Committee

arXiv:2506.20876v1 Announce Type: new Abstract: Technological progress has led to concrete advancements in tasks that were regarded as challenging, such as automatic fact-checking. Interest in adopting these systems for public health and medicine has grown due to the high-stakes nature of medical decisions and challenges in critically appraising a vast and diverse medical literature. Evidence-based medicine connects to every individual, and yet the nature of it is highly technical, rendering the medical literacy of majority users inadequate to sufficiently navigate the domain. Such problems with medical communication ripens the ground for end-to-end fact-checking agents: check a claim against current medical literature and return with an evidence-backed verdict. And yet, such systems remain largely unused. To understand this, we present the first study examining how clinical experts verify real claims from social media by synthesizing medical evidence. In searching for this upper-bound, we reveal fundamental challenges in end-to-end fact-checking when applied to medicine: Difficulties connecting claims in the wild to scientific evidence in the form of clinical trials; ambiguities in underspecified claims mixed with mismatched intentions; and inherently subjective veracity labels. We argue that fact-checking should be approached and evaluated as an interactive communication problem, rather than an end-to-end process.

arXiv:2506.20430v1 Announce Type: new Abstract: Rare diseases collectively affect over 300 million individuals worldwide, yet timely and accurate diagnosis remains a pervasive challenge. This is largely due to their clinical heterogeneity, low individual prevalence, and the limited familiarity most clinicians have with rare conditions. Here, we introduce DeepRare, the first rare disease diagnosis agentic system powered by a large language model (LLM), capable of processing heterogeneous clinical inputs. The system generates ranked diagnostic hypotheses for rare diseases, each accompanied by a transparent chain of reasoning that links intermediate analytic steps to verifiable medical evidence. DeepRare comprises three key components: a central host with a long-term memory module; specialized agent servers responsible for domain-specific analytical tasks integrating over 40 specialized tools and web-scale, up-to-date medical knowledge sources, ensuring access to the most current clinical information. This modular and scalable design enables complex diagnostic reasoning while maintaining traceability and adaptability. We evaluate DeepRare on eight datasets. The system demonstrates exceptional diagnostic performance among 2,919 diseases, achieving 100% accuracy for 1013 diseases. In HPO-based evaluations, DeepRare significantly outperforms other 15 methods, like traditional bioinformatics diagnostic tools, LLMs, and other agentic systems, achieving an average Recall@1 score of 57.18% and surpassing the second-best method (Reasoning LLM) by a substantial margin of 23.79 percentage points. For multi-modal input scenarios, DeepRare achieves 70.60% at Recall@1 compared to Exomiser’s 53.20% in 109 cases. Manual verification of reasoning chains by clinical experts achieves 95.40% agreements. Furthermore, the DeepRare system has been implemented as a user-friendly web application http://raredx.cn/doctor.

arXiv:2506.19750v2 Announce Type: replace Abstract: Symptom Checkers (SCs) provide users with personalized medical information. To prevent performance degradation from algorithm updates, SC developers must evaluate diagnostic performance changes for individual diseases before deployment. However, acquiring sufficient evaluation data for rare diseases is difficult, and manually creating numerous clinical vignettes is costly and impractical. This study proposes and validates a novel Synthetic Vignette Simulation Approach to evaluate diagnostic performance changes for individual rare diseases following SC algorithm updates. We used disease-phenotype annotations from the Human Phenotype Ontology (HPO), a knowledge database for rare diseases, to generate synthetic vignettes. With these, we simulated SC interviews to estimate the impact of algorithm updates on real-world diagnostic performance. The method’s effectiveness was evaluated retrospectively by comparing estimated values with actual metric changes using the $R^2$ coefficient. The experiment included eight past SC algorithm updates. For updates on diseases with frequency information in HPO (n=5), the $R^2$ for Recall@8 change was 0.831 ($p$=0.031), and for Precision@8 change, it was 0.78 ($p$=0.047), indicating the method can predict post-deployment performance. In contrast, large prediction errors occurred for diseases without frequency information (n=3), highlighting its importance. Our method enables pre-deployment evaluation of SC algorithm changes for individual rare diseases using a publicly available, expert-created knowledge base. This transparent and low-cost approach allows developers to efficiently improve diagnostic performance for rare diseases, potentially enhancing support for early diagnosis.

arXiv:2403.08059v3 Announce Type: replace-cross Abstract: Language promptable X-ray image segmentation would enable greater flexibility for human-in-the-loop workflows in diagnostic and interventional precision medicine. Prior efforts have contributed task-specific models capable of solving problems within a narrow scope, but expanding to broader use requires additional data, annotations, and training time. Recently, language-aligned foundation models (LFMs) — machine learning models trained on large amounts of highly variable image and text data thus enabling broad applicability — have emerged as promising tools for automated image analysis. Existing foundation models for medical image analysis focus on scenarios and modalities where large, richly annotated datasets are available. However, the X-ray imaging modality features highly variable image appearance and applications, from diagnostic chest X-rays to interventional fluoroscopy, with varying availability of data. To pave the way toward an LFM for comprehensive and language-aligned analysis of arbitrary medical X-ray images, we introduce FluoroSAM, a language-promptable variant of the Segment Anything Model, trained from scratch on 3M synthetic X-ray images from a wide variety of human anatomies, imaging geometries, and viewing angles. These include pseudo-ground truth masks for 128 organ types and 464 tools with associated text descriptions. FluoroSAM is capable of segmenting myriad anatomical structures and tools based on natural language prompts, thanks to the novel incorporation of vector quantization (VQ) of text embeddings in the training process. We demonstrate FluoroSAM’s performance quantitatively on real X-ray images and showcase on several applications how FluoroSAM is a key enabler for rich human-machine interaction in the X-ray image acquisition and analysis context. Code is available at https://github.com/arcadelab/fluorosam.

arXiv:2506.19998v1 Announce Type: new Abstract: REST APIs play important roles in enriching the action space of web agents, yet most API-based agents rely on curated and uniform toolsets that do not reflect the complexity of real-world APIs. Building tool-using agents for arbitrary domains remains a major challenge, as it requires reading unstructured API documentation, testing APIs and inferring correct parameters. We propose Doc2Agent, a scalable pipeline to build agents that can call Python-based tools generated from API documentation. Doc2Agent generates executable tools from API documentations and iteratively refines them using a code agent. We evaluate our approach on real-world APIs, WebArena APIs, and research APIs, producing validated tools. We achieved a 55% relative performance improvement with 90% lower cost compared to direct API calling on WebArena benchmark. A domain-specific agent built for glycomaterial science further demonstrates the pipeline’s adaptability to complex, knowledge-rich tasks. Doc2Agent offers a generalizable solution for building tool agents from unstructured API documentation at scale.

arXiv:2506.20073v1 Announce Type: new Abstract: Spatio-temporal data mining plays a pivotal role in informed decision making across diverse domains. However, existing models are often restricted to narrow tasks, lacking the capacity for multi-task inference and complex long-form reasoning that require generation of in-depth, explanatory outputs. These limitations restrict their applicability to real-world, multi-faceted decision scenarios. In this work, we introduce STReason, a novel framework that integrates the reasoning strengths of large language models (LLMs) with the analytical capabilities of spatio-temporal models for multi-task inference and execution. Without requiring task-specific finetuning, STReason leverages in-context learning to decompose complex natural language queries into modular, interpretable programs, which are then systematically executed to generate both solutions and detailed rationales. To facilitate rigorous evaluation, we construct a new benchmark dataset and propose a unified evaluation framework with metrics specifically designed for long-form spatio-temporal reasoning. Experimental results show that STReason significantly outperforms advanced LLM baselines across all metrics, particularly excelling in complex, reasoning-intensive spatio-temporal scenarios. Human evaluations further validate STReason’s credibility and practical utility, demonstrating its potential to reduce expert workload and broaden the applicability to real-world spatio-temporal tasks. We believe STReason provides a promising direction for developing more capable and generalizable spatio-temporal reasoning systems.

arXiv:2502.00258v2 Announce Type: replace-cross Abstract: Large Language Models (LLMs) have demonstrated exceptional performance in natural language processing tasks, yet their massive size makes serving them inefficient and costly. Semi-structured pruning has emerged as an effective method for model acceleration, but existing approaches are suboptimal because they focus on local, layer-wise optimizations using heuristic rules, failing to leverage global feedback. We present ProxSparse, a learning-based framework for mask selection enabled by regularized optimization. ProxSparse transforms the rigid, non-differentiable mask selection process into a smoother optimization procedure, allowing gradual mask exploration with flexibility. ProxSparse does not involve additional weight updates once the mask is determined. Our extensive evaluations on 7 widely used models show that ProxSparse consistently outperforms previously proposed semi-structured mask selection methods with significant improvement, demonstrating the effectiveness of our learned approach towards semi-structured pruning.

July/August 25Guest edited by Edward Faulkner ’03 May/June 25Guest edited by Frank Rubin ’62 March/April 25Guest edited by Michael S. Branicky ’03 January/February 25Guest edited by Dan Katz ’03 November/December 24Guest edited by Edward Faulkner ’03 September/October 24Guest edited by Mark Douma ’63 and Frank Rubin ’62 July/August 24Puzzle Corner Editor Emeritus Allan Gottlieb ’67 signs off September/October 23Edited by Allan Gottlieb ’67 May/June 23Edited by Allan Gottlieb ’67 January/February 23Edited by Allan Gottlieb ’67 Allan Gottlieb ’67 launched Puzzle Corner in 1966 and edited the column for 58 years. It first appeared in the MIT student-run magazine Tech Engineering News (now defunct) and began running in Technology Review in the summer of 1966. Back issues from 1966 through 2022 are available at cs.nyu.edu/~gottlieb/tr.

arXiv:2506.19113v1 Announce Type: new Abstract: The discourse around toxicity and LLMs in NLP largely revolves around detection tasks. This work shifts the focus to evaluating LLMs’ reasoning about toxicity — from their explanations that justify a stance — to enhance their trustworthiness in downstream tasks. Despite extensive research on explainability, it is not straightforward to adopt existing methods to evaluate free-form toxicity explanation due to their over-reliance on input text perturbations, among other challenges. To account for these, we propose a novel, theoretically-grounded multi-dimensional criterion, Human-Aligned Faithfulness (HAF), that measures the extent to which LLMs’ free-form toxicity explanations align with those of a rational human under ideal conditions. We develop six metrics, based on uncertainty quantification, to comprehensively evaluate haf of LLMs’ toxicity explanations with no human involvement, and highlight how “non-ideal” the explanations are. We conduct several experiments on three Llama models (of size up to 70B) and an 8B Ministral model on five diverse toxicity datasets. Our results show that while LLMs generate plausible explanations to simple prompts, their reasoning about toxicity breaks down when prompted about the nuanced relations between the complete set of reasons, the individual reasons, and their toxicity stances, resulting in inconsistent and nonsensical responses. We open-source our code and LLM-generated explanations at https://github.com/uofthcdslab/HAF.

arXiv:2506.19835v1 Announce Type: new Abstract: Recent advancements in medical Large Language Models (LLMs) have showcased their powerful reasoning and diagnostic capabilities. Despite their success, current unified multimodal medical LLMs face limitations in knowledge update costs, comprehensiveness, and flexibility. To address these challenges, we introduce the Modular Multi-Agent Framework for Multi-Modal Medical Diagnosis (MAM). Inspired by our empirical findings highlighting the benefits of role assignment and diagnostic discernment in LLMs, MAM decomposes the medical diagnostic process into specialized roles: a General Practitioner, Specialist Team, Radiologist, Medical Assistant, and Director, each embodied by an LLM-based agent. This modular and collaborative framework enables efficient knowledge updates and leverages existing medical LLMs and knowledge bases. Extensive experimental evaluations conducted on a wide range of publicly accessible multimodal medical datasets, incorporating text, image, audio, and video modalities, demonstrate that MAM consistently surpasses the performance of modality-specific LLMs. Notably, MAM achieves significant performance improvements ranging from 18% to 365% compared to baseline models. Our code is released at https://github.com/yczhou001/MAM.