxification". Our method is built upon the observation that prepending a negative steering prompt can effectively induce PLMs to generate toxic content. At the same time, we are inspired by the recent research in the interpretability field, which formulates the evolving contextualized representations within the PLM as an information stream facilitated by the attention layers. Drawing on this idea, we devise a method to identify the toxification direction from the normal generation process to the one prompted with the negative prefix, and then steer the generation to the reversed direction by manipulating the information movement within the attention layers. Experimental results show that our approach, without any fine-tuning or extra components, can achieve comparable performance with state-of-the-art methods.

Recently, various studies have been directed towards exploring dense passage retrieval techniques employing pre-trained language models, among which the masked auto-encoder (MAE) pre-training architecture has emerged as the most promising. The conventional MAE framework relies on leveraging the passage reconstruction of decoder to bolster the text representation ability of encoder, thereby enhancing the performance of resulting dense retrieval systems. Within the context of building the representation ability of the encoder through passage reconstruction of decoder, it is reasonable to postulate that a ``more demanding'' decoder will necessitate a corresponding increase in the encoder's ability. To this end, we propose a novel token importance aware masking strategy based on pointwise mutual information to intensify the challenge of the decoder. Importantly, our approach can be implemented in an unsupervised manner, without adding additional expenses to the pre-training phase. Our experiments verify that the proposed method is both effective and robust on large-scale supervised passage retrieval datasets and out-of-domain zero-shot retrieval benchmarks.

The dominant paradigm for neural text generation is left-to-right decoding from autoregressive language models. Constrained or controllable generation under complex lexical constraints, however, requires foresight to plan ahead feasible future paths. Drawing inspiration from the A* search algorithm, we propose NeuroLogic A*esque, a decoding algorithm that incorporates heuristic estimates of future cost. We develop efficient lookahead heuristics that are efficient for large-scale language models, making our method a drop-in replacement for common techniques such as beam search and top-k sampling. To enable constrained generation, we build on NeuroLogic decoding (Lu et al., 2021), combining its flexibility in incorporating logical constraints with A*esque estimates of future constraint satisfaction. Our approach outperforms competitive baselines on five generation tasks, and achieves new state-of-the-art performance on table-to-text generation, constrained machine translation, and keyword-constrained generation. The improvements are particularly notable on tasks that require complex constraint satisfaction or in few-shot or zero-shot settings. NeuroLogic A*esque illustrates the power of decoding for improving and enabling new capabilities of large-scale language models.

Recent advances in reasoning models have demonstrated significant improvements in accuracy, particularly for complex tasks such as mathematical reasoning, by employing detailed and comprehensive reasoning processes. However, generating these lengthy reasoning sequences is computationally expensive and time-consuming. To address this inefficiency, we leverage the inherent parallelizability of certain tasks to accelerate the reasoning process. Specifically, when multiple parallel reasoning branches exist, we decode multiple tokens per step using a specialized attention mask, processing them within a single sequence, avoiding additional memory usage. Experimental results show that our method achieves over 100% speedup in decoding time while maintaining the answer quality.

Large Multi-modal Models (LMMs) have recently demonstrated remarkable abilities in visual context understanding and coherent response generation. However, alongside these advancements, the issue of hallucinations has emerged as a significant challenge, producing erroneous responses that are unrelated to the visual contents. In this paper, we introduce a novel contrastive-based decoding method, COuntering DEscription Contrastive Decoding (CODE), which leverages self-generated descriptions as contrasting references during the decoding phase of LMMs to address hallucination issues. CODE utilizes the comprehensive descriptions from model itself as visual counterpart to correct and improve response alignment with actual visual content. By dynamically adjusting the information flow and distribution of next-token predictions in the LMM's vocabulary, CODE enhances the coherence and informativeness of generated responses. Extensive experiments demonstrate that our method significantly reduces hallucinations and improves cross-modal consistency across various benchmarks and cutting-edge LMMs. Our method provides a simple yet effective decoding strategy that can be integrated to existing LMM frameworks without additional training.

Large language models (LLMs) have demonstrated remarkable capabilities across various tasks. However, their widespread application is hindered by the resource-intensive decoding process. To address this challenge, current approaches have incorporated additional decoding heads to enable parallel prediction of multiple subsequent tokens, thereby achieving inference acceleration. Nevertheless, the accuracy of these decoding heads falls short of the auto-regressive decoding approach. In light of these limitations, we propose Chimera, a novel framework specifically designed for speculative sampling. Within this framework, we introduce a lightweight draft model that effectively utilizes previously generated tokens to predict subsequent words. To ensure both accuracy and efficiency, we present two strategies within the lightweight draft model. Firstly, we focus on capturing short-range dependencies at the bottom layer. Secondly, we leverage the readily available representations from the original LLM.Through empirical evaluation on the Vicuna and LlaMA-2 series, Chimera demonstrates impressive results, achieving an average latency speedup ratio of 2.7x compared to the vanilla auto-regressive decoding approach. This highlights the potential of our proposed framework in significantly improving the efficiency of large language models during the decoding process.

Quite surprisingly, exact maximum a posteriori (MAP) decoding of neural language generators frequently leads to low-quality results. Rather, most state-of-the-art results on language generation tasks are attained using beam search despite its overwhelmingly high search error rate. This implies that the MAP objective alone does not express the properties we desire in text, which merits the question: if beam search is the answer, what was the question? We frame beam search as the exact solution to a different decoding objective in order to gain insights into why high probability under a model alone may not indicate adequacy. We find that beam search enforces uniform information density in text, a property motivated by cognitive science. We suggest a set of decoding objectives that explicitly enforce this property and find that exact decoding with these objectives alleviates the problems encountered when decoding poorly calibrated language generation models. Additionally, we analyze the text produced using various decoding strategies and see that, in our neural machine translation experiments, the extent to which this property is adhered to strongly correlates with BLEU.

We study lossless acceleration for seq2seq generation with a novel decoding algorithm -- Aggressive Decoding. Unlike the previous efforts (e.g., non-autoregressive decoding) speeding up seq2seq generation at the cost of quality loss, our approach aims to yield the identical (or better) generation compared with autoregressive decoding but in a significant speedup, achieved by innovative cooperation of aggressive decoding and verification that are both efficient due to parallel computing. We propose two Aggressive Decoding paradigms for 2 kinds of seq2seq tasks: 1) For the seq2seq tasks whose inputs and outputs are highly similar (e.g., Grammatical Error Correction), we propose Input-guided Aggressive Decoding (IAD) that aggressively copies from the input sentence as drafted decoded tokens to verify in parallel; 2) For other general seq2seq tasks (e.g., Machine Translation), we propose Generalized Aggressive Decoding (GAD) that first employs an additional non-autoregressive decoding model for aggressive decoding and then verifies in parallel in the autoregressive manner. We test Aggressive Decoding on the most popular 6-layer Transformer model on GPU in multiple seq2seq tasks: 1) For IAD, we show that it can introduce a 7x-9x speedup for the Transformer in Grammatical Error Correction and Text Simplification tasks with the identical results as greedy decoding; 2) For GAD, we observe a 3x-5x speedup with the identical or even better quality in two important seq2seq tasks: Machine Translation and Abstractive Summarization. Moreover, Aggressive Decoding can benefit even more from stronger computing devices that are better at parallel computing. Given the lossless quality as well as significant and promising speedup, we believe Aggressive Decoding may potentially evolve into a de facto standard for efficient and lossless seq2seq generation in the near future.

Large language models (LLMs) often suffer from context faithfulness hallucinations, where outputs deviate from retrieved information due to insufficient context utilization and high output uncertainty. Our uncertainty evaluation experiments reveal a strong correlation between high uncertainty and hallucinations. We hypothesize that attention mechanisms encode signals indicative of contextual utilization, validated through probing analysis. Based on these insights, we propose Dynamic Attention-Guided Context Decoding (DAGCD), a lightweight framework that integrates attention distributions and uncertainty signals in a single-pass decoding process. Experiments across QA datasets demonstrate DAGCD's effectiveness, achieving significant improvements in faithfulness and robustness while maintaining computational efficiency.

Multi-hop Question Answering (MHQA) adds layers of complexity to question answering, making it more challenging. When Language Models (LMs) are prompted with multiple search results, they are tasked not only with retrieving relevant information but also employing multi-hop reasoning across the information sources. Although LMs perform well on traditional question-answering tasks, the causal mask can hinder their capacity to reason across complex contexts. In this paper, we explore how LMs respond to multi-hop questions by permuting search results (retrieved documents) under various configurations. Our study reveals interesting findings as follows: 1) Encoder-decoder models, such as the ones in the Flan-T5 family, generally outperform causal decoder-only LMs in MHQA tasks, despite being significantly smaller in size; 2) altering the order of gold documents reveals distinct trends in both Flan T5 models and fine-tuned decoder-only models, with optimal performance observed when the document order aligns with the reasoning chain order; 3) enhancing causal decoder-only models with bi-directional attention by modifying the causal mask can effectively boost their end performance. In addition to the above, we conduct a thorough investigation of the distribution of LM attention weights in the context of MHQA. Our experiments reveal that attention weights tend to peak at higher values when the resulting answer is correct. We leverage this finding to heuristically improve LMs' performance on this task. Our code is publicly available at https://github.com/hwy9855/MultiHopQA-Reasoning.

Transformer-based Large Language Models (LLMs) are the state-of-the-art for natural language tasks. Recent work has attempted to decode, by reverse engineering the role of linear layers, the internal mechanisms by which LLMs arrive at their final predictions for text completion tasks. Yet little is known about the specific role of attention heads in producing the final token prediction. We propose Attention Lens, a tool that enables researchers to translate the outputs of attention heads into vocabulary tokens via learned attention-head-specific transformations called lenses. Preliminary findings from our trained lenses indicate that attention heads play highly specialized roles in language models. The code for Attention Lens is available at github.com/msakarvadia/AttentionLens.

One of the roadblocks to a better understanding of neural networks' internals is polysemanticity, where neurons appear to activate in multiple, semantically distinct contexts. Polysemanticity prevents us from identifying concise, human-understandable explanations for what neural networks are doing internally. One hypothesised cause of polysemanticity is superposition, where neural networks represent more features than they have neurons by assigning features to an overcomplete set of directions in activation space, rather than to individual neurons. Here, we attempt to identify those directions, using sparse autoencoders to reconstruct the internal activations of a language model. These autoencoders learn sets of sparsely activating features that are more interpretable and monosemantic than directions identified by alternative approaches, where interpretability is measured by automated methods. Ablating these features enables precise model editing, for example, by removing capabilities such as pronoun prediction, while disrupting model behaviour less than prior techniques. This work indicates that it is possible to resolve superposition in language models using a scalable, unsupervised method. Our method may serve as a foundation for future mechanistic interpretability work, which we hope will enable greater model transparency and steerability.

Although Large Language Models (LLMs) excel in reasoning and generation for language tasks, they are not specifically designed for multimodal challenges. Training Multimodal Large Language Models (MLLMs), however, is resource-intensive and constrained by various training limitations. In this paper, we propose the Modular-based Visual Contrastive Decoding (MVCD) framework to move this obstacle. Our framework leverages LLMs' In-Context Learning (ICL) capability and the proposed visual contrastive-example decoding (CED), specifically tailored for this framework, without requiring any additional training. By converting visual signals into text and focusing on contrastive output distributions during decoding, we can highlight the new information introduced by contextual examples, explore their connections, and avoid over-reliance on prior encoded knowledge. MVCD enhances LLMs' visual perception to make it see and reason over the input visuals. To demonstrate MVCD's effectiveness, we conduct experiments with four LLMs across five question answering datasets. Our results not only show consistent improvement in model accuracy but well explain the effective components inside our decoding strategy. Our code will be available at https://github.com/Pbhgit/MVCD.

The inference process in Large Language Models (LLMs) is often limited due to the absence of parallelism in the auto-regressive decoding process, resulting in most operations being restricted by the memory bandwidth of accelerators. While methods such as speculative decoding have been suggested to address this issue, their implementation is impeded by the challenges associated with acquiring and maintaining a separate draft model. In this paper, we present Medusa, an efficient method that augments LLM inference by adding extra decoding heads to predict multiple subsequent tokens in parallel. Using a tree-based attention mechanism, Medusa constructs multiple candidate continuations and verifies them simultaneously in each decoding step. By leveraging parallel processing, Medusa introduces only minimal overhead in terms of single-step latency while substantially reducing the number of decoding steps required. We present two levels of fine-tuning procedures for Medusa to meet the needs of different use cases: Medusa-1: Medusa is directly fine-tuned on top of a frozen backbone LLM, enabling lossless inference acceleration. Medusa-2: Medusa is fine-tuned together with the backbone LLM, enabling better prediction accuracy of Medusa heads and higher speedup but needing a special training recipe that preserves the backbone model's capabilities. Moreover, we propose several extensions that improve or expand the utility of Medusa, including a self-distillation to handle situations where no training data is available and a typical acceptance scheme to boost the acceptance rate while maintaining generation quality. We evaluate Medusa on models of various sizes and training procedures. Our experiments demonstrate that Medusa-1 can achieve over 2.2x speedup without compromising generation quality, while Medusa-2 further improves the speedup to 2.3-3.6x.

Aligning foundation models is essential for their safe and trustworthy deployment. However, traditional fine-tuning methods are computationally intensive and require updating billions of model parameters. A promising alternative, alignment via decoding, adjusts the response distribution directly without model updates to maximize a target reward r, thus providing a lightweight and adaptable framework for alignment. However, principled decoding methods rely on oracle access to an optimal Q-function (Q^*), which is often unavailable in practice. Hence, prior SoTA methods either approximate this Q^* using Q^{pi_{sft}} (derived from the reference SFT model) or rely on short-term rewards, resulting in sub-optimal decoding performance. In this work, we propose Transfer Q^*, which implicitly estimates the optimal value function for a target reward r through a baseline model rho_{BL} aligned with a baseline reward rho_{BL} (which can be different from the target reward r). Theoretical analyses of Transfer Q^* provide a rigorous characterization of its optimality, deriving an upper bound on the sub-optimality gap and identifying a hyperparameter to control the deviation from the pre-trained reference SFT model based on user needs. Our approach significantly reduces the sub-optimality gap observed in prior SoTA methods and demonstrates superior empirical performance across key metrics such as coherence, diversity, and quality in extensive tests on several synthetic and real datasets.

To answer one-to-many factual queries (e.g., listing cities of a country), a language model (LM) must simultaneously recall knowledge and avoid repeating previous answers. How are these two subtasks implemented and integrated internally? Across multiple datasets and models, we identify a promote-then-suppress mechanism: the model first recalls all answers, and then suppresses previously generated ones. Specifically, LMs use both the subject and previous answer tokens to perform knowledge recall, with attention propagating subject information and MLPs promoting the answers. Then, attention attends to and suppresses previous answer tokens, while MLPs amplify the suppression signal. Our mechanism is corroborated by extensive experimental evidence: in addition to using early decoding and causal tracing, we analyze how components use different tokens by introducing both Token Lens, which decodes aggregated attention updates from specified tokens, and a knockout method that analyzes changes in MLP outputs after removing attention to specified tokens. Overall, we provide new insights into how LMs' internal components interact with different input tokens to support complex factual recall. Code is available at https://github.com/Lorenayannnnn/how-lms-answer-one-to-many-factual-queries.

Existing methods enhance the training of detection transformers by incorporating an auxiliary one-to-many assignment. In this work, we treat the model as a multi-task framework, simultaneously performing one-to-one and one-to-many predictions. We investigate the roles of each component in the transformer decoder across these two training targets, including self-attention, cross-attention, and feed-forward network. Our empirical results demonstrate that any independent component in the decoder can effectively learn both targets simultaneously, even when other components are shared. This finding leads us to propose a multi-route training mechanism, featuring a primary route for one-to-one prediction and two auxiliary training routes for one-to-many prediction. We enhance the training mechanism with a novel instructive self-attention that dynamically and flexibly guides object queries for one-to-many prediction. The auxiliary routes are removed during inference, ensuring no impact on model architecture or inference cost. We conduct extensive experiments on various baselines, achieving consistent improvements as shown in Figure 1. Project page: https://visual-ai.github.io/mrdetr

In this work, we undertake the challenge of augmenting the existing generative capabilities of pre-trained text-only large language models (LLMs) with multi-modal generation capability while satisfying two core constraints: C1 preserving the preservation of original language generative capabilities with negligible performance degradation, and C2 adhering to a small parameter budget to learn the new modality, ensuring scalability and efficiency. In contrast to current approaches that add dedicated modules, thereby significantly increasing the parameter count, we propose a method that leverages the underutilized capacity inherent in deep models. Specifically, we exploit the parameter redundancy within Mixture-of-Experts (MoEs) as a source of additional capacity for learning a new modality, enabling better parameter efficiency (C1). Moreover, we preserve the original language generation capabilities by applying low-rank adaptation exclusively to the tokens of the new modality (C2). Furthermore, we introduce a novel parameter initialization scheme based on the Gromov-Wasserstein distance to improve convergence and training stability. Through an extensive analysis of the routing mechanism, we uncover the emergence of modality-specific pathways and decreased redundancy within the experts that can efficiently unlock multi-modal generative capabilities. Overall, our method can be seamlessly applied to a wide range of contemporary LLMs, providing a new pathway for transitioning from uni-modal to multi-modal architectures.

Deployment of autoregressive large language models (LLMs) is costly, and as these models increase in size, the associated costs will become even more considerable. Consequently, different methods have been proposed to accelerate the token generation process and reduce costs. Speculative decoding (SD) is among the most promising approaches to speed up the LLM decoding process by verifying multiple tokens in parallel and using an auxiliary smaller draft model to generate the possible tokens. In SD, usually, one draft model is used to serve a specific target model; however, in practice, LLMs are diverse, and we might need to deal with many target models or more than one target model simultaneously. In this scenario, it is not clear which draft model should be used for which target model, and searching among different draft models or training customized draft models can further increase deployment costs. In this paper, we first introduce a novel multi-target scenario for the deployment of draft models for faster inference. Then, we present a novel, more efficient sorted speculative decoding mechanism that outperforms regular baselines in multi-target settings. We evaluated our method on Spec-Bench in different settings, including base models such as Vicuna 7B, 13B, and LLama Chat 70B. Our results suggest that our draft models perform better than baselines for multiple target models at the same time.

Predicting gene function from its DNA sequence is a fundamental challenge in biology. Many deep learning models have been proposed to embed DNA sequences and predict their enzymatic function, leveraging information in public databases linking DNA sequences to an enzymatic function label. However, much of the scientific community's knowledge of biological function is not represented in these categorical labels, and is instead captured in unstructured text descriptions of mechanisms, reactions, and enzyme behavior. These descriptions are often captured alongside DNA sequences in biological databases, albeit in an unstructured manner. Deep learning of models predicting enzymatic function are likely to benefit from incorporating this multi-modal data encoding scientific knowledge of biological function. There is, however, no dataset designed for machine learning algorithms to leverage this multi-modal information. Here we propose a novel dataset and benchmark suite that enables the exploration and development of large multi-modal neural network models on gene DNA sequences and natural language descriptions of gene function. We present baseline performance on benchmarks for both unsupervised and supervised tasks that demonstrate the difficulty of this modeling objective, while demonstrating the potential benefit of incorporating multi-modal data types in function prediction compared to DNA sequences alone. Our dataset is at: https://hoarfrost-lab.github.io/BioTalk/.

Scene text recognition (STR) methods have struggled to attain high accuracy and fast inference speed. Autoregressive (AR)-based models implement the recognition in a character-by-character manner, showing superiority in accuracy but with slow inference speed. Alternatively, parallel decoding (PD)-based models infer all characters in a single decoding pass, offering faster inference speed but generally worse accuracy. We first present an empirical study of AR decoding in STR, and discover that the AR decoder not only models linguistic context, but also provides guidance on visual context perception. Consequently, we propose Context Perception Parallel Decoder (CPPD) to predict the character sequence in a PD pass. CPPD devises a character counting module to infer the occurrence count of each character, and a character ordering module to deduce the content-free reading order and placeholders. Meanwhile, the character prediction task associates the placeholders with characters. They together build a comprehensive recognition context. We construct a series of CPPD models and also plug the proposed modules into existing STR decoders. Experiments on both English and Chinese benchmarks demonstrate that the CPPD models achieve highly competitive accuracy while running approximately 8x faster than their AR-based counterparts. Moreover, the plugged models achieve significant accuracy improvements. Code is at https://github.com/PaddlePaddle/PaddleOCR/blob/dygraph/doc/doc_en/algorithm_rec_cppd_en.md{this https URL}.

Non-autoregressive (nAR) models for machine translation (MT) manifest superior decoding speed when compared to autoregressive (AR) models, at the expense of impaired fluency of their outputs. We improve the fluency of a nAR model with connectionist temporal classification (CTC) by employing additional features in the scoring model used during beam search decoding. Since the beam search decoding in our model only requires to run the network in a single forward pass, the decoding speed is still notably higher than in standard AR models. We train models for three language pairs: German, Czech, and Romanian from and into English. The results show that our proposed models can be more efficient in terms of decoding speed and still achieve a competitive BLEU score relative to AR models.

Autoregressive decoding of large language models (LLMs) is memory bandwidth bounded, resulting in high latency and significant wastes of the parallel processing power of modern accelerators. Existing methods for accelerating LLM decoding often require a draft model (e.g., speculative decoding), which is nontrivial to obtain and unable to generalize. In this paper, we introduce Lookahead decoding, an exact, parallel decoding algorithm that accelerates LLM decoding without needing auxiliary models or data stores. It allows trading per-step log(FLOPs) to reduce the number of total decoding steps, is more parallelizable on single or multiple modern accelerators, and is compatible with concurrent memory-efficient attention (e.g., FlashAttention). Our implementation of Lookahead decoding can speed up autoregressive decoding by up to 1.8x on MT-bench and 4x with strong scaling on multiple GPUs in code completion tasks. Our code is avialable at https://github.com/hao-ai-lab/LookaheadDecoding

We propose a novel speculative decoding method tailored for multi-sample reasoning scenarios, such as self-consistency and Best-of-N sampling. Our method exploits the intrinsic consensus of parallel generation paths to synthesize high-quality draft tokens without requiring auxiliary models or external databases. By dynamically analyzing structural patterns across parallel reasoning paths through a probabilistic aggregation mechanism, it identifies consensus token sequences that align with the decoding distribution. Evaluations on mathematical reasoning benchmarks demonstrate a substantial improvement in draft acceptance rates over baselines, while reducing the latency in draft token construction. This work establishes a paradigm shift for efficient multi-sample inference, enabling seamless integration of speculative decoding with sampling-based reasoning techniques.

Understanding molecules is key to understanding organisms and driving advances in drug discovery, requiring interdisciplinary knowledge across chemistry and biology. Although large molecular language models have achieved notable success in interpreting molecular structures, their instruction datasets are limited to the specific knowledge from task-oriented datasets and do not fully cover the fundamental characteristics of molecules, hindering their abilities as general-purpose molecular assistants. To address this issue, we propose Mol-LLaMA, a large molecular language model that grasps the general knowledge centered on molecules via multi-modal instruction tuning. To this end, we design key data types that encompass the fundamental features of molecules, incorporating essential knowledge from molecular structures. In addition, to improve understanding of molecular features, we introduce a module that integrates complementary information from different molecular encoders, leveraging the distinct advantages of different molecular representations. Our experimental results demonstrate that Mol-LLaMA is capable of comprehending the general features of molecules and generating relevant responses to users' queries with detailed explanations, implying its potential as a general-purpose assistant for molecular analysis.

A key goal in mechanistic interpretability is circuit analysis: finding sparse subgraphs of models corresponding to specific behaviors or capabilities. However, MLP sublayers make fine-grained circuit analysis on transformer-based language models difficult. In particular, interpretable features -- such as those found by sparse autoencoders (SAEs) -- are typically linear combinations of extremely many neurons, each with its own nonlinearity to account for. Circuit analysis in this setting thus either yields intractably large circuits or fails to disentangle local and global behavior. To address this we explore transcoders, which seek to faithfully approximate a densely activating MLP layer with a wider, sparsely-activating MLP layer. We successfully train transcoders on language models with 120M, 410M, and 1.4B parameters, and find them to perform at least on par with SAEs in terms of sparsity, faithfulness, and human-interpretability. We then introduce a novel method for using transcoders to perform weights-based circuit analysis through MLP sublayers. The resulting circuits neatly factorize into input-dependent and input-invariant terms. Finally, we apply transcoders to reverse-engineer unknown circuits in the model, and we obtain novel insights regarding the greater-than circuit in GPT2-small. Our results suggest that transcoders can prove effective in decomposing model computations involving MLPs into interpretable circuits. Code is available at https://github.com/jacobdunefsky/transcoder_circuits.

Fiber tractography is a cornerstone of neuroimaging, enabling the detailed mapping of the brain's white matter pathways through diffusion MRI. This is crucial for understanding brain connectivity and function, making it a valuable tool in neurological applications. Despite its importance, tractography faces challenges due to its complexity and susceptibility to false positives, misrepresenting vital pathways. To address these issues, recent strategies have shifted towards deep learning, utilizing supervised learning, which depends on precise ground truth, or reinforcement learning, which operates without it. In this work, we propose Tract-RLFormer, a network utilizing both supervised and reinforcement learning, in a two-stage policy refinement process that markedly improves the accuracy and generalizability across various data-sets. By employing a tract-specific approach, our network directly delineates the tracts of interest, bypassing the traditional segmentation process. Through rigorous validation on datasets such as TractoInferno, HCP, and ISMRM-2015, our methodology demonstrates a leap forward in tractography, showcasing its ability to accurately map the brain's white matter tracts.

Parallel decoding methods such as Jacobi decoding show promise for more efficient LLM inference as it breaks the sequential nature of the LLM decoding process and transforms it into parallelizable computation. However, in practice, it achieves little speedup compared to traditional autoregressive (AR) decoding, primarily because Jacobi decoding seldom accurately predicts more than one token in a single fixed-point iteration step. To address this, we develop a new approach aimed at realizing fast convergence from any state to the fixed point on a Jacobi trajectory. This is accomplished by refining the target LLM to consistently predict the fixed point given any state as input. Extensive experiments demonstrate the effectiveness of our method, showing 2.4times to 3.4times improvements in generation speed while preserving generation quality across both domain-specific and open-domain benchmarks.

Language models (LMs) often struggle to pay enough attention to the input context, and generate texts that are unfaithful or contain hallucinations. To mitigate this issue, we present context-aware decoding (CAD), which follows a contrastive output distribution that amplifies the difference between the output probabilities when a model is used with and without context. Our experiments show that CAD, without additional training, significantly improves the faithfulness of different LM families, including OPT, GPT, LLaMA and FLAN-T5 for summarization tasks (e.g., 14.3% gain for LLaMA in factuality metrics). Furthermore, CAD is particularly effective in overriding a model's prior knowledge when it contradicts the provided context, leading to substantial improvements in tasks where resolving the knowledge conflict is essential.

We create a reusable Transformer, BrainBERT, for intracranial recordings bringing modern representation learning approaches to neuroscience. Much like in NLP and speech recognition, this Transformer enables classifying complex concepts, i.e., decoding neural data, with higher accuracy and with much less data by being pretrained in an unsupervised manner on a large corpus of unannotated neural recordings. Our approach generalizes to new subjects with electrodes in new positions and to unrelated tasks showing that the representations robustly disentangle the neural signal. Just like in NLP where one can study language by investigating what a language model learns, this approach opens the door to investigating the brain by what a model of the brain learns. As a first step along this path, we demonstrate a new analysis of the intrinsic dimensionality of the computations in different areas of the brain. To construct these representations, we combine a technique for producing super-resolution spectrograms of neural data with an approach designed for generating contextual representations of audio by masking. In the future, far more concepts will be decodable from neural recordings by using representation learning, potentially unlocking the brain like language models unlocked language.

Speculative Decoding (SD) is a technique to accelerate the inference of Large Language Models (LLMs) by using a lower complexity draft model to propose candidate tokens verified by a larger target model. To further improve efficiency, Multi-Candidate Speculative Decoding (MCSD) improves upon this by sampling multiple candidate tokens from the draft model at each step and verifying them in parallel, thus increasing the chances of accepting a token and reducing generation time. Existing MCSD methods rely on the draft model to initialize the multi-candidate sequences and use static length and tree attention structure for draft generation. However, such an approach suffers from the draft and target model's output distribution differences, especially in dynamic generation context. In this work, we introduce an improved version of MCSD that includes a target model initialized multi-candidate process, dynamic sliced topology-aware causal mask for dynamic length adjustment, and decision models to optimize early stopping. Our framework improves the acceptance rate, defined as the ratio of the longest draft sequence length accepted by the target model over the maximum draft sequence length, by a maximum of 164% and gains a maximum of 75% generation speed up over the MCSD baseline. We also conduct an ablation study to evaluate the impact of the decision model.

Readers can have different goals with respect to the text they are reading. Can these goals be decoded from the pattern of their eye movements over the text? In this work, we examine for the first time whether it is possible to decode two types of reading goals that are common in daily life: information seeking and ordinary reading. Using large scale eye-tracking data, we apply to this task a wide range of state-of-the-art models for eye movements and text that cover different architectural and data representation strategies, and further introduce a new model ensemble. We systematically evaluate these models at three levels of generalization: new textual item, new participant, and the combination of both. We find that eye movements contain highly valuable signals for this task. We further perform an error analysis which builds on prior empirical findings on differences between ordinary reading and information seeking and leverages rich textual annotations. This analysis reveals key properties of textual items and participant eye movements that contribute to the difficulty of the task.

While interpretability research has shed light on some internal algorithms utilized by transformer-based LLMs, reasoning in natural language, with its deep contextuality and ambiguity, defies easy categorization. As a result, formulating clear and motivating questions for circuit analysis that rely on well-defined in-domain and out-of-domain examples required for causal interventions is challenging. Although significant work has investigated circuits for specific tasks, such as indirect object identification (IOI), deciphering natural language reasoning through circuits remains difficult due to its inherent complexity. In this work, we take initial steps to characterize causal reasoning in LLMs by analyzing clear-cut cause-and-effect sentences like "I opened an umbrella because it started raining," where causal interventions may be possible through carefully crafted scenarios using GPT-2 small. Our findings indicate that causal syntax is localized within the first 2-3 layers, while certain heads in later layers exhibit heightened sensitivity to nonsensical variations of causal sentences. This suggests that models may infer reasoning by (1) detecting syntactic cues and (2) isolating distinct heads in the final layers that focus on semantic relationships.

Despite the remarkable advances in language modeling, current mainstream decoding methods still struggle to generate texts that align with human texts across different aspects. In particular, sampling-based methods produce less-repetitive texts which are often disjunctive in discourse, while search-based methods maintain topic coherence at the cost of increased repetition. Overall, these methods fall short in achieving holistic alignment across a broad range of aspects. In this work, we frame decoding from a language model as an optimization problem with the goal of strictly matching the expected performance with human texts measured by multiple metrics of desired aspects simultaneously. The resulting decoding distribution enjoys an analytical solution that scales the input language model distribution via a sequence-level energy function defined by these metrics. And most importantly, we prove that this induced distribution is guaranteed to improve the perplexity on human texts, which suggests a better approximation to the underlying distribution of human texts. To facilitate tractable sampling from this globally normalized distribution, we adopt the Sampling-Importance-Resampling technique. Experiments on various domains and model scales demonstrate the superiority of our method in metrics alignment with human texts and human evaluation over strong baselines.

Prior works on detoxification are scattered in the sense that they do not cover all aspects of detoxification needed in a real-world scenario. Notably, prior works restrict the task of developing detoxification models to only a seen subset of platforms, leaving the question of how the models would perform on unseen platforms unexplored. Additionally, these works do not address non-detoxifiability, a phenomenon whereby the toxic text cannot be detoxified without altering the meaning. We propose GreenLLaMA, the first comprehensive end-to-end detoxification framework, which attempts to alleviate the aforementioned limitations. We first introduce a cross-platform pseudo-parallel corpus applying multi-step data processing and generation strategies leveraging ChatGPT. We then train a suite of detoxification models with our cross-platform corpus. We show that our detoxification models outperform the SoTA model trained with human-annotated parallel corpus. We further introduce explanation to promote transparency and trustworthiness. GreenLLaMA additionally offers a unique paraphrase detector especially dedicated for the detoxification task to tackle the non-detoxifiable cases. Through experimental analysis, we demonstrate the effectiveness of our cross-platform corpus and the robustness of GreenLLaMA against adversarial toxicity.

The dominance of large decoder-only language models has overshadowed encoder-decoder architectures, despite their fundamental efficiency advantages in sequence processing. For small language models (SLMs) - those with 1 billion parameters or fewer - our systematic analysis across GPU, CPU, and NPU platforms reveals that encoder-decoder architectures achieve 47% lower first-token latency and 4.7x higher throughput compared to decoder-only models on edge devices. These gains may be attributed to encoder-decoder's one-time input processing and efficient separation of understanding and generation phases. We introduce a novel knowledge distillation framework that enables encoder-decoder models to leverage capabilities from large scalable decoder-only teachers while preserving their architectural advantages, achieving up to 6 average performance points improvement across diverse tasks, with significant gains in asymmetric sequence tasks where input and output distributions can benefit from different processing approaches. When combined with modern advances like Rotary Positional Embeddings (RoPE) and Vision encoders, our systematic investigation demonstrates that encoder-decoder architectures provide a more practical path toward deploying capable language models in resource-constrained environments. Our findings challenge the prevailing trend toward decoder-only scaling, showing that architectural choices become increasingly crucial as parameter budgets decrease, particularly for on-device and edge deployments where computational efficiency is paramount.

Autoregressive language models demonstrate excellent performance in various scenarios. However, the inference efficiency is limited by its one-step-one-word generation mode, which has become a pressing problem recently as the models become increasingly larger. Speculative decoding employs a "draft and then verify" mechanism to allow multiple tokens to be generated in one step, realizing lossless acceleration. Existing methods mainly adopt fixed heuristic draft structures, which fail to adapt to different situations to maximize the acceptance length during verification. To alleviate this dilemma, we proposed OPT-Tree, an algorithm to construct adaptive and scalable draft trees. It searches the optimal tree structure that maximizes the mathematical expectation of the acceptance length in each decoding step. Experimental results reveal that OPT-Tree outperforms the existing draft structures and achieves a speed-up ratio of up to 3.2 compared with autoregressive decoding. If the draft model is powerful enough and the node budget is sufficient, it can generate more than ten tokens in a single step. Our code is available at https://github.com/Jikai0Wang/OPT-Tree.

Identifying reliable synthesis pathways in materials chemistry is a complex task, particularly in polymer science, due to the intricate and often non-unique nomenclature of macromolecules. To address this challenge, we propose an agent system that integrates large language models (LLMs) and knowledge graphs (KGs). By leveraging LLMs' powerful capabilities for extracting and recognizing chemical substance names, and storing the extracted data in a structured knowledge graph, our system fully automates the retrieval of relevant literatures, extraction of reaction data, database querying, construction of retrosynthetic pathway trees, further expansion through the retrieval of additional literature and recommendation of optimal reaction pathways. A novel Multi-branched Reaction Pathway Search (MBRPS) algorithm enables the exploration of all pathways, with a particular focus on multi-branched ones, helping LLMs overcome weak reasoning in multi-branched paths. This work represents the first attempt to develop a fully automated retrosynthesis planning agent tailored specially for macromolecules powered by LLMs. Applied to polyimide synthesis, our new approach constructs a retrosynthetic pathway tree with hundreds of pathways and recommends optimized routes, including both known and novel pathways, demonstrating its effectiveness and potential for broader applications.

Commonsense reasoning is a pivotal skill for large language models, yet it presents persistent challenges in specific tasks requiring this competence. Traditional fine-tuning approaches can be resource-intensive and potentially compromise a model's generalization capacity. Furthermore, state-of-the-art language models like GPT-3.5 and Claude are primarily accessible through API calls, which makes fine-tuning models challenging. To address these challenges, we draw inspiration from the outputs of large models for tailored tasks and semi-automatically developed a set of novel prompts from several perspectives, including task-relevance, supportive evidence generation (e.g. chain-of-thought and knowledge), diverse path decoding to aid the model. Experimental results on ProtoQA dataset demonstrate that with better designed prompts we can achieve the new state-of-art(SOTA) on the ProtoQA leaderboard, improving the Max Answer@1 score by 8%, Max Incorrect@1 score by 4% (breakthrough 50% for the first time) compared to the previous SOTA model and achieved an improvement on StrategyQA and CommonsenseQA2.0 (3% and 1%, respectively). Furthermore, with the generated Chain-of-Thought and knowledge, we can improve the interpretability of the model while also surpassing the previous SOTA models. We hope that our work can provide insight for the NLP community to develop better prompts and explore the potential of large language models for more complex reasoning tasks.

The generation speed of LLMs are bottlenecked by autoregressive decoding, where tokens are predicted sequentially one by one. Alternatively, diffusion large language models (dLLMs) theoretically allow for parallel token generation, but in practice struggle to achieve the speed of autoregressive models without significantly sacrificing quality. We therefore introduce adaptive parallel decoding (APD), a novel method that dynamically adjusts the number of tokens sampled in parallel. We achieve this by defining a multiplicative mixture between the dLLM marginal probabilities and the joint probability of sequences under a small auxiliary autoregressive model. This inverts the standard setup of speculative decoding, where the goal is to sample from a large autoregressive verifier by drafting from a smaller model. We further optimize APD by enabling KV caching and limiting the size of the masked input. Altogether, our method puts forward three tunable parameters to flexibly tradeoff throughput and quality. We show that APD provides markedly higher throughput with minimal quality degradations on downstream benchmarks.

Multimodal Large Language Models (MLLMs) have emerged as a central focus in both industry and academia, but often suffer from biases introduced by visual and language priors, which can lead to multimodal hallucination. These biases arise from the visual encoder and the Large Language Model (LLM) backbone, affecting the attention mechanism responsible for aligning multimodal inputs. Existing decoding-based mitigation methods focus on statistical correlations and overlook the causal relationships between attention mechanisms and model output, limiting their effectiveness in addressing these biases. To tackle this issue, we propose a causal inference framework termed CausalMM that applies structural causal modeling to MLLMs, treating modality priors as a confounder between attention mechanisms and output. Specifically, by employing backdoor adjustment and counterfactual reasoning at both the visual and language attention levels, our method mitigates the negative effects of modality priors and enhances the alignment of MLLM's inputs and outputs, with a maximum score improvement of 65.3% on 6 VLind-Bench indicators and 164 points on MME Benchmark compared to conventional methods. Extensive experiments validate the effectiveness of our approach while being a plug-and-play solution. Our code is available at: https://github.com/The-Martyr/CausalMM

Chain-of-Thought (CoT) prompting has significantly enhanced the reasoning abilities of large language models. However, recent studies have shown that models can still perform complex reasoning tasks even when the CoT is replaced with filler(hidden) characters (e.g., "..."), leaving open questions about how models internally process and represent reasoning steps. In this paper, we investigate methods to decode these hidden characters in transformer models trained with filler CoT sequences. By analyzing layer-wise representations using the logit lens method and examining token rankings, we demonstrate that the hidden characters can be recovered without loss of performance. Our findings provide insights into the internal mechanisms of transformer models and open avenues for improving interpretability and transparency in language model reasoning.

General-purpose text decoding approaches are usually adopted for dialogue response generation. Although the quality of the generated responses can be improved with dialogue-specific encoding methods, conversational decoding methods are still under-explored. Inspired by wu2023learning that a good dialogue feature space should follow the rules of locality and isotropy, we present a fine-grained conversational decoding method, termed isotropic and proximal search (IPS). Our method is designed to generate the semantic-concentrated response, while still maintaining informativeness and discrimination against the context. Experiments show that our approach outperforms existing decoding strategies in the dialogue field across both automatic and human evaluation metrics. More in-depth analyses further confirm the effectiveness of our approach.

In the pursuit to understand the intricacies of human brain's visual processing, reconstructing dynamic visual experiences from brain activities emerges as a challenging yet fascinating endeavor. While recent advancements have achieved success in reconstructing static images from non-invasive brain recordings, the domain of translating continuous brain activities into video format remains underexplored. In this work, we introduce NeuroCine, a novel dual-phase framework to targeting the inherent challenges of decoding fMRI data, such as noises, spatial redundancy and temporal lags. This framework proposes spatial masking and temporal interpolation-based augmentation for contrastive learning fMRI representations and a diffusion model enhanced by dependent prior noise for video generation. Tested on a publicly available fMRI dataset, our method shows promising results, outperforming the previous state-of-the-art models by a notable margin of {20.97%}, {31.00%} and {12.30%} respectively on decoding the brain activities of three subjects in the fMRI dataset, as measured by SSIM. Additionally, our attention analysis suggests that the model aligns with existing brain structures and functions, indicating its biological plausibility and interpretability.

We show that autoregressive decoding of a transformer-based language model can realize universal computation, without external intervention or modification of the model's weights. Establishing this result requires understanding how a language model can process arbitrarily long inputs using a bounded context. For this purpose, we consider a generalization of autoregressive decoding where, given a long input, emitted tokens are appended to the end of the sequence as the context window advances. We first show that the resulting system corresponds to a classical model of computation, a Lag system, that has long been known to be computationally universal. By leveraging a new proof, we show that a universal Turing machine can be simulated by a Lag system with 2027 production rules. We then investigate whether an existing large language model can simulate the behaviour of such a universal Lag system. We give an affirmative answer by showing that a single system-prompt can be developed for gemini-1.5-pro-001 that drives the model, under deterministic (greedy) decoding, to correctly apply each of the 2027 production rules. We conclude that, by the Church-Turing thesis, prompted gemini-1.5-pro-001 with extended autoregressive (greedy) decoding is a general purpose computer.

Recent progress in large language models (LLMs) has demonstrated the ability to learn and leverage Internet-scale knowledge through pre-training with autoregressive models. Unfortunately, applying such models to settings with embodied agents, such as robots, is challenging due to their lack of experience with the physical world, inability to parse non-language observations, and ignorance of rewards or safety constraints that robots may require. On the other hand, language-conditioned robotic policies that learn from interaction data can provide the necessary grounding that allows the agent to be correctly situated in the real world, but such policies are limited by the lack of high-level semantic understanding due to the limited breadth of the interaction data available for training them. Thus, if we want to make use of the semantic knowledge in a language model while still situating it in an embodied setting, we must construct an action sequence that is both likely according to the language model and also realizable according to grounded models of the environment. We frame this as a problem similar to probabilistic filtering: decode a sequence that both has high probability under the language model and high probability under a set of grounded model objectives. We demonstrate this guided decoding strategy is able to solve complex, long-horizon embodiment tasks in a robotic setting by leveraging the knowledge of both models. The project's website can be found at grounded-decoding.github.io.

RNA plays a pivotal role in translating genetic instructions into functional outcomes, underscoring its importance in biological processes and disease mechanisms. Despite the emergence of numerous deep learning approaches for RNA, particularly universal RNA language models, there remains a significant lack of standardized benchmarks to assess the effectiveness of these methods. In this study, we introduce the first comprehensive RNA benchmark BEACON (BEnchmArk for COmprehensive RNA Task and Language Models). First, BEACON comprises 13 distinct tasks derived from extensive previous work covering structural analysis, functional studies, and engineering applications, enabling a comprehensive assessment of the performance of methods on various RNA understanding tasks. Second, we examine a range of models, including traditional approaches like CNNs, as well as advanced RNA foundation models based on language models, offering valuable insights into the task-specific performances of these models. Third, we investigate the vital RNA language model components from the tokenizer and positional encoding aspects. Notably, our findings emphasize the superiority of single nucleotide tokenization and the effectiveness of Attention with Linear Biases (ALiBi) over traditional positional encoding methods. Based on these insights, a simple yet strong baseline called BEACON-B is proposed, which can achieve outstanding performance with limited data and computational resources. The datasets and source code of our benchmark are available at https://github.com/terry-r123/RNABenchmark.

Large Language Models (LLMs) typically generate outputs token by token using a fixed compute budget, leading to inefficient resource utilization. To address this shortcoming, recent advancements in mixture of expert (MoE) models, speculative decoding, and early exit strategies leverage the insight that computational demands can vary significantly based on the complexity and nature of the input. However, identifying optimal routing patterns for dynamic execution remains an open challenge, limiting the full potential of these adaptive methods. To address this need, we study adaptive computation in LLMs more systematically. We propose a novel framework that integrates smaller auxiliary modules within each Feed-Forward Network layer of the LLM. This design enables dynamic routing of tokens based on task complexity: tokens can be processed by either the small or big modules at each layer, or even bypass certain layers entirely. This allows us to introduce a novel notion of a token's difficulty, defined by its potential to benefit from additional computational resources. Importantly, by employing oracles to identify optimal patterns of adaptive computations, we gain valuable insights into the internal workings of LLMs and the routing processes in a simplified heterogeneous MoE setup. We show that trained routers operate differently from oracles and often yield suboptimal solutions. Notably, activating a large module in just one layer outperforms models that use large modules across all layers, underscoring the gap between practical implementations of routing in MoE models and theoretical optima for adaptive computation.

Reliably generating structured outputs has become a critical capability for modern language model (LM) applications. Constrained decoding has emerged as the dominant technology across sectors for enforcing structured outputs during generation. Despite its growing adoption, little has been done with the systematic evaluation of the behaviors and performance of constrained decoding. Constrained decoding frameworks have standardized around JSON Schema as a structured data format, with most uses guaranteeing constraint compliance given a schema. However, there is poor understanding of the effectiveness of the methods in practice. We present an evaluation framework to assess constrained decoding approaches across three critical dimensions: efficiency in generating constraint-compliant outputs, coverage of diverse constraint types, and quality of the generated outputs. To facilitate this evaluation, we introduce JSONSchemaBench, a benchmark for constrained decoding comprising 10K real-world JSON schemas that encompass a wide range of constraints with varying complexity. We pair the benchmark with the existing official JSON Schema Test Suite and evaluate six state-of-the-art constrained decoding frameworks, including Guidance, Outlines, Llamacpp, XGrammar, OpenAI, and Gemini. Through extensive experiments, we gain insights into the capabilities and limitations of constrained decoding on structured generation with real-world JSON schemas. Our work provides actionable insights for improving constrained decoding frameworks and structured generation tasks, setting a new standard for evaluating constrained decoding and structured generation. We release JSONSchemaBench at https://github.com/guidance-ai/jsonschemabench

Large language models (LLMs) have demonstrated remarkable capabilities in tasks requiring reasoning and multi-step problem-solving through the use of chain-of-thought (CoT) prompting. However, generating the full CoT process results in significantly longer output sequences, leading to increased computational costs and latency during inference. To address this challenge, we propose a novel approach to compress the CoT process through semantic alignment, enabling more efficient decoding while preserving the benefits of CoT reasoning. Our method introduces an auxiliary CoT model that learns to generate and compress the full thought process into a compact special token representation semantically aligned with the original CoT output. This compressed representation is then integrated into the input of the Hidden Chain-of-Thought (HCoT) model. The training process follows a two-stage procedure: First, the CoT model is optimized to generate the compressed token representations aligned with the ground-truth CoT outputs using a contrastive loss. Subsequently, with the CoT model parameters frozen, the HCoT model is fine-tuned to generate accurate subsequent predictions conditioned on the prefix instruction and the compressed CoT representations from the CoT model. Extensive experiments across three challenging domains - mathematical reasoning, agent invocation, and question answering - demonstrate that our semantic compression approach achieves competitive or improved performance compared to the full CoT baseline, while providing significant speedups of at least 1.5x in decoding time. Moreover, incorporating contrastive learning objectives further enhances the quality of the compressed representations, leading to better CoT prompting and improved task accuracy. Our work paves the way for more efficient exploitation of multi-step reasoning capabilities in LLMs across a wide range of applications.

Models for question answering, dialogue agents, and summarization often interpret the meaning of a sentence in a rich context and use that meaning in a new context. Taking excerpts of text can be problematic, as key pieces may not be explicit in a local window. We isolate and define the problem of sentence decontextualization: taking a sentence together with its context and rewriting it to be interpretable out of context, while preserving its meaning. We describe an annotation procedure, collect data on the Wikipedia corpus, and use the data to train models to automatically decontextualize sentences. We present preliminary studies that show the value of sentence decontextualization in a user facing task, and as preprocessing for systems that perform document understanding. We argue that decontextualization is an important subtask in many downstream applications, and that the definitions and resources provided can benefit tasks that operate on sentences that occur in a richer context.

Pre-trained text encoders have rapidly advanced the state of the art on many NLP tasks. We focus on one such model, BERT, and aim to quantify where linguistic information is captured within the network. We find that the model represents the steps of the traditional NLP pipeline in an interpretable and localizable way, and that the regions responsible for each step appear in the expected sequence: POS tagging, parsing, NER, semantic roles, then coreference. Qualitative analysis reveals that the model can and often does adjust this pipeline dynamically, revising lower-level decisions on the basis of disambiguating information from higher-level representations.

Self-consistency-based approaches, which involve repeatedly sampling multiple outputs and selecting the most consistent one as the final response, prove to be remarkably effective in improving the factual accuracy of large language models. Nonetheless, existing methods usually have strict constraints on the task format, largely limiting their applicability. In this paper, we present Integrative Decoding (ID), to unlock the potential of self-consistency in open-ended generation tasks. ID operates by constructing a set of inputs, each prepended with a previously sampled response, and then processes them concurrently, with the next token being selected by aggregating of all their corresponding predictions at each decoding step. In essence, this simple approach implicitly incorporates self-consistency in the decoding objective. Extensive evaluation shows that ID consistently enhances factuality over a wide range of language models, with substantial improvements on the TruthfulQA (+11.2%), Biographies (+15.4%) and LongFact (+8.5%) benchmarks. The performance gains amplify progressively as the number of sampled responses increases, indicating the potential of ID to scale up with repeated sampling.

The ability to generate natural language sequences from source code snippets has a variety of applications such as code summarization, documentation, and retrieval. Sequence-to-sequence (seq2seq) models, adopted from neural machine translation (NMT), have achieved state-of-the-art performance on these tasks by treating source code as a sequence of tokens. We present {scriptsize CODE2SEQ}: an alternative approach that leverages the syntactic structure of programming languages to better encode source code. Our model represents a code snippet as the set of compositional paths in its abstract syntax tree (AST) and uses attention to select the relevant paths while decoding. We demonstrate the effectiveness of our approach for two tasks, two programming languages, and four datasets of up to 16M examples. Our model significantly outperforms previous models that were specifically designed for programming languages, as well as state-of-the-art NMT models. An interactive online demo of our model is available at http://code2seq.org. Our code, data and trained models are available at http://github.com/tech-srl/code2seq.

Accelerating the inference of large language models (LLMs) is a critical challenge in generative AI. Speculative decoding (SD) methods offer substantial efficiency gains by generating multiple tokens using a single target forward pass. However, existing SD approaches require the drafter and target models to share the same vocabulary, thus limiting the pool of possible drafters, often necessitating the training of a drafter from scratch. We present three new SD methods that remove this shared-vocabulary constraint. All three methods preserve the target distribution (i.e., they are lossless) and work with off-the-shelf models without requiring additional training or modifications. Empirically, on summarization, programming, and long-context tasks, our algorithms achieve significant speedups over standard autoregressive decoding. By enabling any off-the-shelf model to serve as drafter and requiring no retraining, this work substantially broadens the applicability of the SD framework in practice.

Speculative decoding is an inference-acceleration method for large language models (LLMs) where a small language model generates a draft-token sequence which is further verified by the target LLM in parallel. Recent works have advanced this method by establishing a draft-token tree, achieving superior performance over a single-sequence speculative decoding. However, those works independently generate tokens at each level of the tree, not leveraging the tree's entire diversifiability. Besides, their empirical superiority has been shown for fixed length of sequences, implicitly granting more computational resource to LLM for the tree-based methods. None of the existing works has conducted empirical studies with fixed target computational budgets despite its importance to resource-bounded devices. We present Recursive Speculative Decoding (RSD), a novel tree-based method that samples draft tokens without replacement and maximizes the diversity of the tree. During RSD's drafting, the tree is built by either Gumbel-Top-k trick that draws tokens without replacement in parallel or Stochastic Beam Search that samples sequences without replacement while early-truncating unlikely draft sequences and reducing the computational cost of LLM. We empirically evaluate RSD with Llama 2 and OPT models, showing that RSD outperforms the baseline methods, consistently for fixed draft sequence length and in most cases for fixed computational budgets at LLM.

Existing speculative decoding methods typically require additional model structure and training processes to assist the model for draft token generation. This makes the migration of acceleration methods to the new model more costly and more demanding on device memory. To address this problem, we propose the Make Some Noise (MSN) training framework as a replacement for the supervised fine-tuning stage of the large language model. The training method simply introduces some noise at the input for the model to learn the denoising task. It significantly enhances the parallel decoding capability of the model without affecting the original task capability. In addition, we propose a tree-based retrieval-augmented Jacobi (TR-Jacobi) decoding strategy to further improve the inference speed of MSN models. Experiments in both the general and code domains have shown that MSN can improve inference speed by 2.3-2.7x times without compromising model performance. The MSN model also achieves comparable acceleration ratios to the SOTA model with additional model structure on Spec-Bench.

Fine-tuned language models use greedy decoding to answer reading comprehension questions with relative success. However, this approach does not ensure that the answer is a span in the given passage, nor does it guarantee that it is the most probable one. Does greedy decoding actually perform worse than an algorithm that does adhere to these properties? To study the performance and optimality of greedy decoding, we present exact-extract, a decoding algorithm that efficiently finds the most probable answer span in the context. We compare the performance of T5 with both decoding algorithms on zero-shot and few-shot extractive question answering. When no training examples are available, exact-extract significantly outperforms greedy decoding. However, greedy decoding quickly converges towards the performance of exact-extract with the introduction of a few training examples, becoming more extractive and increasingly likelier to generate the most probable span as the training set grows. We also show that self-supervised training can bias the model towards extractive behavior, increasing performance in the zero-shot setting without resorting to annotated examples. Overall, our results suggest that pretrained language models are so good at adapting to extractive question answering, that it is often enough to fine-tune on a small training set for the greedy algorithm to emulate the optimal decoding strategy.

In recent years, graph representation learning has undergone a paradigm shift, driven by the emergence and proliferation of graph neural networks (GNNs) and their heterogeneous counterparts. Heterogeneous GNNs have shown remarkable success in extracting low-dimensional embeddings from complex graphs that encompass diverse entity types and relationships. While meta-path-based techniques have long been recognized for their ability to capture semantic affinities among nodes, their dependence on manual specification poses a significant limitation. In contrast, matrix-focused methods accelerate processing by utilizing structural cues but often overlook contextual richness. In this paper, we challenge the current paradigm by introducing ontology as a fundamental semantic primitive within complex graphs. Our goal is to integrate the strengths of both matrix-centric and meta-path-based approaches into a unified framework. We propose perturbation Ontology-based Graph Attention Networks (POGAT), a novel methodology that combines ontology subgraphs with an advanced self-supervised learning paradigm to achieve a deep contextual understanding. The core innovation of POGAT lies in our enhanced homogeneous perturbing scheme designed to generate rigorous negative samples, encouraging the model to explore minimal contextual features more thoroughly. Through extensive empirical evaluations, we demonstrate that POGAT significantly outperforms state-of-the-art baselines, achieving a groundbreaking improvement of up to 10.78\% in F1-score for the critical task of link prediction and 12.01\% in Micro-F1 for the critical task of node classification.

We demonstrate text as a strong cross-modal interface. Rather than relying on deep embeddings to connect image and language as the interface representation, our approach represents an image as text, from which we enjoy the interpretability and flexibility inherent to natural language. We employ an autoencoder that uses a pre-trained text-to-image diffusion model for decoding. The encoder is trained to transform an input image into text, which is then fed into the fixed text-to-image diffusion decoder to reconstruct the original input -- a process we term De-Diffusion. Experiments validate both the precision and comprehensiveness of De-Diffusion text representing images, such that it can be readily ingested by off-the-shelf text-to-image tools and LLMs for diverse multi-modal tasks. For example, a single De-Diffusion model can generalize to provide transferable prompts for different text-to-image tools, and also achieves a new state of the art on open-ended vision-language tasks by simply prompting large language models with few-shot examples.

Quality Estimation (QE) models for Neural Machine Translation (NMT) predict the quality of the hypothesis without having access to the reference. An emerging research direction in NMT involves the use of QE models, which have demonstrated high correlations with human judgment and can enhance translations through Quality-Aware Decoding. Although several approaches have been proposed based on sampling multiple candidate translations and picking the best candidate, none have integrated these models directly into the decoding process. In this paper, we address this by proposing a novel token-level QE model capable of reliably scoring partial translations. We build a uni-directional QE model for this, as decoder models are inherently trained and efficient on partial sequences. We then present a decoding strategy that integrates the QE model for Quality-Aware decoding and demonstrate that the translation quality improves when compared to the N-best list re-ranking with state-of-the-art QE models (up to 1.39 XCOMET-XXL uparrow). Finally, we show that our approach provides significant benefits in document translation tasks, where the quality of N-best lists is typically suboptimal. Code can be found at https://ai4lt.iar.kit.edu/english/projects\_kontextmt.php

Open-ended text generation with autoregressive language models (LMs) is one of the core tasks in natural language processing. However, maximization-based decoding methods (e.g., greedy/beam search) often lead to the degeneration problem, i.e., the generated text is unnatural and contains undesirable repetitions. Existing solutions to this problem either introduce randomness prone to incoherence or require a look-ahead mechanism that demands extra computational overhead. In this study, we formulate open-ended text generation from a new perspective, i.e., we view it as an exploration process within a directed graph. Thereby, we understand the phenomenon of degeneration as circular loops within the directed graph. Based on our formulation, we propose a novel decoding method -- momentum decoding -- which encourages the LM to greedily explore new nodes outside the current graph. Meanwhile, it also allows the LM to return to the existing nodes with a momentum downgraded by a pre-defined resistance function. We extensively test our approach on three benchmarks from different domains through automatic and human evaluations. The results show that momentum decoding performs comparably with the current state of the art while enjoying notably improved inference speed and computation FLOPs. Furthermore, we conduct a detailed analysis to reveal the merits and inner workings of our approach. Our codes and other related resources are publicly available at https://github.com/gmftbyGMFTBY/MomentumDecoding.

How to decode human vision through neural signals has attracted a long-standing interest in neuroscience and machine learning. Modern contrastive learning and generative models improved the performance of fMRI-based visual decoding and reconstruction. However, the high cost and low temporal resolution of fMRI limit their applications in brain-computer interfaces (BCIs), prompting a high need for EEG-based visual reconstruction. In this study, we present an EEG-based visual reconstruction framework. It consists of a plug-and-play EEG encoder called the Adaptive Thinking Mapper (ATM), which is aligned with image embeddings, and a two-stage EEG guidance image generator that first transforms EEG features into image priors and then reconstructs the visual stimuli with a pre-trained image generator. Our approach allows EEG embeddings to achieve superior performance in image classification and retrieval tasks. Our two-stage image generation strategy vividly reconstructs images seen by humans. Furthermore, we analyzed the impact of signals from different time windows and brain regions on decoding and reconstruction. The versatility of our framework is demonstrated in the magnetoencephalogram (MEG) data modality. We report that EEG-based visual decoding achieves SOTA performance, highlighting the portability, low cost, and high temporal resolution of EEG, enabling a wide range of BCI applications. The code of ATM is available at https://github.com/dongyangli-del/EEG_Image_decode.

In the rapidly evolving landscape of artificial intelligence, multi-modal large language models are emerging as a significant area of interest. These models, which combine various forms of data input, are becoming increasingly popular. However, understanding their internal mechanisms remains a complex task. Numerous advancements have been made in the field of explainability tools and mechanisms, yet there is still much to explore. In this work, we present a novel interactive application aimed towards understanding the internal mechanisms of large vision-language models. Our interface is designed to enhance the interpretability of the image patches, which are instrumental in generating an answer, and assess the efficacy of the language model in grounding its output in the image. With our application, a user can systematically investigate the model and uncover system limitations, paving the way for enhancements in system capabilities. Finally, we present a case study of how our application can aid in understanding failure mechanisms in a popular large multi-modal model: LLaVA.

In Recurrent Neural Networks (RNNs), encoding information in a suboptimal or erroneous way can impact the quality of representations based on later elements in the sequence and subsequently lead to wrong predictions and a worse model performance. In humans, challenging cases like garden path sentences (an instance of this being the infamous "The horse raced past the barn fell") can lead their language understanding astray. However, they are still able to correct their representation accordingly and recover when new information is encountered. Inspired by this, I propose an augmentation to standard RNNs in form of a gradient-based correction mechanism: This way I hope to enable such models to dynamically adapt their inner representation of a sentence, adding a way to correct deviations as soon as they occur. This could therefore lead to more robust models using more flexible representations, even during inference time. I conduct different experiments in the context of language modeling, where the impact of using such a mechanism is examined in detail. To this end, I look at modifications based on different kinds of time-dependent error signals and how they influence the model performance. Furthermore, this work contains a study of the model's confidence in its predictions during training and for challenging test samples and the effect of the manipulation thereof. Lastly, I also study the difference in behavior of these novel models compared to a standard LSTM baseline and investigate error cases in detail to identify points of future research. I show that while the proposed approach comes with promising theoretical guarantees and an appealing intuition, it is only able to produce minor improvements over the baseline due to challenges in its practical application and the efficacy of the tested model variants.

We introduce a new approach to systematically map features discovered by sparse autoencoder across consecutive layers of large language models, extending earlier work that examined inter-layer feature links. By using a data-free cosine similarity technique, we trace how specific features persist, transform, or first appear at each stage. This method yields granular flow graphs of feature evolution, enabling fine-grained interpretability and mechanistic insights into model computations. Crucially, we demonstrate how these cross-layer feature maps facilitate direct steering of model behavior by amplifying or suppressing chosen features, achieving targeted thematic control in text generation. Together, our findings highlight the utility of a causal, cross-layer interpretability framework that not only clarifies how features develop through forward passes but also provides new means for transparent manipulation of large language models.

Recent advances in interpretability suggest we can project weights and hidden states of transformer-based language models (LMs) to their vocabulary, a transformation that makes them human interpretable and enables us to assign semantics to what was seen only as numerical vectors. In this paper, we interpret LM attention heads and memory values, the vectors the models dynamically create and recall while processing a given input. By analyzing the tokens they represent through this projection, we identify patterns in the information flow inside the attention mechanism. Based on these discoveries, we create a tool to visualize a forward pass of Generative Pre-trained Transformers (GPTs) as an interactive flow graph, with nodes representing neurons or hidden states and edges representing the interactions between them. Our visualization simplifies huge amounts of data into easy-to-read plots that reflect why models output their results. We demonstrate the utility of our modeling by identifying the effect LM components have on the intermediate processing in the model before outputting a prediction. For instance, we discover that layer norms are used as semantic filters and find neurons that act as regularization vectors.

Given a language model (LM), maximum probability is a poor decoding objective for open-ended generation, because it produces short and repetitive text. On the other hand, sampling can often produce incoherent text that drifts from the original topics. We propose contrastive decoding (CD), a reliable decoding approach that optimizes a contrastive objective subject to a plausibility constraint. The contrastive objective returns the difference between the likelihood under a large LM (called the expert, e.g. OPT-13B) and a small LM (called the amateur, e.g. OPT-125M), and the constraint ensures that the outputs are plausible. CD is inspired by the fact that the failures of larger LMs (e.g., repetition, incoherence) are even more prevalent in smaller LMs, and that this difference signals which texts should be preferred. CD requires zero additional training, and produces higher quality text than decoding from the larger LM alone. It also works across model scales (OPT-13B and GPT2-1.5B) and significantly outperforms four strong decoding algorithms (e.g., nucleus, top-k) in automatic and human evaluations across wikipedia, news and story domains.

Large language models (LLMs) have shown impressive capabilities in adapting to various tasks when provided with task-specific instructions. However, LLMs using standard decoding strategies often struggle with deviations from the inputs. Intuitively, compliant LLM outputs should reflect the information present in the input, which can be measured by point-wise mutual information (PMI) scores. Therefore, we propose Diver, a novel approach that enhances LLM Decoding through span-level PMI verification. During inference, Diver first identifies divergence steps that may lead to multiple candidate spans. Subsequently, it calculates the PMI scores by assessing the log-likelihood gains of the input if the candidate spans are generated. Finally, the optimal span is selected based on the PMI re-ranked output distributions. We evaluate our method across various downstream tasks, and empirical results demonstrate that Diver significantly outperforms existing decoding methods in both performance and versatility.

We propose an acceleration scheme for large language models (LLMs) through Speculative Decoding with Semantic Adaptive Tokens (SDSAT). The primary objective of this design is to enhance the LLM model's ability to generate draft tokens more accurately without compromising the model's accuracy. The core strategies involve: 1) Fine-tune the model by incorporating semantic adaptive tokens that possess flexible decoding capabilities without changing its structure, allowing them to generate high-quality draft tokens. 2) By employing a training method that does not affect the standard tokens, the model can acquire parallel decoding abilities atop its original framework with minimal training overhead. 3) We have designed the "two-step-draft-then-verify" generation strategies using both greedy search and nucleus sampling. Experiments conducted on the CodeLlama-13B and 7B models have yielded speed increases of over 3.5X and 3.0X, respectively. Please refer to https://github.com/hasuoshenyun/SDSAT.

Diffusion-based large language models (Diffusion LLMs) have shown promise for non-autoregressive text generation with parallel decoding capabilities. However, the practical inference speed of open-sourced Diffusion LLMs often lags behind autoregressive models due to the lack of Key-Value (KV) Cache and quality degradation when decoding multiple tokens simultaneously. To bridge this gap, we introduce a novel block-wise approximate KV Cache mechanism tailored for bidirectional diffusion models, enabling cache reuse with negligible performance drop. Additionally, we identify the root cause of generation quality degradation in parallel decoding as the disruption of token dependencies under the conditional independence assumption. To address this, we propose a confidence-aware parallel decoding strategy that selectively decodes tokens exceeding a confidence threshold, mitigating dependency violations and maintaining generation quality. Experimental results on LLaDA and Dream models across multiple LLM benchmarks demonstrate up to 27.6times throughput improvement with minimal accuracy loss, closing the performance gap with autoregressive models and paving the way for practical deployment of Diffusion LLMs.

Large Language Models (LLMs) often hallucinate, producing unfaithful or factually incorrect outputs by misrepresenting the provided context or incorrectly recalling internal knowledge. Recent studies have identified specific attention heads within the Transformer architecture, known as retrieval heads, responsible for extracting relevant contextual information. We hypothesise that masking these retrieval heads can induce hallucinations and that contrasting the outputs of the base LLM and the masked LLM can reduce hallucinations. To this end, we propose Decoding by Contrasting Retrieval Heads (DeCoRe), a novel training-free decoding strategy that amplifies information found in the context and model parameters. DeCoRe mitigates potentially hallucinated responses by dynamically contrasting the outputs of the base LLM and the masked LLM, using conditional entropy as a guide. Our extensive experiments confirm that DeCoRe significantly improves performance on tasks requiring high contextual faithfulness, such as summarisation (XSum by 18.6%), instruction following (MemoTrap by 10.9%), and open-book question answering (NQ-Open by 2.4% and NQ-Swap by 5.5%).

Diffusion models have emerged as the new state-of-the-art family of deep generative models, and their promising potentials for text generation have recently attracted increasing attention. Existing studies mostly adopt a single encoder architecture with partially noising processes for conditional text generation, but its degree of flexibility for conditional modeling is limited. In fact, the encoder-decoder architecture is naturally more flexible for its detachable encoder and decoder modules, which is extensible to multilingual and multimodal generation tasks for conditions and target texts. However, the encoding process of conditional texts lacks the understanding of target texts. To this end, a spiral interaction architecture for encoder-decoder text diffusion (DiffuSIA) is proposed. Concretely, the conditional information from encoder is designed to be captured by the diffusion decoder, while the target information from decoder is designed to be captured by the conditional encoder. These two types of information flow run through multilayer interaction spirally for deep fusion and understanding. DiffuSIA is evaluated on four text generation tasks, including paraphrase, text simplification, question generation, and open-domain dialogue generation. Experimental results show that DiffuSIA achieves competitive performance among previous methods on all four tasks, demonstrating the effectiveness and generalization ability of the proposed method.

Unlocking deep, interpretable biological reasoning from complex genomic data is a major AI challenge hindering scientific discovery. Current DNA foundation models, despite strong sequence representation, struggle with multi-step reasoning and lack inherent transparent, biologically intuitive explanations. We introduce BioReason, a pioneering architecture that, for the first time, deeply integrates a DNA foundation model with a Large Language Model (LLM). This novel connection enables the LLM to directly process and reason with genomic information as a fundamental input, fostering a new form of multimodal biological understanding. BioReason's sophisticated multi-step reasoning is developed through supervised fine-tuning and targeted reinforcement learning, guiding the system to generate logical, biologically coherent deductions. On biological reasoning benchmarks including KEGG-based disease pathway prediction - where accuracy improves from 88% to 97% - and variant effect prediction, BioReason demonstrates an average 15% performance gain over strong single-modality baselines. BioReason reasons over unseen biological entities and articulates decision-making through interpretable, step-by-step biological traces, offering a transformative approach for AI in biology that enables deeper mechanistic insights and accelerates testable hypothesis generation from genomic data. Data, code, and checkpoints are publicly available at https://github.com/bowang-lab/BioReason

Human readers can efficiently comprehend scrambled words, a phenomenon known as Typoglycemia, primarily by relying on word form; if word form alone is insufficient, they further utilize contextual cues for interpretation. While advanced large language models (LLMs) exhibit similar abilities, the underlying mechanisms remain unclear. To investigate this, we conduct controlled experiments to analyze the roles of word form and contextual information in semantic reconstruction and examine LLM attention patterns. Specifically, we first propose SemRecScore, a reliable metric to quantify the degree of semantic reconstruction, and validate its effectiveness. Using this metric, we study how word form and contextual information influence LLMs' semantic reconstruction ability, identifying word form as the core factor in this process. Furthermore, we analyze how LLMs utilize word form and find that they rely on specialized attention heads to extract and process word form information, with this mechanism remaining stable across varying levels of word scrambling. This distinction between LLMs' fixed attention patterns primarily focused on word form and human readers' adaptive strategy in balancing word form and contextual information provides insights into enhancing LLM performance by incorporating human-like, context-aware mechanisms.

Interpretability methods seek to understand language model representations, yet the outputs of most such methods -- circuits, vectors, scalars -- are not immediately human-interpretable. In response, we introduce LatentQA, the task of answering open-ended questions about model activations in natural language. Towards solving LatentQA, we propose Latent Interpretation Tuning (LIT), which finetunes a decoder LLM on a dataset of activations and associated question-answer pairs, similar to how visual instruction tuning trains on question-answer pairs associated with images. We use the decoder for diverse reading applications, such as extracting relational knowledge from representations or uncovering system prompts governing model behavior. Our decoder also specifies a differentiable loss that we use to control models, such as debiasing models on stereotyped sentences and controlling the sentiment of generations. Finally, we extend LatentQA to reveal harmful model capabilities, such as generating recipes for bioweapons and code for hacking.

Large language models (LLMs) have recently shown remarkable performance across a wide range of tasks. However, the substantial number of parameters in LLMs contributes to significant latency during model inference. This is particularly evident when utilizing autoregressive decoding methods, which generate one token in a single forward process, thereby not fully capitalizing on the parallel computing capabilities of GPUs. In this paper, we propose a novel parallel decoding approach, namely hidden transfer, which decodes multiple successive tokens simultaneously in a single forward pass. The idea is to transfer the intermediate hidden states of the previous context to the pseudo hidden states of the future tokens to be generated, and then the pseudo hidden states will pass the following transformer layers thereby assimilating more semantic information and achieving superior predictive accuracy of the future tokens. Besides, we use the novel tree attention mechanism to simultaneously generate and verify multiple candidates of output sequences, which ensure the lossless generation and further improves the generation efficiency of our method. Experiments demonstrate the effectiveness of our method. We conduct a lot of analytic experiments to prove our motivation. In terms of acceleration metrics, we outperform all the single-model acceleration techniques, including Medusa and Self-Speculative decoding.

This article explores the adaptive relationship between Encoder Layers and Decoder Layers using the SOTA model Helsinki-NLP/opus-mt-de-en, which translates German to English. The specific method involves introducing a bias-free fully connected layer between the Encoder and Decoder, with different initializations of the layer's weights, and observing the outcomes of fine-tuning versus retraining. Four experiments were conducted in total. The results suggest that directly modifying the pre-trained model structure for fine-tuning yields suboptimal performance. However, upon observing the outcomes of the experiments with retraining, this structural adjustment shows significant potential.

Speculative Decoding (SD) is a popular lossless technique for accelerating the inference of Large Language Models (LLMs). We show that the decoding speed of SD frameworks with static draft structures can be significantly improved by incorporating context-aware adaptive draft structures. However, current studies on adaptive draft structures are limited by their performance, modeling approaches, and applicability. In this paper, we introduce AdaEAGLE, the first SD framework that explicitly models adaptive draft structures. AdaEAGLE leverages the Lightweight Draft Length Predictor (LDLP) module to explicitly predict the optimal number of draft tokens during inference to guide the draft model. It achieves comparable speedup results without manual thresholds and allows for deeper, more specialized optimizations. Moreover, together with threshold-based strategies, AdaEAGLE achieves a 1.62times speedup over the vanilla AR decoding and outperforms fixed-length SotA baseline while maintaining output quality.

Current state-of-the-art machine translation systems are based on encoder-decoder architectures, that first encode the input sequence, and then generate an output sequence based on the input encoding. Both are interfaced with an attention mechanism that recombines a fixed encoding of the source tokens based on the decoder state. We propose an alternative approach which instead relies on a single 2D convolutional neural network across both sequences. Each layer of our network re-codes source tokens on the basis of the output sequence produced so far. Attention-like properties are therefore pervasive throughout the network. Our model yields excellent results, outperforming state-of-the-art encoder-decoder systems, while being conceptually simpler and having fewer parameters.

Large language models (LLMs) are increasingly recognized as powerful tools for scientific discovery, particularly in molecular science. A fundamental requirement for these models is the ability to accurately understand molecular structures, commonly encoded in the SMILES representation. However, current LLMs struggle to interpret SMILES, even failing to carry out basic tasks such as counting molecular rings. To address this limitation, we introduce CLEANMOL, a novel framework that formulates SMILES parsing into a suite of clean and deterministic tasks explicitly designed to promote graph-level molecular comprehension. These tasks span from subgraph matching to global graph matching, providing structured supervision aligned with molecular structural properties. We construct a molecular pretraining dataset with adaptive difficulty scoring and pre-train open-source LLMs on these tasks. Our results show that CLEANMOL not only enhances structural comprehension but also achieves the best or competes with the baseline on the Mol-Instructions benchmark.

In the past five years, the use of generative and foundational AI systems has greatly improved the decoding of brain activity. Visual perception, in particular, can now be decoded from functional Magnetic Resonance Imaging (fMRI) with remarkable fidelity. This neuroimaging technique, however, suffers from a limited temporal resolution (approx0.5 Hz) and thus fundamentally constrains its real-time usage. Here, we propose an alternative approach based on magnetoencephalography (MEG), a neuroimaging device capable of measuring brain activity with high temporal resolution (approx5,000 Hz). For this, we develop an MEG decoding model trained with both contrastive and regression objectives and consisting of three modules: i) pretrained embeddings obtained from the image, ii) an MEG module trained end-to-end and iii) a pretrained image generator. Our results are threefold: Firstly, our MEG decoder shows a 7X improvement of image-retrieval over classic linear decoders. Second, late brain responses to images are best decoded with DINOv2, a recent foundational image model. Third, image retrievals and generations both suggest that high-level visual features can be decoded from MEG signals, although the same approach applied to 7T fMRI also recovers better low-level features. Overall, these results, while preliminary, provide an important step towards the decoding -- in real-time -- of the visual processes continuously unfolding within the human brain.

Network interpretation as an effort to reveal the features learned by a network remains largely visualization-based. In this paper, our goal is to tackle semantic network interpretation at both filter and decision level. For filter-level interpretation, we represent the concepts a filter encodes with a probability distribution of visual attributes. The decision-level interpretation is achieved by textual summarization that generates an explanatory sentence containing clues behind a network's decision. A Bayesian inference algorithm is proposed to automatically associate filters and network decisions with visual attributes. Human study confirms that the semantic interpretation is a beneficial alternative or complement to visualization methods. We demonstrate the crucial role that semantic network interpretation can play in understanding a network's failure patterns. More importantly, semantic network interpretation enables a better understanding of the correlation between a model's performance and its distribution metrics like filter selectivity and concept sparseness.

Large Language Models (LLMs) require alignment with human preferences to avoid generating offensive, false, or meaningless content. Recently, low-resource methods for LLM alignment have been popular, while still facing challenges in obtaining both high-quality and aligned content. Motivated by the observation that the difficulty of generating aligned responses is concentrated at the beginning of decoding, we propose a novel framework, Weak-to-Strong Decoding (WSD), to enhance the alignment ability of base models by the guidance of a small aligned model. The small model first drafts well-aligned beginnings, followed by the large base model to continue the rest, controlled by a well-designed auto-switch mechanism. We also collect a new dataset, GenerAlign, to fine-tune a small-sized Pilot-3B as the draft model, which effectively enhances different base models under the WSD framework to outperform all baseline methods, while avoiding degradation on downstream tasks, termed as the alignment tax. Extensive experiments are further conducted to examine the impact of different settings and time efficiency, as well as analyses on the intrinsic mechanisms of WSD in depth.

The integration of biomolecular modeling with natural language (BL) has emerged as a promising interdisciplinary area at the intersection of artificial intelligence, chemistry and biology. This approach leverages the rich, multifaceted descriptions of biomolecules contained within textual data sources to enhance our fundamental understanding and enable downstream computational tasks such as biomolecule property prediction. The fusion of the nuanced narratives expressed through natural language with the structural and functional specifics of biomolecules described via various molecular modeling techniques opens new avenues for comprehensively representing and analyzing biomolecules. By incorporating the contextual language data that surrounds biomolecules into their modeling, BL aims to capture a holistic view encompassing both the symbolic qualities conveyed through language as well as quantitative structural characteristics. In this review, we provide an extensive analysis of recent advancements achieved through cross modeling of biomolecules and natural language. (1) We begin by outlining the technical representations of biomolecules employed, including sequences, 2D graphs, and 3D structures. (2) We then examine in depth the rationale and key objectives underlying effective multi-modal integration of language and molecular data sources. (3) We subsequently survey the practical applications enabled to date in this developing research area. (4) We also compile and summarize the available resources and datasets to facilitate future work. (5) Looking ahead, we identify several promising research directions worthy of further exploration and investment to continue advancing the field. The related resources and contents are updating in https://github.com/QizhiPei/Awesome-Biomolecule-Language-Cross-Modeling.

Neural networks are capable of translating between languages -- in some cases even between two languages where there is little or no access to parallel translations, in what is known as Unsupervised Machine Translation (UMT). Given this progress, it is intriguing to ask whether machine learning tools can ultimately enable understanding animal communication, particularly that of highly intelligent animals. We propose a theoretical framework for analyzing UMT when no parallel translations are available and when it cannot be assumed that the source and target corpora address related subject domains or posses similar linguistic structure. We exemplify this theory with two stylized models of language, for which our framework provides bounds on necessary sample complexity; the bounds are formally proven and experimentally verified on synthetic data. These bounds show that the error rates are inversely related to the language complexity and amount of common ground. This suggests that unsupervised translation of animal communication may be feasible if the communication system is sufficiently complex.

Many applications of text generation require incorporating different constraints to control the semantics or style of generated text. These constraints can be hard (e.g., ensuring certain keywords are included in the output) and soft (e.g., contextualizing the output with the left- or right-hand context). In this paper, we present Energy-based Constrained Decoding with Langevin Dynamics (COLD), a decoding framework which unifies constrained generation as specifying constraints through an energy function, then performing efficient differentiable reasoning over the constraints through gradient-based sampling. COLD decoding is a flexible framework that can be applied directly to off-the-shelf left-to-right language models without the need for any task-specific fine-tuning, as demonstrated through three challenging text generation applications: lexically-constrained generation, abductive reasoning, and counterfactual reasoning. Our experiments on these constrained generation tasks point to the effectiveness of our approach, both in terms of automatic and human evaluation.

While speculative decoding has recently appeared as a promising direction for accelerating the inference of large language models (LLMs), the speedup and scalability are strongly bounded by the token acceptance rate. Prevalent methods usually organize predicted tokens as independent chains or fixed token trees, which fails to generalize to diverse query distributions. In this paper, we propose DySpec, a faster speculative decoding algorithm with a novel dynamic token tree structure. We begin by bridging the draft distribution and acceptance rate from intuitive and empirical clues, and successfully show that the two variables are strongly correlated. Based on this, we employ a greedy strategy to dynamically expand the token tree at run time. Theoretically, we show that our method can achieve optimal results under mild assumptions. Empirically, DySpec yields a higher acceptance rate and speedup than fixed trees. DySpec can drastically improve the throughput and reduce the latency of token generation across various data distribution and model sizes, which significantly outperforms strong competitors, including Specinfer and Sequoia. Under low temperature setting, DySpec can improve the throughput up to 9.1times and reduce the latency up to 9.4times on Llama2-70B. Under high temperature setting, DySpec can also improve the throughput up to 6.21times, despite the increasing difficulty of speculating more than one token per step for draft model.

While recent advancements in vision-language models have revolutionized multi-modal understanding, it remains unclear whether they possess the capabilities of comprehending the generated images. Compared to real data, synthetic images exhibit a higher degree of diversity in both content and style, for which there are significant difficulties for the models to fully apprehend. To this end, we present a large-scale dataset, JourneyDB, for multi-modal visual understanding in generative images. Our curated dataset covers 4 million diverse and high-quality generated images paired with the text prompts used to produce them. We further design 4 benchmarks to quantify the performance of generated image understanding in terms of both content and style interpretation. These benchmarks include prompt inversion, style retrieval, image captioning and visual question answering. Lastly, we assess the performance of current state-of-the-art multi-modal models when applied to JourneyDB, and provide an in-depth analysis of their strengths and limitations in generated content understanding. We hope the proposed dataset and benchmarks will facilitate the research in the field of generative content understanding. The dataset will be available on https://journeydb.github.io.

Large Language Models (LLMs) demonstrate exceptional performance across diverse tasks by leveraging both pre-trained knowledge (i.e., parametric knowledge) and external knowledge (i.e., contextual knowledge). While substantial efforts have been made to leverage both forms of knowledge, scenarios in which the model lacks any relevant knowledge remain underexplored. Such limitations can result in issues like hallucination, causing reduced reliability and potential risks in high-stakes applications. To address such limitations, this paper extends the task scope to encompass cases where the user's request cannot be fulfilled due to the lack of relevant knowledge. To this end, we introduce Contrastive Decoding with Abstention (CDA), a training-free decoding method that empowers LLMs to generate responses when relevant knowledge is available and to abstain otherwise. CDA evaluates the relevance of each knowledge for a given query, adaptively determining which knowledge to prioritize or which to completely ignore. Extensive experiments with four LLMs on three question-answering datasets demonstrate that CDA can effectively perform accurate generation and abstention simultaneously. These findings highlight CDA's potential to broaden the applicability of LLMs, enhancing reliability and preserving user trust.

We present X-Decoder, a generalized decoding model that can predict pixel-level segmentation and language tokens seamlessly. X-Decodert takes as input two types of queries: (i) generic non-semantic queries and (ii) semantic queries induced from text inputs, to decode different pixel-level and token-level outputs in the same semantic space. With such a novel design, X-Decoder is the first work that provides a unified way to support all types of image segmentation and a variety of vision-language (VL) tasks. Further, our design enables seamless interactions across tasks at different granularities and brings mutual benefits by learning a common and rich pixel-level visual-semantic understanding space, without any pseudo-labeling. After pretraining on a mixed set of a limited amount of segmentation data and millions of image-text pairs, X-Decoder exhibits strong transferability to a wide range of downstream tasks in both zero-shot and finetuning settings. Notably, it achieves (1) state-of-the-art results on open-vocabulary segmentation and referring segmentation on eight datasets; (2) better or competitive finetuned performance to other generalist and specialist models on segmentation and VL tasks; and (3) flexibility for efficient finetuning and novel task composition (e.g., referring captioning and image editing). Code, demo, video, and visualization are available at https://x-decoder-vl.github.io.

Machine learning, notably deep learning, has significantly propelled molecular investigations within the biochemical sphere. Traditionally, modeling for such research has centered around a handful of paradigms. For instance, the prediction paradigm is frequently deployed for tasks such as molecular property prediction. To enhance the generation and decipherability of purely data-driven models, scholars have integrated biochemical domain knowledge into these molecular study models. This integration has sparked a surge in paradigm transfer, which is solving one molecular learning task by reformulating it as another one. With the emergence of Large Language Models, these paradigms have demonstrated an escalating trend towards harmonized unification. In this work, we delineate a literature survey focused on knowledge-informed molecular learning from the perspective of paradigm transfer. We classify the paradigms, scrutinize their methodologies, and dissect the contribution of domain knowledge. Moreover, we encapsulate prevailing trends and identify intriguing avenues for future exploration in molecular learning.

Speculative decoding has emerged as a widely adopted method to accelerate large language model inference without sacrificing the quality of the model outputs. While this technique has facilitated notable speed improvements by enabling parallel sequence verification, its efficiency remains inherently limited by the reliance on incremental token generation in existing draft models. To overcome this limitation, this paper proposes an adaptation of speculative decoding which uses discrete diffusion models to generate draft sequences. This allows parallelization of both the drafting and verification steps, providing significant speed-ups to the inference process. Our proposed approach, Speculative Diffusion Decoding (SpecDiff), is validated on standard language generation benchmarks and empirically demonstrated to provide a up to 8.7x speed-up over standard generation processes and up to 2.5x speed-up over existing speculative decoding approaches.

Massively multilingual machine translation models allow for the translation of a large number of languages with a single model, but have limited performance on low- and very-low-resource translation directions. Pivoting via high-resource languages remains a strong strategy for low-resource directions, and in this paper we revisit ways of pivoting through multiple languages. Previous work has used a simple averaging of probability distributions from multiple paths, but we find that this performs worse than using a single pivot, and exacerbates the hallucination problem because the same hallucinations can be probable across different paths. As an alternative, we propose MaxEns, a combination strategy that is biased towards the most confident predictions, hypothesising that confident predictions are less prone to be hallucinations. We evaluate different strategies on the FLORES benchmark for 20 low-resource language directions, demonstrating that MaxEns improves translation quality for low-resource languages while reducing hallucination in translations, compared to both direct translation and an averaging approach. On average, multi-pivot strategies still lag behind using English as a single pivot language, raising the question of how to identify the best pivoting strategy for a given translation direction.

Large Language Models (LLMs) have demonstrated exceptional performance across various natural language processing tasks, yet they occasionally tend to yield content that factually inaccurate or discordant with the expected output, a phenomenon empirically referred to as "hallucination". To tackle this issue, recent works have investigated contrastive decoding between the original model and an amateur model with induced hallucination, which has shown promising results. Nonetheless, this method may undermine the output distribution of the original LLM caused by its coarse contrast and simplistic subtraction operation, potentially leading to errors in certain cases. In this paper, we introduce a novel contrastive decoding framework termed LOL (LOwer Layer Matters). Our approach involves concatenating the contrastive decoding of both the final and lower layers between the original model and the amateur model, thereby achieving multi-layer fusion to aid in the mitigation of hallucination. Additionally, we incorporate a truthfulness refocused module that leverages contextual guidance to enhance factual encoding, further capturing truthfulness during contrastive decoding. Extensive experiments conducted on two publicly available datasets illustrate that our proposed LOL framework can substantially alleviate hallucination while surpassing existing baselines in most cases. Compared with the best baseline, we improve by average 4.5 points on all metrics of TruthfulQA. The source code is coming soon.

Despite the remarkable strides made by autoregressive language models, their potential is often hampered by the slow inference speeds inherent in sequential token generation. Blockwise parallel decoding (BPD) was proposed by Stern et al. (2018) as a way to improve inference speed of language models. In this paper, we make two contributions to understanding and improving BPD drafts. We first offer an analysis of the token distributions produced by the BPD prediction heads. Secondly, we use this analysis to inform algorithms to improve BPD inference speed by refining the BPD drafts using small n-gram or neural language models. We empirically show that these refined BPD drafts yield a higher average verified prefix length across tasks.

Effective scaling and a flexible task interface enable large language models to excel at many tasks. We present PaLI (Pathways Language and Image model), a model that extends this approach to the joint modeling of language and vision. PaLI generates text based on visual and textual inputs, and with this interface performs many vision, language, and multimodal tasks, in many languages. To train PaLI, we make use of large pre-trained encoder-decoder language models and Vision Transformers (ViTs). This allows us to capitalize on their existing capabilities and leverage the substantial cost of training them. We find that joint scaling of the vision and language components is important. Since existing Transformers for language are much larger than their vision counterparts, we train a large, 4-billion parameter ViT (ViT-e) to quantify the benefits from even larger-capacity vision models. To train PaLI, we create a large multilingual mix of pretraining tasks, based on a new image-text training set containing 10B images and texts in over 100 languages. PaLI achieves state-of-the-art in multiple vision and language tasks (such as captioning, visual question-answering, scene-text understanding), while retaining a simple, modular, and scalable design.

Large Language Models achieve next-token prediction by transporting a vectorized piece of text (prompt) across an accompanying embedding space under the action of successive transformer layers. The resulting high-dimensional trajectories realize different contextualization, or 'thinking', steps, and fully determine the output probability distribution. We aim to characterize the statistical properties of ensembles of these 'lines of thought.' We observe that independent trajectories cluster along a low-dimensional, non-Euclidean manifold, and that their path can be well approximated by a stochastic equation with few parameters extracted from data. We find it remarkable that the vast complexity of such large models can be reduced to a much simpler form, and we reflect on implications.

We demonstrate that Contrastive Decoding -- a simple, computationally light, and training-free text generation method proposed by Li et al 2022 -- achieves large out-of-the-box improvements over greedy decoding on a variety of reasoning tasks. Originally shown to improve the perceived quality of long-form text generation, Contrastive Decoding searches for strings that maximize a weighted difference in likelihood between strong and weak models. We show that Contrastive Decoding leads LLaMA-65B to outperform LLaMA 2, GPT-3.5 and PaLM 2-L on the HellaSwag commonsense reasoning benchmark, and to outperform LLaMA 2, GPT-3.5 and PaLM-540B on the GSM8K math word reasoning benchmark, in addition to improvements on a collection of other tasks. Analysis suggests that Contrastive Decoding improves over existing methods by preventing some abstract reasoning errors, as well as by avoiding simpler modes such as copying sections of the input during chain-of-thought. Overall, Contrastive Decoding outperforms nucleus sampling for long-form generation and greedy decoding for reasoning tasks, making it a powerful general purpose method for generating text from language models.

Keyphrase Generation (KPG) is a longstanding task in NLP with widespread applications. The advent of sequence-to-sequence (seq2seq) pre-trained language models (PLMs) has ushered in a transformative era for KPG, yielding promising performance improvements. However, many design decisions remain unexplored and are often made arbitrarily. This paper undertakes a systematic analysis of the influence of model selection and decoding strategies on PLM-based KPG. We begin by elucidating why seq2seq PLMs are apt for KPG, anchored by an attention-driven hypothesis. We then establish that conventional wisdom for selecting seq2seq PLMs lacks depth: (1) merely increasing model size or performing task-specific adaptation is not parameter-efficient; (2) although combining in-domain pre-training with task adaptation benefits KPG, it does partially hinder generalization. Regarding decoding, we demonstrate that while greedy search achieves strong F1 scores, it lags in recall compared with sampling-based methods. Based on these insights, we propose DeSel, a likelihood-based decode-select algorithm for seq2seq PLMs. DeSel improves greedy search by an average of 4.7% semantic F1 across five datasets. Our collective findings pave the way for deeper future investigations into PLM-based KPG.

Mechanistic interpretability aims to understand the behavior of neural networks by reverse-engineering their internal computations. However, current methods struggle to find clear interpretations of neural network activations because a decomposition of activations into computational features is missing. Individual neurons or model components do not cleanly correspond to distinct features or functions. We present a novel interpretability method that aims to overcome this limitation by transforming the activations of the network into a new basis - the Local Interaction Basis (LIB). LIB aims to identify computational features by removing irrelevant activations and interactions. Our method drops irrelevant activation directions and aligns the basis with the singular vectors of the Jacobian matrix between adjacent layers. It also scales features based on their importance for downstream computation, producing an interaction graph that shows all computationally-relevant features and interactions in a model. We evaluate the effectiveness of LIB on modular addition and CIFAR-10 models, finding that it identifies more computationally-relevant features that interact more sparsely, compared to principal component analysis. However, LIB does not yield substantial improvements in interpretability or interaction sparsity when applied to language models. We conclude that LIB is a promising theory-driven approach for analyzing neural networks, but in its current form is not applicable to large language models.

We discover a robust self-supervised strategy tailored towards molecular representations for generative masked language models through a series of tailored, in-depth ablations. Using this pre-training strategy, we train BARTSmiles, a BART-like model with an order of magnitude more compute than previous self-supervised molecular representations. In-depth evaluations show that BARTSmiles consistently outperforms other self-supervised representations across classification, regression, and generation tasks setting a new state-of-the-art on 11 tasks. We then quantitatively show that when applied to the molecular domain, the BART objective learns representations that implicitly encode our downstream tasks of interest. For example, by selecting seven neurons from a frozen BARTSmiles, we can obtain a model having performance within two percentage points of the full fine-tuned model on task Clintox. Lastly, we show that standard attribution interpretability methods, when applied to BARTSmiles, highlight certain substructures that chemists use to explain specific properties of molecules. The code and the pretrained model are publicly available.

Pretrained generative models have opened new frontiers in brain decoding by enabling the synthesis of realistic texts and images from non-invasive brain recordings. However, the reliability of such outputs remains questionable--whether they truly reflect semantic activation in the brain, or are merely hallucinated by the powerful generative models. In this paper, we focus on EEG-to-text decoding and address its hallucination issue through the lens of posterior collapse. Acknowledging the underlying mismatch in information capacity between EEG and text, we reframe the decoding task as semantic summarization of core meanings rather than previously verbatim reconstruction of stimulus texts. To this end, we propose the Generative Language Inspection Model (GLIM), which emphasizes learning informative and interpretable EEG representations to improve semantic grounding under heterogeneous and small-scale data conditions. Experiments on the public ZuCo dataset demonstrate that GLIM consistently generates fluent, EEG-grounded sentences without teacher forcing. Moreover, it supports more robust evaluation beyond text similarity, through EEG-text retrieval and zero-shot semantic classification across sentiment categories, relation types, and corpus topics. Together, our architecture and evaluation protocols lay the foundation for reliable and scalable benchmarking in generative brain decoding.

Drafting-then-verifying decoding methods such as speculative decoding are widely adopted training-free methods to accelerate the inference of large language models (LLMs). Instead of employing an autoregressive process to decode tokens sequentially, speculative decoding initially creates drafts with an efficient small model. Then LLMs are required to conduct verification and correction in a non-autoregressive fashion to minimize time overhead. Generating longer drafts can lead to even more significant speedups once verified, but also incurs substantial trial and error costs if it fails. Suffering from the high verification failure probability, existing decoding methods cannot draft too much content for verification at one time, achieving sub-optimal inference acceleration. In this paper, we introduce Ouroboros, which constructs a phrase candidate pool from the verification process of LLMs to provide candidates for draft generation of the small model. Thereby, Ouroboros can further improve the efficiency and effectiveness of the initial drafts. The experimental results on typical text generation tasks show that Ouroboros achieves speedups of up to 1.9x and 2.8x compared to lookahead decoding and speculative decoding, respectively. The source code of Ouroboros is available at https://github.com/thunlp/Ouroboros.

Autoregressive decoding is the only part of sequence-to-sequence models that prevents them from massive parallelization at inference time. Non-autoregressive models enable the decoder to generate all output symbols independently in parallel. We present a novel non-autoregressive architecture based on connectionist temporal classification and evaluate it on the task of neural machine translation. Unlike other non-autoregressive methods which operate in several steps, our model can be trained end-to-end. We conduct experiments on the WMT English-Romanian and English-German datasets. Our models achieve a significant speedup over the autoregressive models, keeping the translation quality comparable to other non-autoregressive models.

The two dominant approaches to neural text generation are fully autoregressive models, using serial beam search decoding, and non-autoregressive models, using parallel decoding with no output dependencies. This work proposes an autoregressive model with sub-linear parallel time generation. Noting that conditional random fields with bounded context can be decoded in parallel, we propose an efficient cascaded decoding approach for generating high-quality output. To parameterize this cascade, we introduce a Markov transformer, a variant of the popular fully autoregressive model that allows us to simultaneously decode with specific autoregressive context cutoffs. This approach requires only a small modification from standard autoregressive training, while showing competitive accuracy/speed tradeoff compared to existing methods on five machine translation datasets.

Autoregressive sampling from large language models has led to state-of-the-art results in several natural language tasks. However, autoregressive sampling generates tokens one at a time making it slow, and even prohibitive in certain tasks. One way to speed up sampling is speculative decoding: use a small model to sample a draft (block or sequence of tokens), and then score all tokens in the draft by the large language model in parallel. A subset of the tokens in the draft are accepted (and the rest rejected) based on a statistical method to guarantee that the final output follows the distribution of the large model. In this work, we provide a principled understanding of speculative decoding through the lens of optimal transport (OT) with membership cost. This framework can be viewed as an extension of the well-known maximal-coupling problem. This new formulation enables us to generalize the speculative decoding method to allow for a set of k candidates at the token-level, which leads to an improved optimal membership cost. We show that the optimal draft selection algorithm (transport plan) can be computed via linear programming, whose best-known runtime is exponential in k. We then propose a valid draft selection algorithm whose acceptance probability is (1-1/e)-optimal multiplicatively. Moreover, it can be computed in time almost linear with size of domain of a single token. Using this new draft selection algorithm, we develop a new autoregressive sampling algorithm called SpecTr, which provides speedup in decoding while ensuring that there is no quality degradation in the decoded output. We experimentally demonstrate that for state-of-the-art large language models, the proposed approach achieves a wall clock speedup of 2.13X, a further 1.37X speedup over speculative decoding on standard benchmarks.

The greatest ambition of mechanistic interpretability is to completely rewrite deep neural networks in a format that is more amenable to human understanding, while preserving their behavior and performance. In this paper, we attempt to partially rewrite a large language model using simple natural language explanations. We first approximate one of the feedforward networks in the LLM with a wider MLP with sparsely activating neurons - a transcoder - and use an automated interpretability pipeline to generate explanations for these neurons. We then replace the first layer of this sparse MLP with an LLM-based simulator, which predicts the activation of each neuron given its explanation and the surrounding context. Finally, we measure the degree to which these modifications distort the model's final output. With our pipeline, the model's increase in loss is statistically similar to entirely replacing the sparse MLP output with the zero vector. We employ the same protocol, this time using a sparse autoencoder, on the residual stream of the same layer and obtain similar results. These results suggest that more detailed explanations are needed to improve performance substantially above the zero ablation baseline.

We address prevailing challenges of the brain-powered research, departing from the observation that the literature hardly recover accurate spatial information and require subject-specific models. To address these challenges, we propose UMBRAE, a unified multimodal decoding of brain signals. First, to extract instance-level conceptual and spatial details from neural signals, we introduce an efficient universal brain encoder for multimodal-brain alignment and recover object descriptions at multiple levels of granularity from subsequent multimodal large language model (MLLM). Second, we introduce a cross-subject training strategy mapping subject-specific features to a common feature space. This allows a model to be trained on multiple subjects without extra resources, even yielding superior results compared to subject-specific models. Further, we demonstrate this supports weakly-supervised adaptation to new subjects, with only a fraction of the total training data. Experiments demonstrate that UMBRAE not only achieves superior results in the newly introduced tasks but also outperforms methods in well established tasks. To assess our method, we construct and share with the community a comprehensive brain understanding benchmark BrainHub. Our code and benchmark are available at https://weihaox.github.io/UMBRAE.

Large language models (LLMs) have shown extraordinary performance in various language tasks, but high computational requirements hinder their widespread deployment. Speculative decoding, which uses amateur models to predict the generation of expert models, has been proposed as a way to accelerate LLM inference. However, speculative decoding focuses on acceleration instead of making the best use of the token distribution from amateur models. We proposed Speculative Contrastive Decoding (SCD), an accelerated decoding method leveraging the natural contrast between expert and amateur models in speculative decoding. Comprehensive evaluations on four benchmarks show that SCD can achieve similar acceleration factors as speculative decoding while further improving the generation quality as the contrastive decoding. The analysis of token probabilities further demonstrates the compatibility between speculative and contrastive decoding. Overall, SCD provides an effective approach to enhance the decoding quality of LLMs while saving computational resources.

Large Reasoning Models (LRMs) are criticized for the excessively lengthy Chain-of-Thought (CoT) to derive the final answer, suffering from high first-token and overall latency. Typically, the CoT of LRMs mixes multiple thinking units; each unit attempts to produce a candidate answer to the original query. Hence, a natural idea to improve efficiency is to reduce the unit number. Yet, the fact that the thinking units in vanilla CoT cannot be explicitly managed renders doing so challenging. This paper introduces Multi-Turn Decomposition (MinD) to decode conventional CoT into a sequence of explicit, structured, and turn-wise interactions to bridge the gap. In MinD, the model provides a multi-turn response to the query, where each turn embraces a thinking unit and yields a corresponding answer. The subsequent turns can reflect, verify, revise, or explore alternative approaches to both the thinking and answer parts of earlier ones. This not only makes the answer delivered more swiftly, but also enables explicit controls over the iterative reasoning process (i.e., users may halt or continue at any turn). We follow a supervised fine-tuning (SFT) then reinforcement learning (RL) paradigm to realize MinD. We first rephrase the outputs of an LRM into multi-turn formats by prompting another LLM, and then tune the LRM with such data. Observing that the tuned model tends to consume even more tokens than the original one (probably due to that the multi-turn formats introduce additional answer tokens), we advocate leveraging RL algorithms like GRPO to prioritize correct outputs with fewer turns. Trained on the MATH dataset using R1-Distill models, MinD can achieve up to ~70% reduction in both output token usage and time to first token (TTFT), while maintaining competitive performance on reasoning benchmarks such as MATH-500, AIME24, AMC23, and GPQA-Diamond.

Aligning large language models (LLMs) with human preferences is essential for their applications. Recently, decoding-time alignment has emerged as an effective plug-and-play technique that avoids fine-tuning model parameters. This approach retains the general utility of pretrained LLMs but often suffers from significant inefficiencies during decoding, primarily due to wasted token generation and excessive reward evaluations. To address these challenges, we introduce Cascade Reward Sampling (CARDS) to resolve both efficiency bottlenecks in decoding-time alignment. Specifically, we develop a segment-level rejection sampling algorithm that minimizes redundant computations of both LLMs and reward models (RMs). Central to CARDS is an uncertainty-based segmentation mechanism, which ensures the accuracy of RMs evaluations on incomplete segments. Furthermore, we provide a detailed analysis of reward scores on segments to elucidate the improved alignment performance. Experimental results demonstrate that CARDS significantly improves decoding efficiency, alignment quality, and general utility compared to existing decoding-time alignment methods, achieving approximately a 70% reduction in decoding time and over 90% win-ties in utility and safety benchmarks.

Generating Chain-of-Thought (CoT) before deriving the answer can effectively improve the reasoning capabilities of large language models (LLMs) and significantly improve the accuracy of the generated answer. However, in most cases, the length of the generated CoT is much longer than the desired final answer, which results in additional decoding costs. Furthermore, existing research has discovered that shortening the reasoning steps in CoT, even while preserving the key information, diminishes LLMs' abilities. These phenomena make it difficult to use LLMs and CoT in many real-world applications that only require the final answer and are sensitive to latency, such as search and recommendation. To reduce the costs of model decoding and shorten the length of the generated CoT, this paper presents Conditioned Compressed Chain-of-Thought (C3oT), a CoT compression framework that involves a compressor to compress an original longer CoT into a shorter CoT while maintaining key information and interpretability, a conditioned training method to train LLMs with both longer CoT and shorter CoT simultaneously to learn the corresponding relationships between them, and a conditioned inference method to gain the reasoning ability learned from longer CoT by generating shorter CoT. We conduct experiments over four datasets from arithmetic and commonsense scenarios, showing that the proposed method is capable of compressing the length of generated CoT by up to more than 50% without compromising its effectiveness.

While instruction-tuned language models have demonstrated impressive zero-shot generalization, these models often struggle to generate accurate responses when faced with instructions that fall outside their training set. This paper presents Instructive Decoding (ID), a simple yet effective approach that augments the efficacy of instruction-tuned models. Specifically, ID adjusts the logits for next-token prediction in a contrastive manner, utilizing predictions generated from a manipulated version of the original instruction, referred to as a noisy instruction. This noisy instruction aims to elicit responses that could diverge from the intended instruction yet remain plausible. We conduct experiments across a spectrum of such noisy instructions, ranging from those that insert semantic noise via random words to others like 'opposite' that elicit the deviated responses. Our approach achieves considerable performance gains across various instruction-tuned models and tasks without necessitating any additional parameter updates. Notably, utilizing 'opposite' as the noisy instruction in ID, which exhibits the maximum divergence from the original instruction, consistently produces the most significant performance gains across multiple models and tasks.

In-context learning (ICL) is one of the most powerful and most unexpected capabilities to emerge in recent transformer-based large language models (LLMs). Yet the mechanisms that underlie it are poorly understood. In this paper, we demonstrate that comparable ICL capabilities can be acquired by an alternative sequence prediction learning method using clone-structured causal graphs (CSCGs). Moreover, a key property of CSCGs is that, unlike transformer-based LLMs, they are {\em interpretable}, which considerably simplifies the task of explaining how ICL works. Specifically, we show that it uses a combination of (a) learning template (schema) circuits for pattern completion, (b) retrieving relevant templates in a context-sensitive manner, and (c) rebinding of novel tokens to appropriate slots in the templates. We go on to marshall evidence for the hypothesis that similar mechanisms underlie ICL in LLMs. For example, we find that, with CSCGs as with LLMs, different capabilities emerge at different levels of overparameterization, suggesting that overparameterization helps in learning more complex template (schema) circuits. By showing how ICL can be achieved with small models and datasets, we open up a path to novel architectures, and take a vital step towards a more general understanding of the mechanics behind this important capability.

Transformer based language models exhibit intelligent behaviors such as understanding natural language, recognizing patterns, acquiring knowledge, reasoning, planning, reflecting and using tools. This paper explores how their underlying mechanics give rise to intelligent behaviors. Towards that end, we propose framing Transformer dynamics as movement through embedding space. Examining Transformers through this perspective reveals key insights, establishing a Theory of Transformers: 1) Intelligent behaviours map to paths in Embedding Space which, the Transformer random-walks through during inferencing. 2) LM training learns a probability distribution over all possible paths. `Intelligence' is learnt by assigning higher probabilities to paths representing intelligent behaviors. No learning can take place in-context; context only narrows the subset of paths sampled during decoding. 5) The Transformer is a self-mapping composition function, folding a context sequence into a context-vector such that it's proximity to a token-vector reflects its co-occurrence and conditioned probability. Thus, the physical arrangement of vectors in Embedding Space determines path probabilities. 6) Context vectors are composed by aggregating features of the sequence's tokens via a process we call the encoding walk. Attention contributes a - potentially redundant - association-bias to this process. 7) This process is comprised of two principal operation types: filtering (data independent) and aggregation (data dependent). This generalization unifies Transformers with other sequence models. Building upon this foundation, we formalize a popular semantic interpretation of embeddings into a ``concept-space theory'' and find some evidence of it's validity.