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Jul 11

ProLLaMA: A Protein Large Language Model for Multi-Task Protein Language Processing

Large Language Models (LLMs), including GPT-x and LLaMA2, have achieved remarkable performance in multiple Natural Language Processing (NLP) tasks. Under the premise that protein sequences constitute the protein language, Protein Large Language Models (ProLLMs) trained on protein corpora excel at de novo protein sequence generation. However, as of now, unlike LLMs in NLP, no ProLLM is capable of multiple tasks in the Protein Language Processing (PLP) field. This prompts us to delineate the inherent limitations in current ProLLMs: (i) the lack of natural language capabilities, (ii) insufficient instruction understanding, and (iii) high training resource demands. To address these challenges, we introduce a training framework to transform any general LLM into a ProLLM capable of handling multiple PLP tasks. Specifically, our framework utilizes low-rank adaptation and employs a two-stage training approach, and it is distinguished by its universality, low overhead, and scalability. Through training under this framework, we propose the ProLLaMA model, the first known ProLLM to handle multiple PLP tasks simultaneously. Experiments show that ProLLaMA achieves state-of-the-art results in the unconditional protein sequence generation task. In the controllable protein sequence generation task, ProLLaMA can design novel proteins with desired functionalities. In the protein property prediction task, ProLLaMA achieves nearly 100\% accuracy across many categories. The latter two tasks are beyond the reach of other ProLLMs. Code is available at https://github.com/Lyu6PosHao/ProLLaMA.

Zebra-Llama: Towards Extremely Efficient Hybrid Models

With the growing demand for deploying large language models (LLMs) across diverse applications, improving their inference efficiency is crucial for sustainable and democratized access. However, retraining LLMs to meet new user-specific requirements is prohibitively expensive and environmentally unsustainable. In this work, we propose a practical and scalable alternative: composing efficient hybrid language models from existing pre-trained models. Our approach, Zebra-Llama, introduces a family of 1B, 3B, and 8B hybrid models by combining State Space Models (SSMs) and Multi-head Latent Attention (MLA) layers, using a refined initialization and post-training pipeline to efficiently transfer knowledge from pre-trained Transformers. Zebra-Llama achieves Transformer-level accuracy with near-SSM efficiency using only 7-11B training tokens (compared to trillions of tokens required for pre-training) and an 8B teacher. Moreover, Zebra-Llama dramatically reduces KV cache size -down to 3.9%, 2%, and 2.73% of the original for the 1B, 3B, and 8B variants, respectively-while preserving 100%, 100%, and >97% of average zero-shot performance on LM Harness tasks. Compared to models like MambaInLLaMA, X-EcoMLA, Minitron, and Llamba, Zebra-Llama consistently delivers competitive or superior accuracy while using significantly fewer tokens, smaller teachers, and vastly reduced KV cache memory. Notably, Zebra-Llama-8B surpasses Minitron-8B in few-shot accuracy by 7% while using 8x fewer training tokens, over 12x smaller KV cache, and a smaller teacher (8B vs. 15B). It also achieves 2.6x-3.8x higher throughput (tokens/s) than MambaInLlama up to a 32k context length. We will release code and model checkpoints upon acceptance.

X-EcoMLA: Upcycling Pre-Trained Attention into MLA for Efficient and Extreme KV Compression

Multi-head latent attention (MLA) is designed to optimize KV cache memory through low-rank key-value joint compression. Rather than caching keys and values separately, MLA stores their compressed latent representations, reducing memory overhead while maintaining the performance. While MLA improves memory efficiency without compromising language model accuracy, its major limitation lies in its integration during the pre-training phase, requiring models to be trained from scratch. This raises a key question: can we use MLA's benefits fully or partially in models that have already been pre-trained with different attention mechanisms? In this paper, we propose X-EcoMLA to deploy post training distillation to enable the upcycling of Transformer-based attention into an efficient hybrid MLA variant through lightweight post-training adaptation, bypassing the need for extensive pre-training. We demonstrate that leveraging the dark knowledge of a well-trained model can enhance training accuracy and enable extreme KV cache compression in MLA without compromising model performance. The experimental results show that our proposed method can effectively compress the KV cache while preserving the performance on the benchmarks; specifically, for Llama3.2-1B-Instruct baseline, a 6.4x compression achieves the same average score by using only 3.6B training tokens and 70 GPU hours on AMD MI300, whereas a 10.6x compression have less than 0.1\% average score drop with 7B training tokens and 140 GPU hours.

CodeARC: Benchmarking Reasoning Capabilities of LLM Agents for Inductive Program Synthesis

Inductive program synthesis, or programming by example, requires synthesizing functions from input-output examples that generalize to unseen inputs. While large language model agents have shown promise in programming tasks guided by natural language, their ability to perform inductive program synthesis is underexplored. Existing evaluation protocols rely on static sets of examples and held-out tests, offering no feedback when synthesized functions are incorrect and failing to reflect real-world scenarios such as reverse engineering. We propose CodeARC, the Code Abstraction and Reasoning Challenge, a new evaluation framework where agents interact with a hidden target function by querying it with new inputs, synthesizing candidate functions, and iteratively refining their solutions using a differential testing oracle. This interactive setting encourages agents to perform function calls and self-correction based on feedback. We construct the first large-scale benchmark for general-purpose inductive program synthesis, featuring 1114 functions. Among 18 models evaluated, o3-mini performs best with a success rate of 52.7%, highlighting the difficulty of this task. Fine-tuning LLaMA-3.1-8B-Instruct on curated synthesis traces yields up to a 31% relative performance gain. CodeARC provides a more realistic and challenging testbed for evaluating LLM-based program synthesis and inductive reasoning.

DeepSeekMoE: Towards Ultimate Expert Specialization in Mixture-of-Experts Language Models

In the era of large language models, Mixture-of-Experts (MoE) is a promising architecture for managing computational costs when scaling up model parameters. However, conventional MoE architectures like GShard, which activate the top-K out of N experts, face challenges in ensuring expert specialization, i.e. each expert acquires non-overlapping and focused knowledge. In response, we propose the DeepSeekMoE architecture towards ultimate expert specialization. It involves two principal strategies: (1) finely segmenting the experts into mN ones and activating mK from them, allowing for a more flexible combination of activated experts; (2) isolating K_s experts as shared ones, aiming at capturing common knowledge and mitigating redundancy in routed experts. Starting from a modest scale with 2B parameters, we demonstrate that DeepSeekMoE 2B achieves comparable performance with GShard 2.9B, which has 1.5 times the expert parameters and computation. In addition, DeepSeekMoE 2B nearly approaches the performance of its dense counterpart with the same number of total parameters, which set the upper bound of MoE models. Subsequently, we scale up DeepSeekMoE to 16B parameters and show that it achieves comparable performance with LLaMA2 7B, with only about 40% of computations. Further, our preliminary efforts to scale up DeepSeekMoE to 145B parameters consistently validate its substantial advantages over the GShard architecture, and show its performance comparable with DeepSeek 67B, using only 28.5% (maybe even 18.2%) of computations.

MMaDA: Multimodal Large Diffusion Language Models

We introduce MMaDA, a novel class of multimodal diffusion foundation models designed to achieve superior performance across diverse domains such as textual reasoning, multimodal understanding, and text-to-image generation. The approach is distinguished by three key innovations: (i) MMaDA adopts a unified diffusion architecture with a shared probabilistic formulation and a modality-agnostic design, eliminating the need for modality-specific components. This architecture ensures seamless integration and processing across different data types. (ii) We implement a mixed long chain-of-thought (CoT) fine-tuning strategy that curates a unified CoT format across modalities. By aligning reasoning processes between textual and visual domains, this strategy facilitates cold-start training for the final reinforcement learning (RL) stage, thereby enhancing the model's ability to handle complex tasks from the outset. (iii) We propose UniGRPO, a unified policy-gradient-based RL algorithm specifically tailored for diffusion foundation models. Utilizing diversified reward modeling, UniGRPO unifies post-training across both reasoning and generation tasks, ensuring consistent performance improvements. Experimental results demonstrate that MMaDA-8B exhibits strong generalization capabilities as a unified multimodal foundation model. It surpasses powerful models like LLaMA-3-7B and Qwen2-7B in textual reasoning, outperforms Show-o and SEED-X in multimodal understanding, and excels over SDXL and Janus in text-to-image generation. These achievements highlight MMaDA's effectiveness in bridging the gap between pretraining and post-training within unified diffusion architectures, providing a comprehensive framework for future research and development. We open-source our code and trained models at: https://github.com/Gen-Verse/MMaDA

VibeCheck: Discover and Quantify Qualitative Differences in Large Language Models

Large language models (LLMs) often exhibit subtle yet distinctive characteristics in their outputs that users intuitively recognize, but struggle to quantify. These "vibes" - such as tone, formatting, or writing style - influence user preferences, yet traditional evaluations focus primarily on the single axis of correctness. We introduce VibeCheck, a system for automatically comparing a pair of LLMs by discovering identifying traits of a model ("vibes") that are well-defined, differentiating, and user-aligned. VibeCheck iteratively discover vibes from model outputs, then utilizes a panel of LLM judges to quantitatively measure the utility of each vibe. We validate that the vibes generated by VibeCheck align with those found in human discovery and run VibeCheck on pairwise preference data from real-world user conversations with llama-3-70b VS GPT-4. VibeCheck reveals that Llama has a friendly, funny, and somewhat controversial vibe. These vibes predict model identity with 80% accuracy and human preference with 61% accuracy. Lastly, we run VibeCheck on a variety of models and tasks including summarization, math, and captioning to provide insight into differences in model behavior. Some of the vibes we find are that Command X prefers to add concrete intros and conclusions when summarizing in comparison to TNGL, Llama-405b often over-explains its thought process on math problems compared to GPT-4o, and GPT-4 prefers to focus on the mood and emotions of the scene when captioning compared to Gemini-1.5-Flash.

CXR-LLaVA: Multimodal Large Language Model for Interpreting Chest X-ray Images

Purpose: Recent advancements in large language models (LLMs) have expanded their capabilities in a multimodal fashion, potentially replicating the image interpretation of human radiologists. This study aimed to develop open-source multimodal large language model for interpreting chest X-ray images (CXR-LLaVA). We also examined the effect of prompt engineering and model parameters such as temperature and nucleus sampling. Materials and Methods: For training, we collected 659,287 publicly available CXRs: 417,336 CXRs had labels for certain radiographic abnormalities (dataset 1); 241,951 CXRs provided free-text radiology reports (dataset 2). After pre-training the Resnet50 as an image encoder, the contrastive language-image pre-training was used to align CXRs and corresponding radiographic abnormalities. Then, the Large Language Model Meta AI-2 was fine-tuned using dataset 2, which were refined using GPT-4, with generating various question answering scenarios. The code can be found at https://github.com/ECOFRI/CXR_LLaVA. Results: In the test set, we observed that the model's performance fluctuated based on its parameters. On average, it achieved F1 score of 0.34 for five pathologic findings (atelectasis, cardiomegaly, consolidation, edema, and pleural effusion), which was improved to 0.46 through prompt engineering. In the independent set, the model achieved an average F1 score of 0.30 for the same pathologic findings. Notably, for the pediatric chest radiograph dataset, which was unseen during training, the model differentiated abnormal radiographs with an F1 score ranging from 0.84 to 0.85. Conclusion: CXR-LLaVA demonstrates promising potential in CXR interpretation. Both prompt engineering and model parameter adjustments can play pivotal roles in interpreting CXRs.

EXplainable Neural-Symbolic Learning (X-NeSyL) methodology to fuse deep learning representations with expert knowledge graphs: the MonuMAI cultural heritage use case

The latest Deep Learning (DL) models for detection and classification have achieved an unprecedented performance over classical machine learning algorithms. However, DL models are black-box methods hard to debug, interpret, and certify. DL alone cannot provide explanations that can be validated by a non technical audience. In contrast, symbolic AI systems that convert concepts into rules or symbols -- such as knowledge graphs -- are easier to explain. However, they present lower generalisation and scaling capabilities. A very important challenge is to fuse DL representations with expert knowledge. One way to address this challenge, as well as the performance-explainability trade-off is by leveraging the best of both streams without obviating domain expert knowledge. We tackle such problem by considering the symbolic knowledge is expressed in form of a domain expert knowledge graph. We present the eXplainable Neural-symbolic learning (X-NeSyL) methodology, designed to learn both symbolic and deep representations, together with an explainability metric to assess the level of alignment of machine and human expert explanations. The ultimate objective is to fuse DL representations with expert domain knowledge during the learning process to serve as a sound basis for explainability. X-NeSyL methodology involves the concrete use of two notions of explanation at inference and training time respectively: 1) EXPLANet: Expert-aligned eXplainable Part-based cLAssifier NETwork Architecture, a compositional CNN that makes use of symbolic representations, and 2) SHAP-Backprop, an explainable AI-informed training procedure that guides the DL process to align with such symbolic representations in form of knowledge graphs. We showcase X-NeSyL methodology using MonuMAI dataset for monument facade image classification, and demonstrate that our approach improves explainability and performance.

$\textit{X}^2$-DFD: A framework for e${X}$plainable and e${X}$tendable Deepfake Detection

Detecting deepfakes has become an important task. Most existing detection methods provide only real/fake predictions without offering human-comprehensible explanations. Recent studies leveraging MLLMs for deepfake detection have shown improvements in explainability. However, the performance of pre-trained MLLMs (e.g., LLaVA) remains limited due to a lack of understanding of their capabilities for this task and strategies to enhance them. In this work, we empirically assess the strengths and weaknesses of MLLMs specifically in deepfake detection via forgery features analysis. Building on these assessments, we propose a novel framework called {X}^2-DFD, consisting of three core modules. The first module, Model Feature Assessment (MFA), measures the detection capabilities of forgery features intrinsic to MLLMs, and gives a descending ranking of these features. The second module, Strong Feature Strengthening (SFS), enhances the detection and explanation capabilities by fine-tuning the MLLM on a dataset constructed based on the top-ranked features. The third module, Weak Feature Supplementing (WFS), improves the fine-tuned MLLM's capabilities on lower-ranked features by integrating external dedicated deepfake detectors. To verify the effectiveness of this framework, we further present a practical implementation, where an automated forgery features generation, evaluation, and ranking procedure is designed for MFA module; an automated generation procedure of the fine-tuning dataset containing real and fake images with explanations based on top-ranked features is developed for SFS model; an external conventional deepfake detector focusing on blending artifact, which corresponds to a low detection capability in the pre-trained MLLM, is integrated for WFS module. Experiments show that our approach enhances both detection and explanation performance.

Planck 2018 results. V. CMB power spectra and likelihoods

This paper describes the 2018 Planck CMB likelihoods, following a hybrid approach similar to the 2015 one, with different approximations at low and high multipoles, and implementing several methodological and analysis refinements. With more realistic simulations, and better correction and modelling of systematics, we can now make full use of the High Frequency Instrument polarization data. The low-multipole 100x143 GHz EE cross-spectrum constrains the reionization optical-depth parameter tau to better than 15% (in combination with with the other low- and high-ell likelihoods). We also update the 2015 baseline low-ell joint TEB likelihood based on the Low Frequency Instrument data, which provides a weaker tau constraint. At high multipoles, a better model of the temperature-to-polarization leakage and corrections for the effective calibrations of the polarization channels (polarization efficiency or PE) allow us to fully use the polarization spectra, improving the constraints on the LambdaCDM parameters by 20 to 30% compared to TT-only constraints. Tests on the modelling of the polarization demonstrate good consistency, with some residual modelling uncertainties, the accuracy of the PE modelling being the main limitation. Using our various tests, simulations, and comparison between different high-ell implementations, we estimate the consistency of the results to be better than the 0.5sigma level. Minor curiosities already present before (differences between ell<800 and ell>800 parameters or the preference for more smoothing of the C_ell peaks) are shown to be driven by the TT power spectrum and are not significantly modified by the inclusion of polarization. Overall, the legacy Planck CMB likelihoods provide a robust tool for constraining the cosmological model and represent a reference for future CMB observations. (Abridged)

Planck 2018 results. VI. Cosmological parameters

We present cosmological parameter results from the final full-mission Planck measurements of the CMB anisotropies. We find good consistency with the standard spatially-flat 6-parameter LambdaCDM cosmology having a power-law spectrum of adiabatic scalar perturbations (denoted "base LambdaCDM" in this paper), from polarization, temperature, and lensing, separately and in combination. A combined analysis gives dark matter density Omega_c h^2 = 0.120pm 0.001, baryon density Omega_b h^2 = 0.0224pm 0.0001, scalar spectral index n_s = 0.965pm 0.004, and optical depth tau = 0.054pm 0.007 (in this abstract we quote 68,% confidence regions on measured parameters and 95,% on upper limits). The angular acoustic scale is measured to 0.03,% precision, with 100theta_*=1.0411pm 0.0003. These results are only weakly dependent on the cosmological model and remain stable, with somewhat increased errors, in many commonly considered extensions. Assuming the base-LambdaCDM cosmology, the inferred late-Universe parameters are: Hubble constant H_0 = (67.4pm 0.5)km/s/Mpc; matter density parameter Omega_m = 0.315pm 0.007; and matter fluctuation amplitude sigma_8 = 0.811pm 0.006. We find no compelling evidence for extensions to the base-LambdaCDM model. Combining with BAO we constrain the effective extra relativistic degrees of freedom to be N_{rm eff} = 2.99pm 0.17, and the neutrino mass is tightly constrained to sum m_nu< 0.12eV. The CMB spectra continue to prefer higher lensing amplitudes than predicted in base -LambdaCDM at over 2,sigma, which pulls some parameters that affect the lensing amplitude away from the base-LambdaCDM model; however, this is not supported by the lensing reconstruction or (in models that also change the background geometry) BAO data. (Abridged)

BuboGPT: Enabling Visual Grounding in Multi-Modal LLMs

LLMs have demonstrated remarkable abilities at interacting with humans through language, especially with the usage of instruction-following data. Recent advancements in LLMs, such as MiniGPT-4, LLaVA, and X-LLM, further enlarge their abilities by incorporating multi-modal inputs, including image, video, and speech. Despite their effectiveness at generating precise and detailed language understanding of the given modality signal, these LLMs give up the ability to ground specific parts of inputs, thus only constructing a coarse-grained mapping. However, explicit and informative correspondence between text and other modalities will not only improve the user experience but also help to expand the application scenario of multi-modal LLMs. Therefore, we propose BuboGPT, a multi-modal LLM with visual grounding that can perform cross-modal interaction between vision, audio and language, providing fine-grained understanding of visual objects and other given modalities. As a result, BuboGPT is able to point out the specific location of an object in the image, when it is generating response or description for that object. Our contributions are two-fold: 1) An off-the-shelf visual grounding module based on SAM that extracts entities in a sentence and find corresponding masks in the image. 2) A two-stage training scheme and instruction dataset to endow joint text-image-audio understanding. Our experiments show that BuboGPT achieves impressive multi-modality understanding and visual grounding abilities during the interaction with human. It performs consistently well when provided by arbitrary modality combinations (either aligned or unaligned). Our code, model and dataset are available at https://bubo-gpt.github.io .

LLMs Beyond English: Scaling the Multilingual Capability of LLMs with Cross-Lingual Feedback

To democratize large language models (LLMs) to most natural languages, it is imperative to make these models capable of understanding and generating texts in many languages, in particular low-resource ones. While recent multilingual LLMs demonstrate remarkable performance in such capabilities, these LLMs still support a limited number of human languages due to the lack of training data for low-resource languages. Moreover, these LLMs are not yet aligned with human preference for downstream tasks, which is crucial for the success of LLMs in English. In this paper, we introduce xLLaMA-100 and xBLOOM-100 (collectively xLLMs-100), which scale the multilingual capabilities of LLaMA and BLOOM to 100 languages. To do so, we construct two datasets: a multilingual instruction dataset including 100 languages, which represents the largest language coverage to date, and a cross-lingual human feedback dataset encompassing 30 languages. We perform multilingual instruction tuning on the constructed instruction data and further align the LLMs with human feedback using the DPO algorithm on our cross-lingual human feedback dataset. We evaluate the multilingual understanding and generating capabilities of xLLMs-100 on five multilingual benchmarks. Experimental results show that xLLMs-100 consistently outperforms its peers across the benchmarks by considerable margins, defining a new state-of-the-art multilingual LLM that supports 100 languages.