arXiv AI

Large Language Model Agents for Evidence Based Genetic Disease Severity Classification

The paper presents an autonomous AI agent that combines ReAct and Retrieval-Augmented Generation to classify the severity of genetic diseases using 10,211 Human Phenotype Ontology terms. It applies ACMG severity guidelines and ACOG quality-of-life criteria, retrieving PubMed literature to produce interpretable reasoning chains and verify claims. The agent achieved 93.55% accuracy on phenotype-level classification and identified 3,283 autosomal recessive gene pairs with severe presentations, with 95.2% concordance in external validation.

arXiv AI

Sep 7

A Semantic Model of Genetic Evidence: A Step Toward Bridging the Basic-Science-Clinic Gap

The article presents a new semantic model for representing scientific evidence, specifically tailored to genetics, that extends existing standards by adding fine‑grained, domain‑specific structure. It aligns with FHIR Evidence and SEPIO, incorporates a compact vocabulary validated by SHACL, and was tested in a human‑AI annotation pilot on six genetics papers, producing 28 evidence items and 95 source‑anchored assertions. The authors argue that this model advances trustworthy, AI‑ready infrastructure for variant interpretation by providing a reference data model and validation schema for genetic evidence.

By Michael Bouzinier, Dmitry Etin

benchmarks

arXiv AI

Jun 16

LiteOdyssey: A Lightweight Reasoning AI Agent for Interpretable Rare-Disease Diagnosis

arXiv:2606. 16149v1 Announce Type: new Abstract: Most medical AI systems improve by scaling additional machinery: more fine-tuning data, more agents, and/or larger retrieval databases.

By Minh-Ha Nguyen, Erica Gray, Chih-Ting Yang, Rizwan Hamid, Lingyao Li, Siyuan Ma, Thomas A. Cassini, Cathy Shyr

llms agents fine-tuning benchmarks

arXiv AI

Oct 31

Advancing Clinical Genomic Analysis with a Skill-Centred Agent

The paper introduces ClinGeX, a large‑language‑model agent that uses 105 curated executable skills to automate clinical genomic analysis. In benchmark tests, ClinGeX achieved 71.7% macro‑averaged task‑level concordance, outperforming the best comparator at 45.7%. Human‑AI collaboration studies showed ClinGeX significantly improved case‑level concordance across variant analysis, rare disease interpretation, and oncology decision‑making, while also reducing interpretation time.

By Qiaoyu Zheng, Weike Zhao, Yanjie Fan, Ye Cao, Mengqi Jiang, Xiao Zhou, Xiaoman Zhang, Pengcheng Qiu, Yongguo Yu, Yanfeng Wang, Ya Zhang, Chaoyi Wu, Weidi Xie

agents benchmarks

arXiv AI

Sep 10

Teaching agentic AI to generalize expert diagnostic reasoning in rare diseases

arXiv:2606.16149v5 Announce Type: replace Abstract: Rare disease diagnosis depends on expert reasoning that is scarce and difficult to transfer. Large language models rank the correct disease first i...

By Minh-Ha Nguyen, Erica Gray, Bryce A. Schuler, Kevin W. Byram, Chih-Ting Yang, Fan Ma, Hua Xu, Wu-Chen Su, Chao Yan, Wei-Qi Wei, Adam Wright, Lisa Bastarache, Josh F. Peterson, Lingyao Li, Siyuan Ma, Undiagnosed Diseases Network, Rizwan Hamid, Thomas A. Cassini, Cathy Shyr

llms agents benchmarks

arXiv AI

Aug 18

DiagnosisArena: Benchmarking Diagnostic Reasoning for Large Language Models

arXiv:2505. 14107v5 Announce Type: replace-cross Abstract: The emergence of groundbreaking large language models capable of performing complex reasoning tasks holds significant promise for addressing various scientific challenges, including those arising in complex clinical scenarios.

By Yakun Zhu, Zhongzhen Huang, Linjie Mu, Yutong Huang, Wei Nie, Jiaji Liu, Shaoting Zhang, Pengfei Liu, Xiaofan Zhang

llms benchmarks

arXiv AI

Sep 23

Ascent: An Agentic System over the Model Context Protocol for Real-World Clinical Data Analysis

arXiv:2609.24620v1 Announce Type: new Abstract: Answering epidemiological questions from real-world clinical data requires medical coding, schema-aware SQL, and validation of implicit choices about p...

By Angelo Ziletti, Leonardo D'Ambrosi, Melanie Tuchardt, Tim Kondziella

agents nlp data-engineering

arXiv AI

Oct 26

MedCaseAgent: From Multimodal Clinical Evidence to Rare Disease Case Reports

MedCaseAgent is an end‑to‑end agentic reasoning system that generates publication‑quality rare disease case reports from unstructured clinical notes. It combines patient‑level data mining with iterative, tool‑integrated reasoning, dynamically querying medical literature and knowledge bases to maintain clinical fidelity and assess case novelty. The framework is modular, supports multiple backbone LLMs, and is accompanied by a new multimodal case‑report corpus (MedCase‑150K) and evaluation suite (MedCase‑Bench).

By Hongkang Chu, Yifan Shen, Tianjiao Yu, Zhuoqing Zhong, Jianguo Cao, Meihuan Huang, Xu Cao

llms agents multimodal

arXiv Computation and Language

Aug 27

Retrieval-Augmented Agentic Rubric Generation for Reliable Medical Response Evaluation

The paper introduces a retrieval‑augmented multi‑agent framework that automatically generates instance‑specific evaluation rubrics for medical language models. By retrieving authoritative medical evidence, decomposing it into atomic facts, and combining these with user interaction constraints, the system produces fine‑grained criteria that outperform GPT‑4o on HealthBench and LLMEval‑Med. The generated rubrics also guide response refinement, improving medical LLM output quality by 9.2%.

By Yinzhu Chen, Abdine Maiga, Hossein A. Rahmani, Emine Yilmaz

llms rag agents benchmarks safety

arXiv AI

Oct 28

Ontology-guided multi-agent reasoning for explainable differential diagnosis

The paper introduces an ontology‑guided, multi‑agent framework for differential diagnosis that mirrors physicians’ iterative reasoning. By grounding inference in a structured, expert‑curated medical knowledge base, the system produces explicit, auditable reasoning steps, reduces hallucination, and improves transparency. It also identifies key missing symptoms and generates targeted follow‑up questions to lower diagnostic uncertainty.

By Roxana Ramona Szomiu, George Ursu, Adrian Groza

llms rag agents nlp benchmarks safety

arXiv AI

Jul 2

RareDxR1: Autonomous Medical Reasoning for Rare Disease Diagnosis Beyond Human Annotation

arXiv:2607. 00147v1 Announce Type: new Abstract: Rare disease differential diagnosis is a critical yet arduous clinical task, requiring physicians to identify precise phenotypes from complex, unstructured patient symptoms and execute intricate reasoning within a vast search space.

By Deyang Jiang, Haoran Wu, Ziyi Wang, Yiming Rong, Yunlong Zhao, Ye Jin, Bo Xu

llms rag agents reinforcement-learning benchmarks

Hugging Face Trending Papers

Oct 23

MedCaseAgent: From Multimodal Clinical Evidence to Rare Disease Case Reports

Although Large Language Models (LLMs) have demonstrated potential in clinical documentation, generating the rigorous, evidence-based reasoning required for unprecedented, atypical, and rare disease ca...

llms agents multimodal

arXiv AI

Oct 27

Auditing evaluation artifacts and data leakage in large language model systems for rare disease diagnosis

arXiv:2610.33592v1 Announce Type: new Abstract: Augmented large language model (LLM) systems have reported high benchmark accuracies in rare disease diagnosis, yet their real-world clinical utility r...

By Jian Yang, Peilin Liu, Xiaohan Li, Songda Li, Yu Cao, Yuqing Feng, Haomin Li

llms agents benchmarks safety

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