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Aug 12

MAgICoRe: Multi-Agent, Iterative, Coarse-to-Fine Refinement for Reasoning

Large Language Models' (LLM) reasoning can be improved using test-time aggregation strategies, i.e., generating multiple samples and voting among generated samples. While these improve performance, they often reach a saturation point. Refinement offers an alternative by using LLM-generated feedback to improve solution quality. However, refinement introduces 3 key challenges: (1) Excessive refinement: Uniformly refining all instances can over-correct and reduce the overall performance. (2) Inability to localize and address errors: LLMs have a limited ability to self-correct and struggle to identify and correct their own mistakes. (3) Insufficient refinement: Deciding how many iterations of refinement are needed is non-trivial, and stopping too soon could leave errors unaddressed. To tackle these issues, we propose MAgICoRe, which avoids excessive refinement by categorizing problem difficulty as easy or hard, solving easy problems with coarse-grained aggregation and hard ones with fine-grained and iterative multi-agent refinement. To improve error localization, we incorporate external step-wise reward model (RM) scores. Moreover, to ensure effective refinement, we employ a multi-agent loop with three agents: Solver, Reviewer (which generates targeted feedback based on step-wise RM scores), and the Refiner (which incorporates feedback). To ensure sufficient refinement, we re-evaluate updated solutions, iteratively initiating further rounds of refinement. We evaluate MAgICoRe on Llama-3-8B and GPT-3.5 and show its effectiveness across 5 math datasets. Even one iteration of MAgICoRe beats Self-Consistency by 3.4%, Best-of-k by 3.2%, and Self-Refine by 4.0% while using less than half the samples. Unlike iterative refinement with baselines, MAgICoRe continues to improve with more iterations. Finally, our ablations highlight the importance of MAgICoRe's RMs and multi-agent communication.

  • 5 authors
·
Sep 18, 2024

RefineAnything: Multimodal Region-Specific Refinement for Perfect Local Details

We introduce region-specific image refinement as a dedicated problem setting: given an input image and a user-specified region (e.g., a scribble mask or a bounding box), the goal is to restore fine-grained details while keeping all non-edited pixels strictly unchanged. Despite rapid progress in image generation, modern models still frequently suffer from local detail collapse (e.g., distorted text, logos, and thin structures). Existing instruction-driven editing models emphasize coarse-grained semantic edits and often either overlook subtle local defects or inadvertently change the background, especially when the region of interest occupies only a small portion of a fixed-resolution input. We present RefineAnything, a multimodal diffusion-based refinement model that supports both reference-based and reference-free refinement. Building on a counter-intuitive observation that crop-and-resize can substantially improve local reconstruction under a fixed VAE input resolution, we propose Focus-and-Refine, a region-focused refinement-and-paste-back strategy that improves refinement effectiveness and efficiency by reallocating the resolution budget to the target region, while a blended-mask paste-back guarantees strict background preservation. We further introduce a boundary-aware Boundary Consistency Loss to reduce seam artifacts and improve paste-back naturalness. To support this new setting, we construct Refine-30K (20K reference-based and 10K reference-free samples) and introduce RefineEval, a benchmark that evaluates both edited-region fidelity and background consistency. On RefineEval, RefineAnything achieves strong improvements over competitive baselines and near-perfect background preservation, establishing a practical solution for high-precision local refinement. Project Page: https://limuloo.github.io/RefineAnything/.

CraftsMan: High-fidelity Mesh Generation with 3D Native Generation and Interactive Geometry Refiner

We present a novel generative 3D modeling system, coined CraftsMan, which can generate high-fidelity 3D geometries with highly varied shapes, regular mesh topologies, and detailed surfaces, and, notably, allows for refining the geometry in an interactive manner. Despite the significant advancements in 3D generation, existing methods still struggle with lengthy optimization processes, irregular mesh topologies, noisy surfaces, and difficulties in accommodating user edits, consequently impeding their widespread adoption and implementation in 3D modeling software. Our work is inspired by the craftsman, who usually roughs out the holistic figure of the work first and elaborates the surface details subsequently. Specifically, we employ a 3D native diffusion model, which operates on latent space learned from latent set-based 3D representations, to generate coarse geometries with regular mesh topology in seconds. In particular, this process takes as input a text prompt or a reference image and leverages a powerful multi-view (MV) diffusion model to generate multiple views of the coarse geometry, which are fed into our MV-conditioned 3D diffusion model for generating the 3D geometry, significantly improving robustness and generalizability. Following that, a normal-based geometry refiner is used to significantly enhance the surface details. This refinement can be performed automatically, or interactively with user-supplied edits. Extensive experiments demonstrate that our method achieves high efficacy in producing superior-quality 3D assets compared to existing methods. HomePage: https://craftsman3d.github.io/, Code: https://github.com/wyysf-98/CraftsMan

  • 7 authors
·
May 23, 2024 2

Med-REFL: Medical Reasoning Enhancement via Self-Corrected Fine-grained Reflection

Large reasoning models have recently made significant strides in mathematical and code reasoning, yet their success has not transferred smoothly to the medical domain. While multiple factors contribute to this disparity, a critical issue is the inadequate focus on the quality of intermediate reflection steps, which is particularly crucial in high-stakes medical scenarios. To address this challenge, we propose Med-REFL, a \textbf{Med}ical \textbf{R}easoning \textbf{E}nhancement via self-corrected \textbf{F}ine-grained ref\textbf{L}ection. Our method leverages a tree-of-thought approach to decompose medical questions into fine-grained reasoning paths, quantitatively evaluating each step and its subsequent reflections. These assessments enable automatic construction of direct preference optimization data, reducing reliance on expensive expert annotations while guiding models to identify and correct reasoning errors. Experimental results on the MedQA-USMLE benchmark demonstrate Med-REFL achieves consistent improvements, with average gains up to 4.11\%. Notably, it further boosts the state-of-the-art performance of 7B/8B models by an additional 4.13\%. Furthermore, Med-REFL exhibits strong generalization capabilities and robustness across several challenging medical question-answering datasets. Our work illustrates that prioritizing reflection quality leads to more accurate and trustworthy reasoning in medical AI applications. Checkpoints, code, and data can be found https://github.com/TianYin123/Med-REFL{here}.

  • 5 authors
·
Jun 11, 2025 1

Can Generalist Foundation Models Outcompete Special-Purpose Tuning? Case Study in Medicine

Generalist foundation models such as GPT-4 have displayed surprising capabilities in a wide variety of domains and tasks. Yet, there is a prevalent assumption that they cannot match specialist capabilities of fine-tuned models. For example, most explorations to date on medical competency benchmarks have leveraged domain-specific training, as exemplified by efforts on BioGPT and Med-PaLM. We build on a prior study of GPT-4's capabilities on medical challenge benchmarks in the absence of special training. Rather than using simple prompting to highlight the model's out-of-the-box capabilities, we perform a systematic exploration of prompt engineering. We find that prompting innovation can unlock deeper specialist capabilities and show that GPT-4 easily tops prior leading results for medical benchmarks. The prompting methods we explore are general purpose, and make no specific use of domain expertise, removing the need for expert-curated content. Our experimental design carefully controls for overfitting during the prompt engineering process. We introduce Medprompt, based on a composition of several prompting strategies. With Medprompt, GPT-4 achieves state-of-the-art results on all nine of the benchmark datasets in the MultiMedQA suite. The method outperforms leading specialist models such as Med-PaLM 2 by a significant margin with an order of magnitude fewer calls to the model. Steering GPT-4 with Medprompt achieves a 27% reduction in error rate on the MedQA dataset over the best methods to date achieved with specialist models and surpasses a score of 90% for the first time. Beyond medical problems, we show the power of Medprompt to generalize to other domains and provide evidence for the broad applicability of the approach via studies of the strategy on exams in electrical engineering, machine learning, philosophy, accounting, law, nursing, and clinical psychology.

  • 18 authors
·
Nov 27, 2023

GLoRe: When, Where, and How to Improve LLM Reasoning via Global and Local Refinements

State-of-the-art language models can exhibit impressive reasoning refinement capabilities on math, science or coding tasks. However, recent work demonstrates that even the best models struggle to identify when and where to refine without access to external feedback. Outcome-based Reward Models (ORMs), trained to predict correctness of the final answer indicating when to refine, offer one convenient solution for deciding when to refine. Process Based Reward Models (PRMs), trained to predict correctness of intermediate steps, can then be used to indicate where to refine. But they are expensive to train, requiring extensive human annotations. In this paper, we propose Stepwise ORMs (SORMs) which are trained, only on synthetic data, to approximate the expected future reward of the optimal policy or V^{star}. More specifically, SORMs are trained to predict the correctness of the final answer when sampling the current policy many times (rather than only once as in the case of ORMs). Our experiments show that SORMs can more accurately detect incorrect reasoning steps compared to ORMs, thus improving downstream accuracy when doing refinements. We then train global refinement models, which take only the question and a draft solution as input and predict a corrected solution, and local refinement models which also take as input a critique indicating the location of the first reasoning error. We generate training data for both models synthetically by reusing data used to train the SORM. We find combining global and local refinements, using the ORM as a reranker, significantly outperforms either one individually, as well as a best of three sample baseline. With this strategy we can improve the accuracy of a LLaMA-2 13B model (already fine-tuned with RL) on GSM8K from 53\% to 65\% when greedily sampled.

  • 7 authors
·
Feb 13, 2024 1

ReFIne: A Framework for Trustworthy Large Reasoning Models with Reliability, Faithfulness, and Interpretability

Recent advances in long chain-of-thought (CoT) reasoning have largely prioritized answer accuracy and token efficiency, while overlooking aspects critical to trustworthiness. We argue that usable reasoning systems must be trustworthy, characterized by three properties: interpretability, faithfulness, and reliability. To this end, we propose ReFIne, a new training framework that integrates supervised fine-tuning with GRPO to encourage models to: (i) improve interpretability by producing structured, tag-based traces with high-level planning that are easier for humans to follow; (ii) enhance faithfulness by explicitly disclosing the decisive information guiding each solution, with consistent cross-section references; and (iii) promote reliability by providing self-assessments of both the derivation's soundness and the confidence of the final answer. We apply ReFIne to the Qwen3 models at multiple scales (1.7B/4B/8B) and evaluate across mathematical benchmarks of varying difficulty. Our experimental results show that ReFIne models generate clearer and better-structured reasoning traces (interpretability +44.0%), more faithfully expose their underlying decision process (faithfulness +18.8%), and offer informative confidence estimates (reliability +42.4%). These findings highlight an overlooked but important direction: reasoning models should be optimized not only for accuracy, but also for broader dimensions of trustworthiness. Our code is available at: https://github.com/Trustworthy-ML-Lab/Training_Trustworthy_LRM_with_Refine

  • 4 authors
·
Oct 10, 2025 2

Refine Medical Diagnosis Using Generation Augmented Retrieval and Clinical Practice Guidelines

Current medical language models, adapted from large language models (LLMs), typically predict ICD code-based diagnosis from electronic health records (EHRs) because these labels are readily available. However, ICD codes do not capture the nuanced, context-rich reasoning clinicians use for diagnosis. Clinicians synthesize diverse patient data and reference clinical practice guidelines (CPGs) to make evidence-based decisions. This misalignment limits the clinical utility of existing models. We introduce GARMLE-G, a Generation-Augmented Retrieval framework that grounds medical language model outputs in authoritative CPGs. Unlike conventional Retrieval-Augmented Generation based approaches, GARMLE-G enables hallucination-free outputs by directly retrieving authoritative guideline content without relying on model-generated text. It (1) integrates LLM predictions with EHR data to create semantically rich queries, (2) retrieves relevant CPG knowledge snippets via embedding similarity, and (3) fuses guideline content with model output to generate clinically aligned recommendations. A prototype system for hypertension diagnosis was developed and evaluated on multiple metrics, demonstrating superior retrieval precision, semantic relevance, and clinical guideline adherence compared to RAG-based baselines, while maintaining a lightweight architecture suitable for localized healthcare deployment. This work provides a scalable, low-cost, and hallucination-free method for grounding medical language models in evidence-based clinical practice, with strong potential for broader clinical deployment.

  • 8 authors
·
Jun 22, 2025

RefineX: Learning to Refine Pre-training Data at Scale from Expert-Guided Programs

The foundational capabilities of large language models (LLMs) are deeply influenced by the quality of their pre-training corpora. However, enhancing data quality at scale remains a significant challenge, primarily due to the trade-off between refinement effectiveness and processing efficiency. While rule-based filtering remains the dominant paradigm, it typically operates at the document level and lacks the granularity needed to refine specific content within documents. Inspired by emerging work such as ProX, we propose RefineX, a novel framework for large-scale, surgical refinement of pre-training data through programmatic editing tasks. RefineX enables efficient and fine-grained data refinement while reliably preserving the diversity and naturalness of raw text. The core strength of RefineX lies in distilling high-quality, expert-guided end-to-end refinement results into minimal edit-based deletion programs. This high-precision distillation pipeline is used to train an efficient and reliable refine model that can systematically improve every instance in the corpus at scale. We evaluate RefineX across from-scratch pre-training at multiple model scales and find that it consistently outperforms models trained on raw, filtered, or alternatively refined data across diverse downstream tasks. On the 750M model, RefineX yields 2.6%-7.2% average gains on lighteval tasks, and achieves comparable performance using significantly fewer training tokens. Further analysis shows that RefineX reliably enhances text quality with both high efficiency and precision, outperforming prior approaches such as end-to-end generation and Prox-C. These results position RefineX as a scalable, effective, and reliable solution for optimizing pre-training data in modern LLM pipelines.

  • 10 authors
·
Jul 3, 2025 1

SynGP500: A Clinically-Grounded Synthetic Dataset of Australian General Practice Medical Notes

We introduce SynGP500, a clinician-curated collection of 500 synthetic Australian general practice medical notes. The dataset integrates curriculum-based clinical breadth (RACGP 2022 Curriculum), epidemiologically-calibrated prevalence (BEACH study), and diverse consultation contexts. This approach systematically includes both common presentations and less-common curriculum-specified conditions that GPs must recognize but appear infrequently in single practice populations, potentially supporting more generalizable model training than datasets constrained by naturally occurring case distributions. SynGP500 is messy by design, reflecting the authentic complexity of healthcare delivery: telegraphic documentation, typos, patient non-adherence, socioeconomic barriers, and clinician-patient disagreements, unlike sanitized synthetic datasets that obscure clinical realities. Multi-faceted validation demonstrates dataset quality through epidemiological alignment with real Australian GP consultation patterns (BEACH study), stylometric analysis confirming high linguistic variation, semantic diversity analysis demonstrating broad coverage, and exploratory downstream evaluation using self-supervised medical concept extraction, showing F1 improvements. SynGP500 addresses a critical national gap, providing researchers and educators with a resource for developing and evaluating clinical NLP methods for Australian general practice while inherently protecting patient privacy.

  • 1 authors
·
Dec 17, 2025

RefGC-SR^2: Reference-guided Generated Content Super-Resolution and Refinement

Reference-guided generation (e.g., object compositing, customization) has progressed rapidly, yet current pipelines share a fundamental limitation: the object-centric high-resolution reference image (HRRI) provided by users is downsampled to a fixed low-resolution (LR) before being fed into the model, so the fine-grained details are discarded before the output is even produced. In addition, the generation step then introduces its own artifacts (e.g., identity distortion) on top of this loss. Existing reference-guided generated content refinement (RefGCR) methods can correct some of these artifacts but still operate in the LR domain; reference-guided super-resolution (RefSR) methods recover resolution but assume natural-image degradations and ignore the artifact distribution of generative pipelines. To address both gaps in a single formulation, we introduce a new task: reference-guided generated content super-resolution-refinement (RefGC-SR^2), where the original HRRI is reused at the post-processing stage to recover lost details, refine generative artifacts, and upscale the output simultaneously. We construct the first real-world triplet data generation pipeline for this RefGC-SR^2 task, training a diptych-conditioned generator to synthesize paired low-quality anchors that public pretrained models cannot provide. We further present a frequency-aware diffusion transformer model for RefGC-SR^2 that selectively injects fine details from the HRRI while removing generative artifacts. Extensive experiments demonstrate that our RefGC-SR^2 model successfully (i) refines the object identity faithfully with respect to the reference, and (ii) recovers high-resolution details, so that the final result is significantly higher quality and practically more usable compared to existing RefGCR and RefSR baselines.

  • 4 authors
·
Jun 12 2

RefineBench: Evaluating Refinement Capability of Language Models via Checklists

Can language models (LMs) self-refine their own responses? This question is increasingly relevant as a wide range of real-world user interactions involve refinement requests. However, prior studies have largely tested LMs' refinement abilities on verifiable tasks such as competition math or symbolic reasoning with simplified scaffolds, whereas users often pose open-ended queries and provide varying degrees of feedback on what they desire. The recent advent of reasoning models that exhibit self-reflection patterns in their chains-of-thought further motivates this question. To analyze this, we introduce RefineBench, a benchmark of 1,000 challenging problems across 11 domains paired with a checklist-based evaluation framework. We evaluate two refinement modes: (1) guided refinement, where an LM is provided natural language feedback, and (2) self-refinement, where LMs attempt to improve without guidance. In the self-refinement setting, even frontier LMs such as Gemini 2.5 Pro and GPT-5 achieve modest baseline scores of 31.3% and 29.1%, respectively, and most models fail to consistently improve across iterations (e.g., Gemini-2.5-Pro gains only +1.8%, while DeepSeek-R1 declines by -0.1%). By contrast, in guided refinement, both proprietary LMs and large open-weight LMs (>70B) can leverage targeted feedback to refine responses to near-perfect levels within five turns. These findings suggest that frontier LMs require breakthroughs to self-refine their incorrect responses, and that RefineBench provides a valuable testbed for tracking progress.

MedBench v4: A Robust and Scalable Benchmark for Evaluating Chinese Medical Language Models, Multimodal Models, and Intelligent Agents

Recent advances in medical large language models (LLMs), multimodal models, and agents demand evaluation frameworks that reflect real clinical workflows and safety constraints. We present MedBench v4, a nationwide, cloud-based benchmarking infrastructure comprising over 700,000 expert-curated tasks spanning 24 primary and 91 secondary specialties, with dedicated tracks for LLMs, multimodal models, and agents. Items undergo multi-stage refinement and multi-round review by clinicians from more than 500 institutions, and open-ended responses are scored by an LLM-as-a-judge calibrated to human ratings. We evaluate 15 frontier models. Base LLMs reach a mean overall score of 54.1/100 (best: Claude Sonnet 4.5, 62.5/100), but safety and ethics remain low (18.4/100). Multimodal models perform worse overall (mean 47.5/100; best: GPT-5, 54.9/100), with solid perception yet weaker cross-modal reasoning. Agents built on the same backbones substantially improve end-to-end performance (mean 79.8/100), with Claude Sonnet 4.5-based agents achieving up to 85.3/100 overall and 88.9/100 on safety tasks. MedBench v4 thus reveals persisting gaps in multimodal reasoning and safety for base models, while showing that governance-aware agentic orchestration can markedly enhance benchmarked clinical readiness without sacrificing capability. By aligning tasks with Chinese clinical guidelines and regulatory priorities, the platform offers a practical reference for hospitals, developers, and policymakers auditing medical AI.

  • 18 authors
·
Nov 18, 2025

Hybrid guiding: A multi-resolution refinement approach for semantic segmentation of gigapixel histopathological images

Histopathological cancer diagnostics has become more complex, and the increasing number of biopsies is a challenge for most pathology laboratories. Thus, development of automatic methods for evaluation of histopathological cancer sections would be of value. In this study, we used 624 whole slide images (WSIs) of breast cancer from a Norwegian cohort. We propose a cascaded convolutional neural network design, called H2G-Net, for semantic segmentation of gigapixel histopathological images. The design involves a detection stage using a patch-wise method, and a refinement stage using a convolutional autoencoder. To validate the design, we conducted an ablation study to assess the impact of selected components in the pipeline on tumour segmentation. Guiding segmentation, using hierarchical sampling and deep heatmap refinement, proved to be beneficial when segmenting the histopathological images. We found a significant improvement when using a refinement network for postprocessing the generated tumour segmentation heatmaps. The overall best design achieved a Dice score of 0.933 on an independent test set of 90 WSIs. The design outperformed single-resolution approaches, such as cluster-guided, patch-wise high-resolution classification using MobileNetV2 (0.872) and a low-resolution U-Net (0.874). In addition, segmentation on a representative x400 WSI took ~58 seconds, using only the CPU. The findings demonstrate the potential of utilizing a refinement network to improve patch-wise predictions. The solution is efficient and does not require overlapping patch inference or ensembling. Furthermore, we showed that deep neural networks can be trained using a random sampling scheme that balances on multiple different labels simultaneously, without the need of storing patches on disk. Future work should involve more efficient patch generation and sampling, as well as improved clustering.

  • 9 authors
·
Dec 6, 2021

RareBench: Can LLMs Serve as Rare Diseases Specialists?

Generalist Large Language Models (LLMs), such as GPT-4, have shown considerable promise in various domains, including medical diagnosis. Rare diseases, affecting approximately 300 million people worldwide, often have unsatisfactory clinical diagnosis rates primarily due to a lack of experienced physicians and the complexity of differentiating among many rare diseases. In this context, recent news such as "ChatGPT correctly diagnosed a 4-year-old's rare disease after 17 doctors failed" underscore LLMs' potential, yet underexplored, role in clinically diagnosing rare diseases. To bridge this research gap, we introduce RareBench, a pioneering benchmark designed to systematically evaluate the capabilities of LLMs on 4 critical dimensions within the realm of rare diseases. Meanwhile, we have compiled the largest open-source dataset on rare disease patients, establishing a benchmark for future studies in this domain. To facilitate differential diagnosis of rare diseases, we develop a dynamic few-shot prompt methodology, leveraging a comprehensive rare disease knowledge graph synthesized from multiple knowledge bases, significantly enhancing LLMs' diagnostic performance. Moreover, we present an exhaustive comparative study of GPT-4's diagnostic capabilities against those of specialist physicians. Our experimental findings underscore the promising potential of integrating LLMs into the clinical diagnostic process for rare diseases. This paves the way for exciting possibilities in future advancements in this field.

  • 6 authors
·
Feb 9, 2024

GS2Pose: Two-stage 6D Object Pose Estimation Guided by Gaussian Splatting

This paper proposes a new method for accurate and robust 6D pose estimation of novel objects, named GS2Pose. By introducing 3D Gaussian splatting, GS2Pose can utilize the reconstruction results without requiring a high-quality CAD model, which means it only requires segmented RGBD images as input. Specifically, GS2Pose employs a two-stage structure consisting of coarse estimation followed by refined estimation. In the coarse stage, a lightweight U-Net network with a polarization attention mechanism, called Pose-Net, is designed. By using the 3DGS model for supervised training, Pose-Net can generate NOCS images to compute a coarse pose. In the refinement stage, GS2Pose formulates a pose regression algorithm following the idea of reprojection or Bundle Adjustment (BA), referred to as GS-Refiner. By leveraging Lie algebra to extend 3DGS, GS-Refiner obtains a pose-differentiable rendering pipeline that refines the coarse pose by comparing the input images with the rendered images. GS-Refiner also selectively updates parameters in the 3DGS model to achieve environmental adaptation, thereby enhancing the algorithm's robustness and flexibility to illuminative variation, occlusion, and other challenging disruptive factors. GS2Pose was evaluated through experiments conducted on the LineMod dataset, where it was compared with similar algorithms, yielding highly competitive results. The code for GS2Pose will soon be released on GitHub.

  • 3 authors
·
Nov 6, 2024

A deep learning system for differential diagnosis of skin diseases

Skin conditions affect an estimated 1.9 billion people worldwide. A shortage of dermatologists causes long wait times and leads patients to seek dermatologic care from general practitioners. However, the diagnostic accuracy of general practitioners has been reported to be only 0.24-0.70 (compared to 0.77-0.96 for dermatologists), resulting in referral errors, delays in care, and errors in diagnosis and treatment. In this paper, we developed a deep learning system (DLS) to provide a differential diagnosis of skin conditions for clinical cases (skin photographs and associated medical histories). The DLS distinguishes between 26 skin conditions that represent roughly 80% of the volume of skin conditions seen in primary care. The DLS was developed and validated using de-identified cases from a teledermatology practice serving 17 clinical sites via a temporal split: the first 14,021 cases for development and the last 3,756 cases for validation. On the validation set, where a panel of three board-certified dermatologists defined the reference standard for every case, the DLS achieved 0.71 and 0.93 top-1 and top-3 accuracies respectively. For a random subset of the validation set (n=963 cases), 18 clinicians reviewed the cases for comparison. On this subset, the DLS achieved a 0.67 top-1 accuracy, non-inferior to board-certified dermatologists (0.63, p<0.001), and higher than primary care physicians (PCPs, 0.45) and nurse practitioners (NPs, 0.41). The top-3 accuracy showed a similar trend: 0.90 DLS, 0.75 dermatologists, 0.60 PCPs, and 0.55 NPs. These results highlight the potential of the DLS to augment general practitioners to accurately diagnose skin conditions by suggesting differential diagnoses that may not have been considered. Future work will be needed to prospectively assess the clinical impact of using this tool in actual clinical workflows.

  • 22 authors
·
Sep 11, 2019

UGPL: Uncertainty-Guided Progressive Learning for Evidence-Based Classification in Computed Tomography

Accurate classification of computed tomography (CT) images is essential for diagnosis and treatment planning, but existing methods often struggle with the subtle and spatially diverse nature of pathological features. Current approaches typically process images uniformly, limiting their ability to detect localized abnormalities that require focused analysis. We introduce UGPL, an uncertainty-guided progressive learning framework that performs a global-to-local analysis by first identifying regions of diagnostic ambiguity and then conducting detailed examination of these critical areas. Our approach employs evidential deep learning to quantify predictive uncertainty, guiding the extraction of informative patches through a non-maximum suppression mechanism that maintains spatial diversity. This progressive refinement strategy, combined with an adaptive fusion mechanism, enables UGPL to integrate both contextual information and fine-grained details. Experiments across three CT datasets demonstrate that UGPL consistently outperforms state-of-the-art methods, achieving improvements of 3.29%, 2.46%, and 8.08% in accuracy for kidney abnormality, lung cancer, and COVID-19 detection, respectively. Our analysis shows that the uncertainty-guided component provides substantial benefits, with performance dramatically increasing when the full progressive learning pipeline is implemented. Our code is available at: https://github.com/shravan-18/UGPL

  • 4 authors
·
Jul 18, 2025 1

Scaling Gaussian Process Optimization by Evaluating a Few Unique Candidates Multiple Times

Computing a Gaussian process (GP) posterior has a computational cost cubical in the number of historical points. A reformulation of the same GP posterior highlights that this complexity mainly depends on how many unique historical points are considered. This can have important implication in active learning settings, where the set of historical points is constructed sequentially by the learner. We show that sequential black-box optimization based on GPs (GP-Opt) can be made efficient by sticking to a candidate solution for multiple evaluation steps and switch only when necessary. Limiting the number of switches also limits the number of unique points in the history of the GP. Thus, the efficient GP reformulation can be used to exactly and cheaply compute the posteriors required to run the GP-Opt algorithms. This approach is especially useful in real-world applications of GP-Opt with high switch costs (e.g. switching chemicals in wet labs, data/model loading in hyperparameter optimization). As examples of this meta-approach, we modify two well-established GP-Opt algorithms, GP-UCB and GP-EI, to switch candidates as infrequently as possible adapting rules from batched GP-Opt. These versions preserve all the theoretical no-regret guarantees while improving practical aspects of the algorithms such as runtime, memory complexity, and the ability of batching candidates and evaluating them in parallel.

  • 5 authors
·
Jan 30, 2022

Capabilities of GPT-4 on Medical Challenge Problems

Large language models (LLMs) have demonstrated remarkable capabilities in natural language understanding and generation across various domains, including medicine. We present a comprehensive evaluation of GPT-4, a state-of-the-art LLM, on medical competency examinations and benchmark datasets. GPT-4 is a general-purpose model that is not specialized for medical problems through training or engineered to solve clinical tasks. Our analysis covers two sets of official practice materials for the USMLE, a three-step examination program used to assess clinical competency and grant licensure in the United States. We also evaluate performance on the MultiMedQA suite of benchmark datasets. Beyond measuring model performance, experiments were conducted to investigate the influence of test questions containing both text and images on model performance, probe for memorization of content during training, and study probability calibration, which is of critical importance in high-stakes applications like medicine. Our results show that GPT-4, without any specialized prompt crafting, exceeds the passing score on USMLE by over 20 points and outperforms earlier general-purpose models (GPT-3.5) as well as models specifically fine-tuned on medical knowledge (Med-PaLM, a prompt-tuned version of Flan-PaLM 540B). In addition, GPT-4 is significantly better calibrated than GPT-3.5, demonstrating a much-improved ability to predict the likelihood that its answers are correct. We also explore the behavior of the model qualitatively through a case study that shows the ability of GPT-4 to explain medical reasoning, personalize explanations to students, and interactively craft new counterfactual scenarios around a medical case. Implications of the findings are discussed for potential uses of GPT-4 in medical education, assessment, and clinical practice, with appropriate attention to challenges of accuracy and safety.

  • 5 authors
·
Mar 20, 2023

SYNFAC-EDIT: Synthetic Imitation Edit Feedback for Factual Alignment in Clinical Summarization

Large Language Models (LLMs) such as GPT & Llama have demonstrated significant achievements in summarization tasks but struggle with factual inaccuracies, a critical issue in clinical NLP applications where errors could lead to serious consequences. To counter the high costs and limited availability of expert-annotated data for factual alignment, this study introduces an innovative pipeline that utilizes >100B parameter GPT variants like GPT-3.5 & GPT-4 to act as synthetic experts to generate high-quality synthetics feedback aimed at enhancing factual consistency in clinical note summarization. Our research primarily focuses on edit feedback generated by these synthetic feedback experts without additional human annotations, mirroring and optimizing the practical scenario in which medical professionals refine AI system outputs. Although such 100B+ parameter GPT variants have proven to demonstrate expertise in various clinical NLP tasks, such as the Medical Licensing Examination, there is scant research on their capacity to act as synthetic feedback experts and deliver expert-level edit feedback for improving the generation quality of weaker (<10B parameter) LLMs like GPT-2 (1.5B) & Llama 2 (7B) in clinical domain. So in this work, we leverage 100B+ GPT variants to act as synthetic feedback experts offering expert-level edit feedback, that is used to reduce hallucinations and align weaker (<10B parameter) LLMs with medical facts using two distinct alignment algorithms (DPO & SALT), endeavoring to narrow the divide between AI-generated content and factual accuracy. This highlights the substantial potential of LLM-based synthetic edits in enhancing the alignment of clinical factuality.

umassnlp UMass NLP
·
Feb 21, 2024

FormalGeo: An Extensible Formalized Framework for Olympiad Geometric Problem Solving

This is the first paper in a series of work we have accomplished over the past three years. In this paper, we have constructed a consistent formal plane geometry system. This will serve as a crucial bridge between IMO-level plane geometry challenges and readable AI automated reasoning. Within this formal framework, we have been able to seamlessly integrate modern AI models with our formal system. AI is now capable of providing deductive reasoning solutions to IMO-level plane geometry problems, just like handling other natural languages, and these proofs are readable, traceable, and verifiable. We propose the geometry formalization theory (GFT) to guide the development of the geometry formal system. Based on the GFT, we have established the FormalGeo, which consists of 88 geometric predicates and 196 theorems. It can represent, validate, and solve IMO-level geometry problems. we also have crafted the FGPS (formal geometry problem solver) in Python. It serves as both an interactive assistant for verifying problem-solving processes and an automated problem solver. We've annotated the formalgeo7k and formalgeo-imo datasets. The former contains 6,981 (expand to 133,818 through data augmentation) geometry problems, while the latter includes 18 (expand to 2,627 and continuously increasing) IMO-level challenging geometry problems. All annotated problems include detailed formal language descriptions and solutions. Implementation of the formal system and experiments validate the correctness and utility of the GFT. The backward depth-first search method only yields a 2.42% problem-solving failure rate, and we can incorporate deep learning techniques to achieve lower one. The source code of FGPS and datasets are available at https://github.com/BitSecret/FGPS.

  • 20 authors
·
Oct 27, 2023

Automated Rubrics for Reliable Evaluation of Medical Dialogue Systems

Large Language Models (LLMs) are increasingly used for clinical decision support, where hallucinations and unsafe suggestions may pose direct risks to patient safety. These risks are particularly challenging as they often manifest as subtle clinical errors that evade detection by generic metrics, while expert-authored fine-grained rubrics remain costly to construct and difficult to scale. In this paper, we propose a retrieval-augmented multi-agent framework designed to automate the generation of instance-specific evaluation rubrics. Our approach grounds evaluation in authoritative medical evidence by decomposing retrieved content into atomic facts and synthesizing them with user interaction constraints to form verifiable, fine-grained evaluation criteria. Evaluated on HealthBench, our framework achieves a Clinical Intent Alignment (CIA) score of 60.12%, a statistically significant improvement over the GPT-4o baseline (55.16%). In discriminative tests, our rubrics yield a mean score delta (μ_Δ = 8.658) and an AUROC of 0.977, nearly doubling the quality separation achieved by GPT-4o baseline (4.972). Beyond evaluation, our rubrics effectively guide response refinement, improving quality by 9.2% (from 59.0% to 68.2%). This provides a scalable and transparent foundation for both evaluating and improving medical LLMs. The code is available at https://anonymous.4open.science/r/Automated-Rubric-Generation-AF3C/.

  • 4 authors
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Jan 21

ARC Prize 2025: Technical Report

The ARC-AGI benchmark series serves as a critical measure of few-shot generalization on novel tasks, a core aspect of intelligence. The ARC Prize 2025 global competition targeted the newly released ARC-AGI-2 dataset, which features greater task complexity compared to its predecessor. The Kaggle competition attracted 1,455 teams and 15,154 entries, with the top score reaching 24% on the ARC-AGI-2 private evaluation set. Paper submissions nearly doubled year-over-year to 90 entries, reflecting the growing research interest in fluid intelligence and abstract reasoning. The defining theme of 2025 is the emergence of the refinement loop -- a per-task iterative program optimization loop guided by a feedback signal. Refinement loops come in a variety of forms, in particular evolutionary program synthesis approaches and application-layer refinements to commercial AI systems. Such refinement loops are also possible in weight space, as evidenced by zero-pretraining deep learning methods which are now achieving competitive performance with remarkably small networks (7M parameters). In parallel, four frontier AI labs (Anthropic, Google DeepMind, OpenAI, and xAI) reported ARC-AGI performance in public model cards in 2025, establishing ARC-AGI as an industry standard benchmark for AI reasoning. However, our analysis indicates that current frontier AI reasoning performance remains fundamentally constrained to knowledge coverage, giving rise to new forms of benchmark contamination. In this paper, we survey the top-performing methods, examine the role of refinement loops in AGI progress, discuss knowledge-dependent overfitting, and preview ARC-AGI-3, which introduces interactive reasoning challenges that require exploration, planning, memory, goal acquisition, and alignment capabilities.

  • 4 authors
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Jan 15

Deep Researcher with Sequential Plan Reflection and Candidates Crossover (Deep Researcher Reflect Evolve)

This paper introduces a novel Deep Researcher architecture designed to generate detailed research reports on complex PhD level topics by addressing the inherent limitations of the Parallel Scaling paradigm. Our system utilizes two key innovations: Sequential Research Plan Refinement via Reflection and a Candidates Crossover algorithm. The sequential refinement process is demonstrated as an efficient method that allows the agent to maintain a centralized Global Research Context, enabling it to look back at current progress, reason about the research plan, and intelligently make changes at runtime. This dynamic adaptation contrasts with parallel approaches, which often suffer from siloed knowledge. The Candidates Crossover algorithm further enhances search efficiency by deploying multiple LLM candidates with varied parameters to explore a larger search space, with their findings synthesized to curate a comprehensive final research response. The process concludes with One Shot Report Generation, ensuring the final document is informed by a unified narrative and high fact density. Powered by the Gemini 2.5 Pro model, our Deep Researcher was evaluated on the DeepResearch Bench, a globally recognized benchmark of 100 doctoral level research tasks. Our architecture achieved an overall score of 46.21, demonstrating superior performance by surpassing leading deep research agents such as Claude Researcher, Nvidia AIQ Research Assistant, Perplexity Research, Kimi Researcher and Grok Deeper Search present on the DeepResearch Bench actively running leaderboard. This performance marginally exceeds our previous work, Static DRA, and reinforces the finding that sequential scaling consistently outperforms the parallel self consistency paradigm.

  • 1 authors
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Jan 28

A Comprehensive Study of GPT-4V's Multimodal Capabilities in Medical Imaging

This paper presents a comprehensive evaluation of GPT-4V's capabilities across diverse medical imaging tasks, including Radiology Report Generation, Medical Visual Question Answering (VQA), and Visual Grounding. While prior efforts have explored GPT-4V's performance in medical image analysis, to the best of our knowledge, our study represents the first quantitative evaluation on publicly available benchmarks. Our findings highlight GPT-4V's potential in generating descriptive reports for chest X-ray images, particularly when guided by well-structured prompts. Meanwhile, its performance on the MIMIC-CXR dataset benchmark reveals areas for improvement in certain evaluation metrics, such as CIDEr. In the domain of Medical VQA, GPT-4V demonstrates proficiency in distinguishing between question types but falls short of the VQA-RAD benchmark in terms of accuracy. Furthermore, our analysis finds the limitations of conventional evaluation metrics like the BLEU scores, advocating for the development of more semantically robust assessment methods. In the field of Visual Grounding, GPT-4V exhibits preliminary promise in recognizing bounding boxes, but its precision is lacking, especially in identifying specific medical organs and signs. Our evaluation underscores the significant potential of GPT-4V in the medical imaging domain, while also emphasizing the need for targeted refinements to fully unlock its capabilities.

  • 10 authors
·
Oct 31, 2023

No Loss, No Gain: Gated Refinement and Adaptive Compression for Prompt Optimization

Prompt engineering is crucial for leveraging the full potential of large language models (LLMs). While automatic prompt optimization offers a scalable alternative to costly manual design, generating effective prompts remains challenging. Existing methods often struggle to stably generate improved prompts, leading to low efficiency, and overlook that prompt optimization easily gets trapped in local optima. Addressing this, we propose GRACE, a framework that integrates two synergistic strategies: Gated Refinement and Adaptive Compression, achieving Efficient prompt optimization. The gated refinement strategy introduces a feedback regulation gate and an update rejection gate, which refine update signals to produce stable and effective prompt improvements. When optimization stagnates, the adaptive compression strategy distills the prompt's core concepts, restructuring the optimization trace and opening new paths. By strategically introducing information loss through refinement and compression, GRACE delivers substantial gains in performance and efficiency. In extensive experiments on 11 tasks across three practical domains, including BIG-Bench Hard (BBH), domain-specific, and general NLP tasks, GRACE achieves significant average relative performance improvements of 4.7%, 4.4% and 2.7% over state-of-the-art methods, respectively. Further analysis shows that GRACE achieves these gains using only 25% of the prompt generation budget required by prior methods, highlighting its high optimization efficiency and low computational overhead. Our code is available at https://github.com/Eric8932/GRACE.

  • 9 authors
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Sep 27, 2025

Lyra: Orchestrating Dual Correction in Automated Theorem Proving

Large Language Models (LLMs) present an intriguing avenue for exploration in the field of formal theorem proving. Nevertheless, their full potential, particularly concerning the mitigation of hallucinations and refinement through prover error messages, remains an area that has yet to be thoroughly investigated. To enhance the effectiveness of LLMs in the field, we introduce the Lyra, a new framework that employs two distinct correction mechanisms: Tool Correction (TC) and Conjecture Correction (CC). To implement Tool Correction in the post-processing of formal proofs, we leverage prior knowledge to utilize predefined prover tools (e.g., Sledgehammer) for guiding the replacement of incorrect tools. Tool Correction significantly contributes to mitigating hallucinations, thereby improving the overall accuracy of the proof. In addition, we introduce Conjecture Correction, an error feedback mechanism designed to interact with prover to refine formal proof conjectures with prover error messages. Compared to the previous refinement framework, the proposed Conjecture Correction refines generation with instruction but does not collect paired (generation, error & refinement) prompts. Our method has achieved state-of-the-art (SOTA) performance on both miniF2F validation (48.0% -> 55.3%) and test (45.5% -> 51.2%). We also present 3 IMO problems solved by Lyra. We believe Tool Correction (post-process for hallucination mitigation) and Conjecture Correction (subgoal adjustment from interaction with environment) could provide a promising avenue for future research in this field.

  • 9 authors
·
Sep 27, 2023

MEDDxAgent: A Unified Modular Agent Framework for Explainable Automatic Differential Diagnosis

Differential Diagnosis (DDx) is a fundamental yet complex aspect of clinical decision-making, in which physicians iteratively refine a ranked list of possible diseases based on symptoms, antecedents, and medical knowledge. While recent advances in large language models (LLMs) have shown promise in supporting DDx, existing approaches face key limitations, including single-dataset evaluations, isolated optimization of components, unrealistic assumptions about complete patient profiles, and single-attempt diagnosis. We introduce a Modular Explainable DDx Agent (MEDDxAgent) framework designed for interactive DDx, where diagnostic reasoning evolves through iterative learning, rather than assuming a complete patient profile is accessible. MEDDxAgent integrates three modular components: (1) an orchestrator (DDxDriver), (2) a history taking simulator, and (3) two specialized agents for knowledge retrieval and diagnosis strategy. To ensure robust evaluation, we introduce a comprehensive DDx benchmark covering respiratory, skin, and rare diseases. We analyze single-turn diagnostic approaches and demonstrate the importance of iterative refinement when patient profiles are not available at the outset. Our broad evaluation demonstrates that MEDDxAgent achieves over 10% accuracy improvements in interactive DDx across both large and small LLMs, while offering critical explainability into its diagnostic reasoning process.

  • 6 authors
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Feb 26, 2025

Automatic Replication of LLM Mistakes in Medical Conversations

Large language models (LLMs) are increasingly evaluated in clinical settings using multi-dimensional rubrics which quantify reasoning quality, safety, and patient-centeredness. Yet, replicating specific mistakes in other LLM models is not straightforward and often requires manual effort. We introduce MedMistake, an automatic pipeline that extracts mistakes LLMs make in patient-doctor conversations and converts them into a benchmark of single-shot QA pairs. Our pipeline (1) creates complex, conversational data between an LLM patient and LLM doctor, (2) runs an evaluation with a committee of 2 LLM judges across a variety of dimensions and (3) creates simplified single-shot QA scenarios from those mistakes. We release MedMistake-All, a dataset of 3,390 single-shot QA pairs where GPT-5 and Gemini 2.5 Pro are currently failing to answer correctly, as judged by two LLM judges. We used medical experts to validate a subset of 211/3390 questions (MedMistake-Bench), which we used to run a final evaluation of 12 frontier LLMs: Claude Opus 4.5, Claude Sonnet 4.5, DeepSeek-Chat, Gemini 2.5 Pro, Gemini 3 Pro, GPT-4o, GPT-5, GPT-5.1, GPT-5.2, Grok 4, Grok 4.1, Mistral Large. We found that GPT models, Claude and Grok obtained the best performance on MedMistake-Bench. We release both the doctor-validated benchmark (MedMistake-Bench), as well as the full dataset (MedMistake-All) at https://huggingface.co/datasets/TheLumos/MedicalMistakeBenchmark.

  • 4 authors
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Dec 24, 2025

BioMedGPT: Open Multimodal Generative Pre-trained Transformer for BioMedicine

Foundation models (FMs) have exhibited remarkable performance across a wide range of downstream tasks in many domains. Nevertheless, general-purpose FMs often face challenges when confronted with domain-specific problems, due to their limited access to the proprietary training data in a particular domain. In biomedicine, there are various biological modalities, such as molecules, proteins, and cells, which are encoded by the language of life and exhibit significant modality gaps with human natural language. In this paper, we introduce BioMedGPT, an open multimodal generative pre-trained transformer (GPT) for biomedicine, to bridge the gap between the language of life and human natural language. BioMedGPT allows users to easily ``communicate'' with diverse biological modalities through free text, which is the first of its kind. BioMedGPT aligns different biological modalities with natural language via a large generative language model, namely, BioMedGPT-LM. We publish BioMedGPT-10B, which unifies the feature spaces of molecules, proteins, and natural language via encoding and alignment. Through fine-tuning, BioMedGPT-10B outperforms or is on par with human and significantly larger general-purpose foundation models on the biomedical QA task. It also demonstrates promising performance in the molecule QA and protein QA tasks, which could greatly accelerate the discovery of new drugs and therapeutic targets. In addition, BioMedGPT-LM-7B is the first large generative language model based on Llama2 in the biomedical domain, therefore is commercial friendly. Both BioMedGPT-10B and BioMedGPT-LM-7B are open-sourced to the research community. In addition, we publish the datasets that are meticulously curated for the alignment of multi-modalities, i.e., PubChemQA and UniProtQA. All the models, codes, and datasets are available at https://github.com/PharMolix/OpenBioMed.

  • 7 authors
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Aug 18, 2023

HealthQA-BR: A System-Wide Benchmark Reveals Critical Knowledge Gaps in Large Language Models

The evaluation of Large Language Models (LLMs) in healthcare has been dominated by physician-centric, English-language benchmarks, creating a dangerous illusion of competence that ignores the interprofessional nature of patient care. To provide a more holistic and realistic assessment, we introduce HealthQA-BR, the first large-scale, system-wide benchmark for Portuguese-speaking healthcare. Comprising 5,632 questions from Brazil's national licensing and residency exams, it uniquely assesses knowledge not only in medicine and its specialties but also in nursing, dentistry, psychology, social work, and other allied health professions. We conducted a rigorous zero-shot evaluation of over 20 leading LLMs. Our results reveal that while state-of-the-art models like GPT 4.1 achieve high overall accuracy (86.6%), this top-line score masks alarming, previously unmeasured deficiencies. A granular analysis shows performance plummets from near-perfect in specialties like Ophthalmology (98.7%) to barely passing in Neurosurgery (60.0%) and, most notably, Social Work (68.4%). This "spiky" knowledge profile is a systemic issue observed across all models, demonstrating that high-level scores are insufficient for safety validation. By publicly releasing HealthQA-BR and our evaluation suite, we provide a crucial tool to move beyond single-score evaluations and toward a more honest, granular audit of AI readiness for the entire healthcare team.

  • 1 authors
·
Jun 16, 2025

Evaluation of GPT-3.5 and GPT-4 for supporting real-world information needs in healthcare delivery

Despite growing interest in using large language models (LLMs) in healthcare, current explorations do not assess the real-world utility and safety of LLMs in clinical settings. Our objective was to determine whether two LLMs can serve information needs submitted by physicians as questions to an informatics consultation service in a safe and concordant manner. Sixty six questions from an informatics consult service were submitted to GPT-3.5 and GPT-4 via simple prompts. 12 physicians assessed the LLM responses' possibility of patient harm and concordance with existing reports from an informatics consultation service. Physician assessments were summarized based on majority vote. For no questions did a majority of physicians deem either LLM response as harmful. For GPT-3.5, responses to 8 questions were concordant with the informatics consult report, 20 discordant, and 9 were unable to be assessed. There were 29 responses with no majority on "Agree", "Disagree", and "Unable to assess". For GPT-4, responses to 13 questions were concordant, 15 discordant, and 3 were unable to be assessed. There were 35 responses with no majority. Responses from both LLMs were largely devoid of overt harm, but less than 20% of the responses agreed with an answer from an informatics consultation service, responses contained hallucinated references, and physicians were divided on what constitutes harm. These results suggest that while general purpose LLMs are able to provide safe and credible responses, they often do not meet the specific information need of a given question. A definitive evaluation of the usefulness of LLMs in healthcare settings will likely require additional research on prompt engineering, calibration, and custom-tailoring of general purpose models.

  • 18 authors
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Apr 26, 2023

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.

  • 13 authors
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Apr 23, 2024 1

PIE: Simulating Disease Progression via Progressive Image Editing

Disease progression simulation is a crucial area of research that has significant implications for clinical diagnosis, prognosis, and treatment. One major challenge in this field is the lack of continuous medical imaging monitoring of individual patients over time. To address this issue, we develop a novel framework termed Progressive Image Editing (PIE) that enables controlled manipulation of disease-related image features, facilitating precise and realistic disease progression simulation. Specifically, we leverage recent advancements in text-to-image generative models to simulate disease progression accurately and personalize it for each patient. We theoretically analyze the iterative refining process in our framework as a gradient descent with an exponentially decayed learning rate. To validate our framework, we conduct experiments in three medical imaging domains. Our results demonstrate the superiority of PIE over existing methods such as Stable Diffusion Walk and Style-Based Manifold Extrapolation based on CLIP score (Realism) and Disease Classification Confidence (Alignment). Our user study collected feedback from 35 veteran physicians to assess the generated progressions. Remarkably, 76.2% of the feedback agrees with the fidelity of the generated progressions. To our best knowledge, PIE is the first of its kind to generate disease progression images meeting real-world standards. It is a promising tool for medical research and clinical practice, potentially allowing healthcare providers to model disease trajectories over time, predict future treatment responses, and improve patient outcomes.

  • 6 authors
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Sep 20, 2023 1

MMedAgent-RL: Optimizing Multi-Agent Collaboration for Multimodal Medical Reasoning

Medical Large Vision-Language Models (Med-LVLMs) have shown strong potential in multimodal diagnostic tasks. However, existing single-agent models struggle to generalize across diverse medical specialties, limiting their performance. Recent efforts introduce multi-agent collaboration frameworks inspired by clinical workflows, where general practitioners (GPs) and specialists interact in a fixed sequence. Despite improvements, these static pipelines lack flexibility and adaptability in reasoning. To address this, we propose MMedAgent-RL, a reinforcement learning (RL)-based multi-agent framework that enables dynamic, optimized collaboration among medical agents. Specifically, we train two GP agents based on Qwen2.5-VL via RL: the triage doctor learns to assign patients to appropriate specialties, while the attending physician integrates the judgments from multi-specialists and its own knowledge to make final decisions. To address the inconsistency in specialist outputs, we introduce a curriculum learning (CL)-guided RL strategy that progressively teaches the attending physician to balance between imitating specialists and correcting their mistakes. Experiments on five medical VQA benchmarks demonstrate that MMedAgent-RL not only outperforms both open-source and proprietary Med-LVLMs, but also exhibits human-like reasoning patterns. Notably, it achieves an average performance gain of 20.7% over supervised fine-tuning baselines.

  • 11 authors
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May 31, 2025

GENIE: Generative Note Information Extraction model for structuring EHR data

Electronic Health Records (EHRs) hold immense potential for advancing healthcare, offering rich, longitudinal data that combines structured information with valuable insights from unstructured clinical notes. However, the unstructured nature of clinical text poses significant challenges for secondary applications. Traditional methods for structuring EHR free-text data, such as rule-based systems and multi-stage pipelines, are often limited by their time-consuming configurations and inability to adapt across clinical notes from diverse healthcare settings. Few systems provide a comprehensive attribute extraction for terminologies. While giant large language models (LLMs) like GPT-4 and LLaMA 405B excel at structuring tasks, they are slow, costly, and impractical for large-scale use. To overcome these limitations, we introduce GENIE, a Generative Note Information Extraction system that leverages LLMs to streamline the structuring of unstructured clinical text into usable data with standardized format. GENIE processes entire paragraphs in a single pass, extracting entities, assertion statuses, locations, modifiers, values, and purposes with high accuracy. Its unified, end-to-end approach simplifies workflows, reduces errors, and eliminates the need for extensive manual intervention. Using a robust data preparation pipeline and fine-tuned small scale LLMs, GENIE achieves competitive performance across multiple information extraction tasks, outperforming traditional tools like cTAKES and MetaMap and can handle extra attributes to be extracted. GENIE strongly enhances real-world applicability and scalability in healthcare systems. By open-sourcing the model and test data, we aim to encourage collaboration and drive further advancements in EHR structurization.

  • 9 authors
·
Jan 30, 2025

DrugGen: Advancing Drug Discovery with Large Language Models and Reinforcement Learning Feedback

Traditional drug design faces significant challenges due to inherent chemical and biological complexities, often resulting in high failure rates in clinical trials. Deep learning advancements, particularly generative models, offer potential solutions to these challenges. One promising algorithm is DrugGPT, a transformer-based model, that generates small molecules for input protein sequences. Although promising, it generates both chemically valid and invalid structures and does not incorporate the features of approved drugs, resulting in time-consuming and inefficient drug discovery. To address these issues, we introduce DrugGen, an enhanced model based on the DrugGPT structure. DrugGen is fine-tuned on approved drug-target interactions and optimized with proximal policy optimization. By giving reward feedback from protein-ligand binding affinity prediction using pre-trained transformers (PLAPT) and a customized invalid structure assessor, DrugGen significantly improves performance. Evaluation across multiple targets demonstrated that DrugGen achieves 100% valid structure generation compared to 95.5% with DrugGPT and produced molecules with higher predicted binding affinities (7.22 [6.30-8.07]) compared to DrugGPT (5.81 [4.97-6.63]) while maintaining diversity and novelty. Docking simulations further validate its ability to generate molecules targeting binding sites effectively. For example, in the case of fatty acid-binding protein 5 (FABP5), DrugGen generated molecules with superior docking scores (FABP5/11, -9.537 and FABP5/5, -8.399) compared to the reference molecule (Palmitic acid, -6.177). Beyond lead compound generation, DrugGen also shows potential for drug repositioning and creating novel pharmacophores for existing targets. By producing high-quality small molecules, DrugGen provides a high-performance medium for advancing pharmaceutical research and drug discovery.

  • 6 authors
·
Nov 19, 2024

ClarifyGPT: Empowering LLM-based Code Generation with Intention Clarification

We introduce a novel framework named ClarifyGPT, which aims to enhance code generation by empowering LLMs with the ability to identify ambiguous requirements and ask targeted clarifying questions. In particular, ClarifyGPT first detects whether a given requirement is ambiguous by performing a code consistency check. If it is ambiguous, ClarifyGPT prompts an LLM to generate targeted clarifying questions. After receiving question responses, ClarifyGPT refines the ambiguous requirement and inputs it into the same LLM to generate a final code solution. To evaluate our ClarifyGPT, we first conduct a human evaluation involving ten participants who use ClarifyGPT for code generation on two publicly available benchmarks: MBPP-sanitized and MBPP-ET. The results show that ClarifyGPT elevates the performance (Pass@1) of GPT-4 from 70.96% to 80.80% on MBPP-sanitized. Furthermore, to perform large-scale automated evaluations of ClarifyGPT across different LLMs and benchmarks without requiring user participation, we introduce a high-fidelity simulation method to simulate user responses. The automated evaluation results also demonstrate that ClarifyGPT can significantly enhance code generation performance compared to the baselines. In particular, ClarifyGPT improves the average performance of GPT-4 and ChatGPT across four benchmarks from 68.02% to 75.75% and from 58.55% to 67.22%, respectively. We believe that ClarifyGPT can effectively facilitate the practical application of LLMs in real-world development environments.

  • 8 authors
·
Oct 17, 2023

Expert Evaluation of Clinical AI Tools on Real Point-of-Care Clinical Queries

Physicians now pose millions of clinical questions to AI tools each week, yet these tools are evaluated largely on hypothetical or exam-style questions, not those actually asked in practice. We report a blinded evaluation built on 620 Real-world Point-Of-Care Queries (Real-POCQi) submitted to the OpenEvidence (OE) platform by physicians spanning 30 specialties, as well as 187 questions from HealthBench. 149 practicing physicians across 36 states made head-to-head comparisons between answers from three frontier general-purpose models (Claude Opus 4.8, Gemini 3.1 Pro, and GPT-5.5) and a specialized clinical tool (OE), with graders matched to each question's specialty. When comparing answers along five dimensions relevant to clinical decision support -- accuracy, clinical utility, source quality, verifiability, & completeness -- physicians scored the specialized tool highest on all axes; in the primary analysis on Real-POCQi, win differences (margins between win and loss rates) ranged from 25 to 39 percentage points (p<0.001). Results remained consistent in sensitivity analyses stratifying by citation display, answer length, OE-user status, and Real-POCQi versus HealthBench. In parallel, LLM judges were found to systematically differ from expert judges, though both generally agreed on the best model. These findings underscore two conclusions: (i) AI tool evaluations should reflect real-world query distributions and use expert judges that mirror the specialization defining modern medicine and (ii) the consistent advantage of the specialized tool over general-purpose models does not necessarily mean that the latter cannot serve similar purposes, but that targeted engineering and customization can yield meaningful gains in performance for its users. We release Real-POCQi as a public benchmark, as well as the prespecified statistical analysis for reproducing results of this study.

  • 8 authors
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Jun 26

Closing the gap between open-source and commercial large language models for medical evidence summarization

Large language models (LLMs) hold great promise in summarizing medical evidence. Most recent studies focus on the application of proprietary LLMs. Using proprietary LLMs introduces multiple risk factors, including a lack of transparency and vendor dependency. While open-source LLMs allow better transparency and customization, their performance falls short compared to proprietary ones. In this study, we investigated to what extent fine-tuning open-source LLMs can further improve their performance in summarizing medical evidence. Utilizing a benchmark dataset, MedReview, consisting of 8,161 pairs of systematic reviews and summaries, we fine-tuned three broadly-used, open-sourced LLMs, namely PRIMERA, LongT5, and Llama-2. Overall, the fine-tuned LLMs obtained an increase of 9.89 in ROUGE-L (95% confidence interval: 8.94-10.81), 13.21 in METEOR score (95% confidence interval: 12.05-14.37), and 15.82 in CHRF score (95% confidence interval: 13.89-16.44). The performance of fine-tuned LongT5 is close to GPT-3.5 with zero-shot settings. Furthermore, smaller fine-tuned models sometimes even demonstrated superior performance compared to larger zero-shot models. The above trends of improvement were also manifested in both human and GPT4-simulated evaluations. Our results can be applied to guide model selection for tasks demanding particular domain knowledge, such as medical evidence summarization.

  • 14 authors
·
Jul 25, 2024

An Exploratory Case Study of LLM-Assisted Refactoring and Gameplay Feature Generation in an Endless Runner Game

Large language models (LLMs) are increasingly used to support software development, but their practical usefulness in applied game-development settings remains underexplored, especially when generated code must be integrated into an existing game software system. This paper presents an exploratory empirical case study of GPT-4o in a custom Python/Pygame endless runner. The study examines six selected development tasks: three localized refactoring tasks and three tasks involving gameplay feature generation. The resulting implementations were evaluated using software metrics, unit tests, and manual gameplay assessments. In this case study, all three selected refactoring tasks were completed successfully in functional terms, whereas only one of the three selected gameplay feature generation tasks resulted in a correctly integrated feature. The findings suggest that, in this setting, GPT-4o handled localized transformations more reliably than tasks requiring new gameplay interactions across multiple existing systems. Given the exploratory single-case design, these results are best interpreted as indicative observations rather than as generalizable evidence of category-level model performance. Overall, the paper contributes a transparent case-based account of the opportunities and limitations of LLM-assisted refactoring and gameplay feature generation in an existing game software system.

VideoRepair: Improving Text-to-Video Generation via Misalignment Evaluation and Localized Refinement

Recent text-to-video (T2V) diffusion models have demonstrated impressive generation capabilities across various domains. However, these models often generate videos that have misalignments with text prompts, especially when the prompts describe complex scenes with multiple objects and attributes. To address this, we introduce VideoRepair, a novel model-agnostic, training-free video refinement framework that automatically identifies fine-grained text-video misalignments and generates explicit spatial and textual feedback, enabling a T2V diffusion model to perform targeted, localized refinements. VideoRepair consists of four stages: In (1) video evaluation, we detect misalignments by generating fine-grained evaluation questions and answering those questions with MLLM. In (2) refinement planning, we identify accurately generated objects and then create localized prompts to refine other areas in the video. Next, in (3) region decomposition, we segment the correctly generated area using a combined grounding module. We regenerate the video by adjusting the misaligned regions while preserving the correct regions in (4) localized refinement. On two popular video generation benchmarks (EvalCrafter and T2V-CompBench), VideoRepair substantially outperforms recent baselines across various text-video alignment metrics. We provide a comprehensive analysis of VideoRepair components and qualitative examples.

  • 4 authors
·
Nov 22, 2024 3

DR.BENCH: Diagnostic Reasoning Benchmark for Clinical Natural Language Processing

The meaningful use of electronic health records (EHR) continues to progress in the digital era with clinical decision support systems augmented by artificial intelligence. A priority in improving provider experience is to overcome information overload and reduce the cognitive burden so fewer medical errors and cognitive biases are introduced during patient care. One major type of medical error is diagnostic error due to systematic or predictable errors in judgment that rely on heuristics. The potential for clinical natural language processing (cNLP) to model diagnostic reasoning in humans with forward reasoning from data to diagnosis and potentially reduce the cognitive burden and medical error has not been investigated. Existing tasks to advance the science in cNLP have largely focused on information extraction and named entity recognition through classification tasks. We introduce a novel suite of tasks coined as Diagnostic Reasoning Benchmarks, DR.BENCH, as a new benchmark for developing and evaluating cNLP models with clinical diagnostic reasoning ability. The suite includes six tasks from ten publicly available datasets addressing clinical text understanding, medical knowledge reasoning, and diagnosis generation. DR.BENCH is the first clinical suite of tasks designed to be a natural language generation framework to evaluate pre-trained language models. Experiments with state-of-the-art pre-trained generative language models using large general domain models and models that were continually trained on a medical corpus demonstrate opportunities for improvement when evaluated in DR. BENCH. We share DR. BENCH as a publicly available GitLab repository with a systematic approach to load and evaluate models for the cNLP community.

  • 7 authors
·
Sep 29, 2022

UltraShape 1.0: High-Fidelity 3D Shape Generation via Scalable Geometric Refinement

In this report, we introduce UltraShape 1.0, a scalable 3D diffusion framework for high-fidelity 3D geometry generation. The proposed approach adopts a two-stage generation pipeline: a coarse global structure is first synthesized and then refined to produce detailed, high-quality geometry. To support reliable 3D generation, we develop a comprehensive data processing pipeline that includes a novel watertight processing method and high-quality data filtering. This pipeline improves the geometric quality of publicly available 3D datasets by removing low-quality samples, filling holes, and thickening thin structures, while preserving fine-grained geometric details. To enable fine-grained geometry refinement, we decouple spatial localization from geometric detail synthesis in the diffusion process. We achieve this by performing voxel-based refinement at fixed spatial locations, where voxel queries derived from coarse geometry provide explicit positional anchors encoded via RoPE, allowing the diffusion model to focus on synthesizing local geometric details within a reduced, structured solution space. Our model is trained exclusively on publicly available 3D datasets, achieving strong geometric quality despite limited training resources. Extensive evaluations demonstrate that UltraShape 1.0 performs competitively with existing open-source methods in both data processing quality and geometry generation. All code and trained models will be released to support future research.

  • 13 authors
·
Dec 24, 2025 4

ReflexiCoder: Teaching Large Language Models to Self-Reflect on Generated Code and Self-Correct It via Reinforcement Learning

While Large Language Models (LLMs) have revolutionized code generation, standard "System 1" approaches, generating solutions in a single forward pass, often hit a performance ceiling when faced with complex algorithmic tasks. Existing iterative refinement strategies attempt to bridge this gap at inference time, yet they predominantly rely on external oracles, execution feedback, or computationally expensive prompt-response cycles. In this work, we propose ReflexiCoder, a novel reinforcement learning (RL) framework that internalizes the structured reasoning trajectory, encompassing initial generation, bug and optimization aware reflection, and self-correction, directly into the model's weights. Unlike prior methods, ReflexiCoder shifts the paradigm from external-dependent refinement to an intrinsic, fully autonomous self-reflection and self-correction capabilities at inference time. We utilize an RL-zero training paradigm with granular reward functions to optimize the entire reflection-correction trajectory, teaching the model how to debug without reliance on ground-truth feedback or execution engines at inference time. Extensive experiments across seven benchmarks demonstrate that our ReflexiCoder-8B establishes a new state-of-the-art (SOTA) among leading open-source models in the 1.5B-14B range, achieving 94.51% (87.20%) on HumanEval (Plus), 81.80% (78.57%) on MBPP (Plus), 35.00% on BigCodeBench, 52.21% on LiveCodeBench, and 37.34% on CodeForces in a single-attempt setting, rivaling or surpassing proprietary models like GPT-5.1. Notably, our framework is significantly more token-efficient than base models, reducing inference-time compute overhead by approximately 40% through disciplined, high-speed reasoning and reflection patterns. Source code is available at https://github.com/juyongjiang/ReflexiCoder.

  • 6 authors
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Mar 5 2

Adaptive Pruning for Increased Robustness and Reduced Computational Overhead in Gaussian Process Accelerated Saddle Point Searches

Gaussian process (GP) regression provides a strategy for accelerating saddle point searches on high-dimensional energy surfaces by reducing the number of times the energy and its derivatives with respect to atomic coordinates need to be evaluated. The computational overhead in the hyperparameter optimization can, however, be large and make the approach inefficient. Failures can also occur if the search ventures too far into regions that are not represented well enough by the GP model. Here, these challenges are resolved by using geometry-aware optimal transport measures and an active pruning strategy using a summation over Wasserstein-1 distances for each atom-type in farthest-point sampling, selecting a fixed-size subset of geometrically diverse configurations to avoid rapidly increasing cost of GP updates as more observations are made. Stability is enhanced by permutation-invariant metric that provides a reliable trust radius for early-stopping and a logarithmic barrier penalty for the growth of the signal variance. These physically motivated algorithmic changes prove their efficacy by reducing to less than a half the mean computational time on a set of 238 challenging configurations from a previously published data set of chemical reactions. With these improvements, the GP approach is established as, a robust and scalable algorithm for accelerating saddle point searches when the evaluation of the energy and atomic forces requires significant computational effort.

  • 2 authors
·
Oct 7, 2025 2

Think Thrice Before You Act: Progressive Thought Refinement in Large Language Models

Recent advancements in large language models (LLMs) have demonstrated that progressive refinement, rather than providing a single answer, results in more accurate and thoughtful outputs. However, existing methods often rely heavily on supervision signals to evaluate previous responses, making it difficult to assess output quality in more open-ended scenarios effectively. Additionally, these methods are typically designed for specific tasks, which limits their generalization to new domains. To address these limitations, we propose Progressive Thought Refinement (PTR), a framework that enables LLMs to refine their responses progressively. PTR operates in two phases: (1) Thought data construction stage: We propose a weak and strong model collaborative selection strategy to build a high-quality progressive refinement dataset to ensure logical consistency from thought to answers, and the answers are gradually refined in each round. (2) Thought-Mask Fine-Tuning Phase: We design a training structure to mask the "thought" and adjust loss weights to encourage LLMs to refine prior thought, teaching them to implicitly understand "how to improve" rather than "what is correct." Experimental results show that PTR significantly enhances LLM performance across ten diverse tasks (avg. from 49.6% to 53.5%) without task-specific fine-tuning. Notably, in more open-ended tasks, LLMs also demonstrate substantial improvements in the quality of responses beyond mere accuracy, suggesting that PTR truly teaches LLMs to self-improve over time.

  • 12 authors
·
Oct 17, 2024

Rethinking Thinking Tokens: LLMs as Improvement Operators

Reasoning training incentivizes LLMs to produce long chains of thought (long CoT), which among other things, allows them to explore solution strategies with self-checking. This results in higher accuracy, but inflates context length, token/compute cost, and answer latency. We ask: Can current models leverage their metacognition to provide other combinations on this Pareto frontier, e.g., better accuracy with lower context length and/or latency? Abstractly, we view the model as an improvement operator on its own "thoughts" with a continuum of possible strategies. We identify an interesting inference family Parallel-Distill-Refine (PDR), which performs the following: (i) generate diverse drafts in parallel; (ii) distill them into a bounded, textual workspace; and (iii) refine conditioned on this workspace, producing an output that seeds the next round. Importantly, context length (hence compute cost) is controllable via degree of parallelism, and is no longer conflated with the total number of generated tokens. We report PDR instantiations of current models that give better accuracy than long CoT while incurring lower latency. Setting degree of parallelism to 1 yields an interesting subcase, Sequential Refinement (SR) (iteratively improve a single candidate answer) which provides performance superior to long CoT. Success of such model orchestrations raises the question whether further training could shift the Pareto frontier. To this end, we train an 8B thinking model with Reinforcement Learning (RL) to make it consistent with PDR as the inference method. On math tasks with verifiable answers, iterative pipelines surpass single-pass baselines at matched sequential budgets, with PDR delivering the largest gains (e.g., +11% on AIME 2024 and +9% on AIME 2025).

  • 9 authors
·
Oct 1, 2025 2

iGRPO: Self-Feedback-Driven LLM Reasoning

Large Language Models (LLMs) have shown promise in solving complex mathematical problems, yet they still fall short of producing accurate and consistent solutions. Reinforcement Learning (RL) is a framework for aligning these models with task-specific rewards, improving overall quality and reliability. Group Relative Policy Optimization (GRPO) is an efficient, value-function-free alternative to Proximal Policy Optimization (PPO) that leverages group-relative reward normalization. We introduce Iterative Group Relative Policy Optimization (iGRPO), a two-stage extension of GRPO that adds dynamic self-conditioning through model-generated drafts. In Stage 1, iGRPO samples multiple exploratory drafts and selects the highest-reward draft using the same scalar reward signal used for optimization. In Stage 2, it appends this best draft to the original prompt and applies a GRPO-style update on draft-conditioned refinements, training the policy to improve beyond its strongest prior attempt. Under matched rollout budgets, iGRPO consistently outperforms GRPO across base models (e.g., Nemotron-H-8B-Base-8K and DeepSeek-R1 Distilled), validating its effectiveness on diverse reasoning benchmarks. Moreover, applying iGRPO to OpenReasoning-Nemotron-7B trained on AceReason-Math achieves new state-of-the-art results of 85.62\% and 79.64\% on AIME24 and AIME25, respectively. Ablations further show that the refinement wrapper generalizes beyond GRPO variants, benefits from a generative judge, and alters learning dynamics by delaying entropy collapse. These results underscore the potential of iterative, self-feedback-based RL for advancing verifiable mathematical reasoning.

nvidia NVIDIA
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Feb 9 2