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Jun 26

PRISMA-DFLLM: An Extension of PRISMA for Systematic Literature Reviews using Domain-specific Finetuned Large Language Models

With the proliferation of open-sourced Large Language Models (LLMs) and efficient finetuning techniques, we are on the cusp of the emergence of numerous domain-specific LLMs that have been finetuned for expertise across specialized fields and applications for which the current general-purpose LLMs are unsuitable. In academia, this technology has the potential to revolutionize the way we conduct systematic literature reviews (SLRs), access knowledge and generate new insights. This paper proposes an AI-enabled methodological framework that combines the power of LLMs with the rigorous reporting guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). By finetuning LLMs on domain-specific academic papers that have been selected as a result of a rigorous SLR process, the proposed PRISMA-DFLLM (for Domain-specific Finetuned LLMs) reporting guidelines offer the potential to achieve greater efficiency, reusability and scalability, while also opening the potential for conducting incremental living systematic reviews with the aid of LLMs. Additionally, the proposed approach for leveraging LLMs for SLRs enables the dissemination of finetuned models, empowering researchers to accelerate advancements and democratize cutting-edge research. This paper presents the case for the feasibility of finetuned LLMs to support rigorous SLRs and the technical requirements for realizing this. This work then proposes the extended PRISMA-DFLLM checklist of reporting guidelines as well as the advantages, challenges, and potential implications of implementing PRISMA-DFLLM. Finally, a future research roadmap to develop this line of AI-enabled SLRs is presented, paving the way for a new era of evidence synthesis and knowledge discovery.

Prismatic Synthesis: Gradient-based Data Diversification Boosts Generalization in LLM Reasoning

Effective generalization in language models depends critically on the diversity of their training data. Yet existing diversity metrics often fall short of this goal, relying on surface-level heuristics that are decoupled from model behavior. This motivates us to ask: What kind of diversity in training data actually drives generalization in language models -- and how can we measure and amplify it? Through large-scale empirical analyses spanning over 300 training runs, carefully controlled for data scale and quality, we show that data diversity can be a strong predictor of generalization in LLM reasoning -- as measured by average model performance on unseen out-of-distribution benchmarks. We introduce G-Vendi, a metric that quantifies diversity via the entropy of model-induced gradients. Despite using a small off-the-shelf proxy model for gradients, G-Vendi consistently outperforms alternative measures, achieving strong correlation (Spearman's rho approx 0.9) with out-of-distribution (OOD) performance on both natural language inference (NLI) and math reasoning tasks. Building on this insight, we present Prismatic Synthesis, a framework for generating diverse synthetic data by targeting underrepresented regions in gradient space. Experimental results show that Prismatic Synthesis consistently improves model performance as we scale synthetic data -- not just on in-distribution test but across unseen, out-of-distribution benchmarks -- significantly outperforming state-of-the-art models that rely on 20 times larger data generator than ours. For example, PrismMath-7B, our model distilled from a 32B LLM, outperforms R1-Distill-Qwen-7B -- the same base model trained on proprietary data generated by 671B R1 -- on 6 out of 7 challenging benchmarks.

Prism: A Framework for Decoupling and Assessing the Capabilities of VLMs

Vision Language Models (VLMs) demonstrate remarkable proficiency in addressing a wide array of visual questions, which requires strong perception and reasoning faculties. Assessing these two competencies independently is crucial for model refinement, despite the inherent difficulty due to the intertwined nature of seeing and reasoning in existing VLMs. To tackle this issue, we present Prism, an innovative framework designed to disentangle the perception and reasoning processes involved in visual question solving. Prism comprises two distinct stages: a perception stage that utilizes a VLM to extract and articulate visual information in textual form, and a reasoning stage that formulates responses based on the extracted visual information using a Large Language Model (LLM). This modular design enables the systematic comparison and assessment of both proprietary and open-source VLM for their perception and reasoning strengths. Our analytical framework provides several valuable insights, underscoring Prism's potential as a cost-effective solution for vision-language tasks. By combining a streamlined VLM focused on perception with a powerful LLM tailored for reasoning, Prism achieves superior results in general vision-language tasks while substantially cutting down on training and operational expenses. Quantitative evaluations show that Prism, when configured with a vanilla 2B LLaVA and freely accessible GPT-3.5, delivers performance on par with VLMs 10 times larger on the rigorous multimodal benchmark MMStar. The project is released at: https://github.com/SparksJoe/Prism.

PrismLayers: Open Data for High-Quality Multi-Layer Transparent Image Generative Models

Generating high-quality, multi-layer transparent images from text prompts can unlock a new level of creative control, allowing users to edit each layer as effortlessly as editing text outputs from LLMs. However, the development of multi-layer generative models lags behind that of conventional text-to-image models due to the absence of a large, high-quality corpus of multi-layer transparent data. In this paper, we address this fundamental challenge by: (i) releasing the first open, ultra-high-fidelity PrismLayers (PrismLayersPro) dataset of 200K (20K) multilayer transparent images with accurate alpha mattes, (ii) introducing a trainingfree synthesis pipeline that generates such data on demand using off-the-shelf diffusion models, and (iii) delivering a strong, open-source multi-layer generation model, ART+, which matches the aesthetics of modern text-to-image generation models. The key technical contributions include: LayerFLUX, which excels at generating high-quality single transparent layers with accurate alpha mattes, and MultiLayerFLUX, which composes multiple LayerFLUX outputs into complete images, guided by human-annotated semantic layout. To ensure higher quality, we apply a rigorous filtering stage to remove artifacts and semantic mismatches, followed by human selection. Fine-tuning the state-of-the-art ART model on our synthetic PrismLayersPro yields ART+, which outperforms the original ART in 60% of head-to-head user study comparisons and even matches the visual quality of images generated by the FLUX.1-[dev] model. We anticipate that our work will establish a solid dataset foundation for the multi-layer transparent image generation task, enabling research and applications that require precise, editable, and visually compelling layered imagery.

The PRISM Alignment Project: What Participatory, Representative and Individualised Human Feedback Reveals About the Subjective and Multicultural Alignment of Large Language Models

Human feedback plays a central role in the alignment of Large Language Models (LLMs). However, open questions remain about the methods (how), domains (where), people (who) and objectives (to what end) of human feedback collection. To navigate these questions, we introduce PRISM, a new dataset which maps the sociodemographics and stated preferences of 1,500 diverse participants from 75 countries, to their contextual preferences and fine-grained feedback in 8,011 live conversations with 21 LLMs. PRISM contributes (i) wide geographic and demographic participation in human feedback data; (ii) two census-representative samples for understanding collective welfare (UK and US); and (iii) individualised feedback where every rating is linked to a detailed participant profile, thus permitting exploration of personalisation and attribution of sample artefacts. We focus on collecting conversations that centre subjective and multicultural perspectives on value-laden and controversial topics, where we expect the most interpersonal and cross-cultural disagreement. We demonstrate the usefulness of PRISM via three case studies of dialogue diversity, preference diversity, and welfare outcomes, showing that it matters which humans set alignment norms. As well as offering a rich community resource, we advocate for broader participation in AI development and a more inclusive approach to technology design.

PRISM: A Multi-Modal Generative Foundation Model for Slide-Level Histopathology

Foundation models in computational pathology promise to unlock the development of new clinical decision support systems and models for precision medicine. However, there is a mismatch between most clinical analysis, which is defined at the level of one or more whole slide images, and foundation models to date, which process the thousands of image tiles contained in a whole slide image separately. The requirement to train a network to aggregate information across a large number of tiles in multiple whole slide images limits these models' impact. In this work, we present a slide-level foundation model for H&E-stained histopathology, PRISM, that builds on Virchow tile embeddings and leverages clinical report text for pre-training. Using the tile embeddings, PRISM produces slide-level embeddings with the ability to generate clinical reports, resulting in several modes of use. Using text prompts, PRISM achieves zero-shot cancer detection and sub-typing performance approaching and surpassing that of a supervised aggregator model. Using the slide embeddings with linear classifiers, PRISM surpasses supervised aggregator models. Furthermore, we demonstrate that fine-tuning of the PRISM slide encoder yields label-efficient training for biomarker prediction, a task that typically suffers from low availability of training data; an aggregator initialized with PRISM and trained on as little as 10% of the training data can outperform a supervised baseline that uses all of the data.

PRISM: Patient Records Interpretation for Semantic Clinical Trial Matching using Large Language Models

Clinical trial matching is the task of identifying trials for which patients may be potentially eligible. Typically, this task is labor-intensive and requires detailed verification of patient electronic health records (EHRs) against the stringent inclusion and exclusion criteria of clinical trials. This process is manual, time-intensive, and challenging to scale up, resulting in many patients missing out on potential therapeutic options. Recent advancements in Large Language Models (LLMs) have made automating patient-trial matching possible, as shown in multiple concurrent research studies. However, the current approaches are confined to constrained, often synthetic datasets that do not adequately mirror the complexities encountered in real-world medical data. In this study, we present the first, end-to-end large-scale empirical evaluation of clinical trial matching using real-world EHRs. Our study showcases the capability of LLMs to accurately match patients with appropriate clinical trials. We perform experiments with proprietary LLMs, including GPT-4 and GPT-3.5, as well as our custom fine-tuned model called OncoLLM and show that OncoLLM, despite its significantly smaller size, not only outperforms GPT-3.5 but also matches the performance of qualified medical doctors. All experiments were carried out on real-world EHRs that include clinical notes and available clinical trials from a single cancer center in the United States.

Primary and Secondary Factor Consistency as Domain Knowledge to Guide Happiness Computing in Online Assessment

Happiness computing based on large-scale online web data and machine learning methods is an emerging research topic that underpins a range of issues, from personal growth to social stability. Many advanced Machine Learning (ML) models with explanations are used to compute the happiness online assessment while maintaining high accuracy of results. However, domain knowledge constraints, such as the primary and secondary relations of happiness factors, are absent from these models, which limits the association between computing results and the right reasons for why they occurred. This article attempts to provide new insights into the explanation consistency from an empirical study perspective. Then we study how to represent and introduce domain knowledge constraints to make ML models more trustworthy. We achieve this through: (1) proving that multiple prediction models with additive factor attributions will have the desirable property of primary and secondary relations consistency, and (2) showing that factor relations with quantity can be represented as an importance distribution for encoding domain knowledge. Factor explanation difference is penalized by the Kullback-Leibler divergence-based loss among computing models. Experimental results using two online web datasets show that domain knowledge of stable factor relations exists. Using this knowledge not only improves happiness computing accuracy but also reveals more significative happiness factors for assisting decisions well.

Primate Face Identification in the Wild

Ecological imbalance owing to rapid urbanization and deforestation has adversely affected the population of several wild animals. This loss of habitat has skewed the population of several non-human primate species like chimpanzees and macaques and has constrained them to co-exist in close proximity of human settlements, often leading to human-wildlife conflicts while competing for resources. For effective wildlife conservation and conflict management, regular monitoring of population and of conflicted regions is necessary. However, existing approaches like field visits for data collection and manual analysis by experts is resource intensive, tedious and time consuming, thus necessitating an automated, non-invasive, more efficient alternative like image based facial recognition. The challenge in individual identification arises due to unrelated factors like pose, lighting variations and occlusions due to the uncontrolled environments, that is further exacerbated by limited training data. Inspired by human perception, we propose to learn representations that are robust to such nuisance factors and capture the notion of similarity over the individual identity sub-manifolds. The proposed approach, Primate Face Identification (PFID), achieves this by training the network to distinguish between positive and negative pairs of images. The PFID loss augments the standard cross entropy loss with a pairwise loss to learn more discriminative and generalizable features, thus making it appropriate for other related identification tasks like open-set, closed set and verification. We report state-of-the-art accuracy on facial recognition of two primate species, rhesus macaques and chimpanzees under the four protocols of classification, verification, closed-set identification and open-set recognition.

Sinogram upsampling using Primal-Dual UNet for undersampled CT and radial MRI reconstruction

Computed tomography and magnetic resonance imaging are two widely used clinical imaging modalities for non-invasive diagnosis. However, both of these modalities come with certain problems. CT uses harmful ionising radiation, and MRI suffers from slow acquisition speed. Both problems can be tackled by undersampling, such as sparse sampling. However, such undersampled data leads to lower resolution and introduces artefacts. Several techniques, including deep learning based methods, have been proposed to reconstruct such data. However, the undersampled reconstruction problem for these two modalities was always considered as two different problems and tackled separately by different research works. This paper proposes a unified solution for both sparse CT and undersampled radial MRI reconstruction, achieved by applying Fourier transform-based pre-processing on the radial MRI and then finally reconstructing both modalities using sinogram upsampling combined with filtered back-projection. The Primal-Dual network is a deep learning based method for reconstructing sparsely-sampled CT data. This paper introduces Primal-Dual UNet, which improves the Primal-Dual network in terms of accuracy and reconstruction speed. The proposed method resulted in an average SSIM of 0.932\textpm0.021 while performing sparse CT reconstruction for fan-beam geometry with a sparsity level of 16, achieving a statistically significant improvement over the previous model, which resulted in 0.919\textpm0.016. Furthermore, the proposed model resulted in 0.903\textpm0.019 and 0.957\textpm0.023 average SSIM while reconstructing undersampled brain and abdominal MRI data with an acceleration factor of 16, respectively - statistically significant improvements over the original model, which resulted in 0.867\textpm0.025 and 0.949\textpm0.025.

RBench-V: A Primary Assessment for Visual Reasoning Models with Multi-modal Outputs

The rapid advancement of native multi-modal models and omni-models, exemplified by GPT-4o, Gemini, and o3, with their capability to process and generate content across modalities such as text and images, marks a significant milestone in the evolution of intelligence. Systematic evaluation of their multi-modal output capabilities in visual thinking processes (also known as multi-modal chain of thought, M-CoT) becomes critically important. However, existing benchmarks for evaluating multi-modal models primarily focus on assessing multi-modal inputs and text-only reasoning while neglecting the importance of reasoning through multi-modal outputs. In this paper, we present a benchmark, dubbed RBench-V, designed to assess models' vision-indispensable reasoning abilities. To construct RBench-V, we carefully hand-pick 803 questions covering math, physics, counting, and games. Unlike previous benchmarks that typically specify certain input modalities, RBench-V presents problems centered on multi-modal outputs, which require image manipulation such as generating novel images and constructing auxiliary lines to support the reasoning process. We evaluate numerous open- and closed-source models on RBench-V, including o3, Gemini 2.5 Pro, Qwen2.5-VL, etc. Even the best-performing model, o3, achieves only 25.8% accuracy on RBench-V, far below the human score of 82.3%, highlighting that current models struggle to leverage multi-modal reasoning. Data and code are available at https://evalmodels.github.io/rbenchv

In-Context Learning through the Bayesian Prism

In-context learning is one of the surprising and useful features of large language models. How it works is an active area of research. Recently, stylized meta-learning-like setups have been devised that train these models on a sequence of input-output pairs (x, f(x)) from a function class using the language modeling loss and observe generalization to unseen functions from the same class. One of the main discoveries in this line of research has been that for several problems such as linear regression, trained transformers learn algorithms for learning functions in context. However, the inductive biases of these models resulting in this behavior are not clearly understood. A model with unlimited training data and compute is a Bayesian predictor: it learns the pretraining distribution. It has been shown that high-capacity transformers mimic the Bayesian predictor for linear regression. In this paper, we show empirical evidence of transformers exhibiting the behavior of this ideal learner across different linear and non-linear function classes. We also extend the previous setups to work in the multitask setting and verify that transformers can do in-context learning in this setup as well and the Bayesian perspective sheds light on this setting also. Finally, via the example of learning Fourier series, we study the inductive bias for in-context learning. We find that in-context learning may or may not have simplicity bias depending on the pretraining data distribution.

Large Language Model for Mental Health: A Systematic Review

Large language models (LLMs) have received much attention and shown their potential in digital health, while their application in mental health is subject to ongoing debate. This systematic review aims to summarize and characterize the use of LLMs in mental health by investigating the strengths and limitations of the latest work in LLMs and discusses the challenges and opportunities for early screening, digital interventions, and other clinical applications in mental health. Following PRISMA guidelines, we examined English articles from PubMed, DBLP Computer Science Bibliography, and IEEE Xplore, published between 1 January 2017, and 1 September 2023, focusing on mental health and LLMs. The review analyzed 32 articles, including mental health analysis using social media datasets (n=13), mental health chatbots (n=10), and other mental health applications (n=9). Findings reveal LLMs' effectiveness in mental health issue detection and the enhancement of telepsychological services through personalised healthcare. Nonetheless, risks like text inconsistencies, hallucinatory content, and the lack of an ethical framework raise concerns about their clinical use. Despite these challenges, the advancement of LLMs underscores their potential as innovative clinical tools, necessitating further research and development. The review emphasizes that LLMs should complement, not replace, professional mental health services.