Biomedical QA

QA: Question Answering

Momentum

2 papers in the last four weeks, against 1 the four weeks before. 0.0% of all new papers.

Jul 13Week of Sep 28

Latest papers 30

Oct 6, 2026cs.CL

SAGE: Semantic Anchor-Guided Evolution for Grounded Medical QA Data Synthesis

Developing reliable models for clinical tasks, such as Medical Question Answering (QA), is severely constrained by the limited availability of high-quality, expert-annotated training data. This challenge is exacerbated by stringent privacy requirements and the impracticality of utilizing large open-source corpora or proprietary cloud APIs within resource-limited clinical settings. To address these obstacles, we introduce SAGE (\textit{Semantic Anchor-Guided Evolution}), a novel data synthesis framework that enables small, locally deployed models to generate high-quality medical training data. SAGE leverages lightweight, publicly available taxonomies such as MeSH as semantic anchors, imposing a structured prior to effectively guide and ground the data generation process. At its core, SAGE iteratively interleaves atomic (individual concept-based) and associative (relation-based) synthesis, bootstrapping training data from minimal seeds. This approach eliminates the need for large collections of medical documents or reliance on external APIs, providing a practical solution for on-premises data creation. Extensive experiments across multiple medical question-answering benchmarks demonstrate that models fine-tuned with SAGE-synthesized data consistently outperform those trained using self-derived or conventional document-based paradigms, highlighting tangible improvements in data efficiency and resource utilization for medical LLM development. Code is available at https://github.com/DIaacKr/SAGE.
Sep 30, 2026cs.CL

Overview of BioASQ 2026: The fourteenth BioASQ Challenge on Large-Scale Biomedical Semantic Indexing and Question Answering

This paper presents an overview of the fourteenth edition of the BioASQ challenge, organized in the context of the Conference and Labs of the Evaluation Forum (CLEF) 2026. BioASQ is an international challenge series that supports progress in biomedical language processing tasks ranging from semantic indexing and information extraction to question answering and summarization. In 2026, BioASQ included six shared tasks: a) Task 14b on biomedical semantic question answering. b) Task Synergy14 on question answering for developing biomedical top- ics. c) Task MultiClinSum-2 on multilingual clinical summarization. d) Task BioNNE-R on extracting relations between nested named entities in Russian and English. e) Task ELCardioCC on clinical coding in cardiology. f) Task GutBrainIE on gut-brain interplay information extrac- tion. Across these six tasks, 87 distinct teams participated, submitting more than 1000 runs overall. As in previous editions, several submissions reached competitive performance, reflecting the continued progress of state-of-the-art methods across biomedical language processing tasks.
Sep 28, 2026cs.CL

Recursive LLM Degradation in Biomedical Question Answering: A Cross-Generation Study

Repeatedly training language models on their own generated data may create a synthetic-data feedback loop in which errors and distributional biases are reintroduced into subsequent training datasets. This paper studies that process in biomedical question answering (QA) using PubMedQA and two Qwen2.5 model sizes, 0.5B and 3B parameters. The study compares a recursive synthetic-data condition, in which generation G(k+1) is trained on answers produced by G(k), against a Human-Control condition that repeatedly uses the original human training data. The study evaluates across four generations from G0-G3 with two random seeds (42 and 123) and a fixed evaluation set of 1,000 expert-labeled samples. The evaluation includes disease and chemical entity F1, context-supported rate, lexical and semantic similarity, answer length, repetition rate, and other evaluation metrics. The Recursive condition for both model sizes and both seeds showed larger declines than the Human-Control condition in disease entity F1, chemical entity F1, context-supported rate, ROUGE-L, and cosine similarity. Under the fixed no-repeat 3-gram decoding constraint, the main observed behavioral change was increased answer length, while the measured 3-gram repetition rate did not increase. The magnitude of the difference-in-change was larger for the 3B model than for the 0.5B model. This difference was particularly apparent in disease F1, context-supported rate, cosine similarity, and answer length. These results show domain-specific changes associated with using recursive synthetic-data training in biomedical QA, but do not establish clinical hallucination rates or universal model collapse.
Aug 31, 2026cs.AI

AdaPath: Query-Adaptive Path-Finding via Path-Bank for Multi-Hop Implicit Biomedical KGQA

Path-finding over knowledge graphs has become an effective way to ground LLM reasoning on multi-hop questions. However, biomedical QA introduces two distinct challenges that general-domain methods are not designed for: (i) queries do not expose intermediate reasoning and can be answered through multiple valid pathways, and (ii) biomedical knowledge graphs are densely connected, so path-finding methods easily take wrong turns. To address these challenges, we propose AdaPath, a path-finding framework that retrieves query-adaptive meta-paths from Path-Bank, which captures both query semantics and biomedical knowledge graph structure. AdaPath provides the missing cues in biomedical queries while effectively pruning dense knowledge graph neighborhoods during multi-hop reasoning. We further release BioStrat-QA, a biomedical KGQA benchmark that stratifies multi-hop queries by how much intermediate reasoning they expose. Across biomedical KGQA benchmarks, AdaPath consistently outperforms baselines, sustaining meaningful path-finding even when multi-hop queries expose less surface information. The source code is available at https://github.com/Jun-Hyeong-Kim/AdaPath.
Aug 6, 2026cs.AI

Research Assistant: AstraZeneca's Agentic System for R&D

We describe Research Assistant, an internal LLM-based system developed at AstraZeneca to help scientists and clinicians explore biomedical questions across a broad range of data sources. The system provides a chat-style interface that brings together evidence from scientific literature, knowledge graphs, chemistry, clinical trials, safety resources, expression data, and internal experimental systems. It supports both a fast mode for direct question answering and a multi-step mode for more complex research tasks. Responses are grounded in retrieved evidence and linked back to the original sources, allowing users to review and further explore the underlying data. In this technical note, we outline the system architecture, the main design choices behind the product, and lessons learned from deploying it at scale to support day-to-day R&D workflows across AstraZeneca.
Aug 2, 2026cs.CL

Retrieval Augmented Biomedical Question Answering with Weak Question Recovery and Neural Reranking for BioASQ Task 14b

This work presents DS@GT ARC BioASQ team's work for a biomedical question answering pipeline, integrating multi-source query expansion, neural reranking, retrieval refinement, and OpenBioLLM-assisted answer generation. The system combines PubMed retrieval with fine-tuned MiniLM-based semantic reranking, Reciprocal Rank Fusion (RRF), and feature-based relevance scoring to improve document ranking quality. To address challenging queries with weak retrieval performance, we introduce a conditional weak-question recovery strategy that applies semantic expansion, relationship-aware augmentation, and selective result merging. A post-retrieval pruning stage further removes redundant or low-relevance snippets while preserving evidence coverage for downstream answer generation. Experimental results on BioASQ evaluation batches demonstrate that the proposed recovery and cleanup strategies substantially improve retrieval robustness and MAP@10 performance on difficult question sets. The final system also incorporates output validation and post-processing steps to ensure formatting consistency and submission reliability across BioASQ phases.
Jul 15, 2026cs.CL

Cost-Pragmatic Quality Gating and Selection-Fusion Multi-Model Combiners for BioASQ Phases A+ and B

We describe our BioASQ Task 14B 2026 system. The work centers on two design decisions: how aggressively to re-retrieve when first-stage retrieval is weak, and how to combine multiple language-model answers. Retrieval unions two parallel pipelines - a hybrid first stage (dense BGE + BM25 + RRF, reaching R@200 = 99.3% on the BioASQ-13b historical archive) and an agent-driven pipeline that decomposes the question over PubMed, Europe PMC, and iCite - with a BGE cross-encoder quality gate flagging weakly-supported questions for selective re-retrieval. On Task 12B 2024 validation, a cost-pragmatic re-retrieval policy beats a skill-strict baseline significantly on list F1 and list precision, at 12% lower re-retrieval cost. Holding prompt and model fixed across val and test 13B (different question sets), list F1 rises by +0.132 absolute on the BioASQ-released gold-input pool, consistent with substantial retrieval-side headroom. For Phase B answering we decompose multi-model ensemble lift into a selection component bounded by the per-question oracle and a fusion component that aggregators can exceed. The decomposition predicts before any experiment that LLM-as-judge wins on selection-dominated metrics (yes/no, multi-reference ROUGE) but is structurally insufficient on the recall component of fusion-friendly metrics (factoid rank-1, list recall). On Task 13B 2025 our synonym-union resolver wins list recall on every head, while GPT-5.5 solo retains the list-F1 lead because the resolver's wider item set costs precision. On the Task 14B 2026 preliminary leaderboard our team places first on the combined-exact aggregate on three of the eight (phase x batch) leaderboards, wins four individual question-type cells, and takes #1 on Phase B b3 ideal.
Jul 13, 2026cs.IR

FAIR GraphRAG: A Retrieval-Augmented Generation Approach for Semantic Data Analysis

Retrieval-Augmented Generation (RAG) addresses the limitations of Large Language Models (LLMs) when providing responses to domain-specific questions. Graph-based RAG approaches, such as GraphRAG, enhance retrieval by capturing semantic relationships within knowledge graphs (KGs). While the FAIR principles (Findability, Accessibility, Interoperability, and Reusability) are becoming prevalent for scientific data management, especially in complex domains such as medicine, existing RAG approaches lack a structured FAIRification of the underlying knowledge resources. This lack limits their potential for FAIR information retrieval in these domains. To address this gap, we introduce FAIR GraphRAG, a novel framework that integrates FAIR Digital Objects (FDOs) as the fundamental units of a graph-based retrieval system. Each graph node represents an FDO that incorporates core data, metadata, persistent identifiers, and semantic links. We leverage LLMs to support schema construction and automated extraction of content and metadata from data sources. The framework was co-designed by physicians and computer scientists to ensure technical and clinical relevance. We apply FAIR GraphRAG to a biomedical dataset in gastroenterology, demonstrating its applicability to RNA-sequencing data. Beyond ensuring adherence to the FAIR principles, FAIR GraphRAG significantly improves question answering accuracy, coverage, and explainability, particularly for complex queries involving metadata and ontology links. This work shows the feasibility of combining FAIR data practices with graph-based retrieval techniques. We see potential for applying our approach to other specialized fields such as education and business.
Jul 12, 2026cs.CL

Capabilities of Claude Fable 5 on Biomedical Challenge Problems

Frontier language models are increasingly evaluated on biomedical benchmarks, but two problems undermine most published evaluations: legacy benchmarks are near-saturated, and open-ended responses are graded by other language models. We evaluate Claude Fable 5, Anthropic's most capable publicly available model, across eight biomedical benchmarks, four text and four multimodal, using deterministic scoring against fixed answer keys throughout. We include two Claude predecessors and GPT-5 as baselines. Refusal is tracked as a distinct outcome in every result table. That decision produces the paper's central finding. Fable 5 refuses between 8.0% and 99.4% of questions depending on the benchmark, a pattern absent in both predecessors and in GPT-5. Once refused items are excluded from the denominator, Fable 5's accuracy exceeds or meets every other model on every benchmark in this study. We identify two distinguishable refusal patterns: one concentrating in basic-science and mechanism content across MedQA and MedXpertQA MM, confirmed independently on two benchmarks using each benchmark's own category labels; and a separate disease-domain pattern on RareBench, where inborn metabolic disease presentations are refused near-universally while adult-onset autoimmune presentations are not. The primary constraint on Fable 5's biomedical usefulness is willingness to engage, not capability once it does.
Jul 7, 2026cs.CL

From Voting to Agent Collaboration: Answer-Type-Aware LLM Pipelines for BioASQ 14b

Biomedical question answering requires not only accurate extraction of information from scientific literature but also reliable integration of evidence across multiple documents. This study presents a question-type-specific large language model (LLM) framework for BioASQ 14b Task B, designed to improve answer robustness and evidence grounding in biomedical question answering. Rather than applying a single prompting strategy to all questions, the framework selects different inference procedures for yes/no, factoid, and list questions according to their distinct reasoning and evaluation requirements. For yes/no questions, snippet shuffling and self-reflection are used to reduce sensitivity to evidence ordering and improve decision stability. For factoid questions, full-snippet input is combined with chain-of-thought-based in-context learning to support accurate biomedical entity identification. For list questions, a multi-agent architecture is employed, in which evidence extraction, candidate generation, answer verification, and final aggregation are handled collaboratively. Preliminary experiments on BioASQ 13b were used to identify effective inference strategies for each question type, and the resulting framework was subsequently evaluated in the official BioASQ 14b Task B challenge. In the official evaluation, our framework showed competitive performance across multiple batches and achieved first place in the factoid subtask of Batch 4. These results demonstrate the effectiveness of combining question-type-specific inference, ensemble prediction, and agent-based verification for reliable biomedical question answering.
Jun 24, 2026cs.CL

Hybrid-IR: Dual-Path Hybrid Retrieval with Iterative Reasoning for Complex Medical Question Answering

Large language models (LLMs) have shown promising performance across a wide range of biomedical applications, including medical question answering (QA), yet they remain prone to hallucinations and outdated knowledge. Although retrieval-augmented generation (RAG) can alleviate this issue by incorporating external documents, there still exist two fundamental limitations. First, medical knowledge is often fragmented across documents, while most RAG methods rely on a single retrieval path, which makes it challenging to jointly preserve fine-grained semantic information and structured global associations. Second, static retrieval strategies are typically insufficient to support deep reasoning that is important in complex medical QA. In this paper, we present a dual-path retrieval framework with an iterative retrieval-reasoning mechanism termed "Hybrid-IR" for complex medical QA. The proposed Hybrid-IR integrates graph-based retrieval for exploration of structured knowledge and dense retrieval for fine-grained semantic matching. Moreover, the reasoning trajectory can be progressively refined through an iterative retrieve-reason loop. Experiments on three widely used medical QA benchmarks demonstrate the effectiveness of our Hybrid-IR.
Jun 20, 2026cs.CL

OpenBioRQ: Unsolved Biomedical Research Questions for Agents

A working citation looks like proof -- but the fact that a link resolves does not mean the cited paper supports the claim. I find that current agentic models rarely fabricate citations (over 99%99\% resolve), yet roughly 15.9%15.9\% link to the wrong paper. Existing benchmarks miss this failure mode: when a question has a fixed answer key, a model can reproduce the expected source from that key rather than independently verifying that the source supports the claim. I introduce \textbf{\openbiorq{}}, a retrieval-grounded agentic benchmark of 12,55312{,}553 unsolved biomedical research questions across 1212 domains that treats open questions as a faithfulness-and-abstention probe. To my knowledge, this is the first biomedical benchmark to combine an agentic setting -- where the model must issue multiple tool calls -- with unsolved questions that have no answer key. Openness is verified against real follow-up evidence rather than a model's parametric knowledge. Difficulty is empirical: I anchor it on questions that three open-weight reference models fail to answer, rather than on subjective hardness labels. On this hardest subset, held-out models from the same lineage as the difficulty anchors solve only ~17%, while three independent frontier agents (Gemini-3-Pro, Opus-4.7, GPT-5.5) span a wide 29-60% range. The benchmark is thus hard, non-saturating (the best agent still leaves ~33-40% unsolved), and discriminating across capability tiers. Beyond difficulty, I observe agentic collapse on the hardest questions, where agents stop using their tools. For the most collapse-prone model, blocking tool access entirely barely changes its score -- so tools stop paying off exactly where they are needed most. A frozen per-question checklist raises inter-judge agreement from Spearman 0.35 to 0.82.
Jun 19, 2026cs.AI

BioInsight: Multi-Agent Orchestration for Interactive Biomedical Knowledge Discovery

Biomedical researchers increasingly use AI-generated analyses and reports to interpret protein-level signals, but static outputs are often insufficient for research decision-making, where users need to inspect evidence, assess uncertainty, compare mechanisms, and refine hypotheses. We present \textsc{BioInsight}, a multi-agent system that moves from static biomedical report generation to interactive evidence-centered interactive interface generation. Given a disease name, a protein association table, and optional cohort metadata, BioInsight organizes disease-specific evidence through typed intermediate artifacts, including ranked pathways, literature evidence packets, protein-level reasoning notes, citation-grounded reports, dashboard schemas, and rendered interactive interfaces. The system decomposes evidence retrieval from mechanistic reasoning, normalizes citations through deterministic components, and converts the same structured evidence used in the report into an interactive interface. We evaluate BioInsight on standardized biomedical QA, challenging protein-function reasoning, and end-to-end biomedical evidence synthesis. Results show that BioInsight achieves best, and suggest that biomedical AI systems should move beyond text-only and static reports toward provenance-preserving, interactive evidence artifacts.
Jun 16, 2026cs.AI

WEQA: Wearable hEalth Question Answering with Query-Adaptive Agentic Reasoning

Language models are remarkably capable at medical question answering, in some cases surpassing the accuracy of general physicians. However, answering questions about wearable health data remains challenging and understudied, as these ubiquitous sensors produce continuous, high-dimensional, and longitudinal data, which is non-trivial to align with text-centric distributions in LLM pretraining. The diversity of sensor modalities and user intents cannot be effectively handled by a fixed reasoning workflow or a single pretrained foundation model. To address these challenges, we propose WEQA, a query-adaptive agent framework that unifies LLM reasoning with specialized wearable analytical and modeling tools. An LLM controller is employed to synthesize execution plans and dynamically route each query to the appropriate combination of sensor analysis and pretrained models, and perform grounded response auditing with external knowledge. We also curate a benchmark spanning four open wearable datasets comprising analytic and predictive tasks in three different health domains. Experiments show that our framework is 24% more accurate than LLM and agentic baselines, and a blinded study with 12 medical experts and 8 users shows substantial gains in usefulness and clinical soundness.
Jun 15, 2026cs.CL

Weaving Multi-Source Evidence for Biomedical Reasoning: The BioMedHop Benchmark and BioWeave Framework

Biomedical question answering (QA) increasingly requires reasoning over interacting entities, where supporting evidence is scattered across biomedical knowledge graphs, literature documents, and web-accessible resources. However, existing biomedical QA benchmarks mainly focus on exam-style knowledge, literature comprehension, or short-range multi-hop inference, leaving source-conditioned graph reasoning and evidence topology construction underexplored. To fill this gap, we introduce BioMedHop, a multi-source graph-grounded benchmark for evaluating biomedical reasoning over structured evidence topologies. BioMedHop contains 10,045 instances across KG, document, web, and hybrid evidence settings, covering shared-neighbor matching, intersection reasoning, path-based reasoning, and counting, with option-based, open-ended, and numeric count renderings. To support this benchmark, we further propose BioWeave, a source-aware reasoning framework that retrieves biomedical KG paths, gathers supporting clues from documents and web sources, assembles them into a unified evidence graph, and verifies answers through entity-level evidence support. Comprehensive experiments show that BioWeave achieves the best overall performance among compared methods on BioMedHop, outperforming the strong hybrid baseline ToG-2 by 10.5% in the overall average. Moreover, BioWeave consistently improves different LLM backbones and enables smaller models, such as Qwen3-4B, to achieve reasoning performance comparable to GPT-4-Turbo.
Jun 2, 2026cs.CL

When Retrieval Doesn't Help: A Large-Scale Study of Biomedical RAG

Medical question answering is a high-stakes setting where factual errors can have serious consequences. Retrieval-augmented generation (RAG) is widely viewed as a promising solution, and prior work has reported substantial gains for large medical QA models. We revisit this assumption across a broad range of open-weight instruction-tuned models spanning 7B to 72B parameters. Across five models, ten biomedical QA datasets, four retrieval methods, and four retrieval corpora, we find that retrieval yields only small and inconsistent improvements over a no-retrieval baseline, typically within 1-2 points. In contrast, the choice of backbone model has a much larger effect than the choice of retriever or corpus, and expert and layman retrieval sources perform similarly in most settings. These results suggest that the main bottleneck is not retrieval quality alone, but the model's limited ability to use retrieved evidence effectively.
May 31, 2026cs.CL

DrugClaw and DrugAudit: A Primary-Source-Grounded Agent and Authority-Aware Benchmark for Drug-Information Question Answering

Drug-information question answering is a high-stakes setting where hallucinated facts can mislead clinical decision-making and the provenance of each cited fact matters as much as the fact itself. We present DrugClaw, a multi-agent retrieval-augmented system that queries a registry of drug and pharmacovigilance skills via a reflection-driven state-machine workflow and returns answers grounded in primary regulatory or peer-reviewed records. We also contribute DrugAudit, a 3,772-item authority-aware benchmark with an evaluation panel that scores upstream-of-gold source match, token-level semantic snippet overlap, and citation faithfulness under a dual-judge LLM-as-judge protocol with inter-judge kappa = 0.88 (almost-perfect). Across DrugAudit plus drug-related subsets of MedQA (751) and PubMedQA (512), DrugClaw is top-1 on every column of the headline table: composite Evidence Index under both judges, judge-mediated answer correctness, primary-source rate (0.918, +10.1 pp over next-best), faithfulness (0.887, +5.9 pp), MedQA (0.920), and PubMedQA (0.693).
May 31, 2026cs.CL

UniD3^3: A Knowledge Graph-Enhanced RAG Framework for Drug-Disease Discovery and Reasoning

Systematic characterization of drug-disease relationships is essential for drug discovery and repurposing, yet is hindered by the heterogeneity and rapid growth of biomedical literature. Existing datasets rely on labor-intensive curation and are often incomplete, while LLM-only approaches suffer from hallucination and weak evidence grounding. We introduce UniD3^3, a unified framework that integrates Large Language Models with Knowledge Graph-enhanced Retrieval-Augmented Generation (KG-RAG) to extract, organize, and validate drug-disease knowledge across Drug-Disease Matching (DDM), Drug Effectiveness Assessment (DEA), and Drug-Target Analysis (DTA). UniD3^3 processes 157,849 PubMed articles with Llama 3.3-70B and constructs knowledge graphs via a dual-stage strategy combining paper-level extraction with KG-level consolidation centered on drug and disease entities. These graphs support KG-RAG-based generation of structured datasets, evaluated through external benchmarks, fuzzy matching with curated resources, and clinician review. UniD3^3 produces six knowledge graphs and large-scale datasets, including 28,915 DDM, 15,042 DEA, and over 4,000 DTA QA pairs. External validation shows strong performance (F1: 0.85-0.87 for DDM/DEA; 0.82 for DTA), with clinician review confirming high reliability (AUROC = 0.90). KG-RAG-augmented models outperform standalone LLMs, and the UniD3^3 chatbot enables interpretable, citation-supported exploration of drug-disease relationships. UniD3^3 provides a scalable, extensible framework for transforming unstructured biomedical literature into high-quality, structured drug-disease knowledge, supporting AI-driven discovery, repurposing, and precision medicine.
May 31, 2026cs.CL

HypothesisMed: Inference-Time Answer Fusion and Structured Hypothesis-Space Reporting for Biomedical Question Answering

Biomedical question answering with large language models is commonly evaluated using answer accuracy, but answer accuracy alone does not indicate whether a model can produce parseable outputs, follow structured reliability instructions, recognize weak answer spaces, or avoid confident incorrect commitments. This paper presents HypothesisMed, an inference-time reliability pipeline for biomedical multiple-choice question answering. It combines direct, chain-of-thought, HypothesisMed-v3 prompting, and answer fusion. The final answer is selected by fusion, while HypothesisMed-v3 supplies SPACE labels and confidence information. SPACE labels mark the answer space as VALID, INCOMPLETE, or CONTRADICTED. We evaluate Qwen2.5-7B, Phi-4-mini, DeepSeek-R1-32B, and BioMistral-7B on MedQA, MedMCQA, and PubMedQA using 1,000 examples per dataset. The pipeline improves weighted accuracy over each model's best direct or chain-of-thought baseline while increasing parse and SPACE coverage. We also scale evaluation to Qwen2.5-7B and Phi-4-mini using 10,183 examples per model. Fusion improves Phi-4-mini accuracy from 0.4296 to 0.5192, while Qwen2.5-7B chain-of-thought remains slightly higher in answer accuracy. However, Qwen2.5-7B fusion achieves complete parse and SPACE coverage with much lower false commitment. A 12,000-example SPACE stress test shows answer-space diagnosis remains difficult, with SPACE accuracy of 0.3074 for Qwen2.5-7B and 0.4168 for Phi-4-mini. These results show that answer accuracy, parseability, structured reliability reporting, calibration behavior, and false-commitment behavior are separable capabilities. The main contribution is not a universal state-of-the-art claim, but a reproducible inference-time framework for evaluating biomedical question answering models as auditable workflow components under structured reliability constraints.
May 21, 2026cs.CL

ChronoMedKG: A Temporally-Grounded Biomedical Knowledge Graph and Benchmark for Clinical Reasoning

Biomedical knowledge graphs (KGs) treat disease associations as static facts, but temporal information is crucial for clinical reasoning, e.g., a symptom diagnostic of one disease at age 3 may imply a different disease at age 13. Existing KGs such as PrimeKG, Hetionet, and iKraph do not encode when a finding becomes clinically relevant over the course of a disease. This limits their usefulness for longitudinal clinical reasoning and retrieval augmentation. We introduce ChronoMedKG, a temporal biomedical knowledge graph that contains 460,497 evidence-linked triples (filtered from 13M raw extractions) covering 13,431 diseases. Each association is tied to temporal components like onset window or progression stage, which are backed by PMID-traceable evidence and a multi-signal credibility score. The graph is constructed through a disease-autonomous multi-agent pipeline in which multiple frontier LLMs independently extract knowledge from PubMed and PMC literature. Only those relations are kept that are supported by multi-model consensus, survive credibility filtering, as well as ontology alignment. ChronoMedKG scored 92.7% agreement against Orphadata and adds temporal grounding for 6,250 diseases absent from HPOA, Orphadata, and Phenopackets, including 1,657 Orphanet-coded rare diseases. We further introduce ChronoTQA, a benchmark of 3,341 questions across eight task types (six temporal plus two static controls), with a 12-question supplementary probe. Frontier LLMs lose roughly 30 points moving from static to temporal questions; ChronoMedKG retrieval rescues 47-65% of their long-tail failures, against 17-29% for HPOA-RAG. As such, ChronoMedKG provides a crucial temporal axis for retrieval-augmented clinical systems that was previously absent.
May 17, 2026cs.CL

BELIEF: Structured Evidence Modeling and Uncertainty-Aware Fusion for Biomedical Question Answering

Biomedical question answering often requires decisions from retrieved literature whose relevance, quality, and support for candidate answers are uneven. Most retrieval-augmented large language model (LLM) methods feed this literature to the model as flat text, leaving evidence reliability and remaining uncertainty largely implicit. We propose BELIEF, a structured evidence modeling and uncertainty-aware fusion framework for closed-set biomedical question answering. Rather than treating retrieved documents as undifferentiated context, BELIEF converts them into evidence objects that record clinical attributes, source quality, question relevance, support strength, and the associated candidate hypothesis. These evidence objects provide a shared basis for two complementary reasoning paths. The symbolic path constructs reliability-weighted basic probability assignments based on Dempster--Shafer (D-S) theory over a finite answer space and performs uncertainty-aware symbolic evidence fusion to estimate belief and residual uncertainty. The neural path uses the same structured evidence for LLM-based semantic inference, while a reliability-aware arbitration module reconciles the symbolic and neural outputs according to belief strength, uncertainty, evidence reliability, and semantic consistency. Experiments on PubMedQA, MedQA, and MedMCQA with five general-purpose LLM backbones show that BELIEF obtains the best result in 25 of 30 backbone--dataset--metric settings. Comparisons with biomedical-domain models indicate that BELIEF is competitive on MedQA and MedMCQA, while specialized biomedical pretraining remains advantageous on PubMedQA. Ablation, complementarity, uncertainty-stratified, and cost analyses further show that BELIEF improves retrieved-evidence utilization by making evidence structure, path disagreement, and decision uncertainty explicit.
May 13, 2026cs.CL

When Evidence Conflicts: Uncertainty and Order Effects in Retrieval-Augmented Biomedical Question Answering

Biomedical retrieval-augmented large language models (LLMs) often face evidence that is incomplete, misleading, or internally contradictory, yet evaluation usually emphasizes answer accuracy under helpful context rather than reliability under conflict. Using HealthContradict, we evaluate six open-weight LLMs under five controlled evidence conditions: no retrieved context, correct-only context, incorrect-only context, and two mixed conditions containing both correct and contradictory documents in opposite orders. In this conflicting-evidence order contrast, where the same two documents are both present and only their order is reversed, accuracy drops for every model and 11.4%--25.2% of predictions flip. To support abstention in these difficult cases, we also evaluate a conflict-aware abstention score that combines model confidence with a detector of evidence conflict. In the two hardest conditions, this score improves selective accuracy over confidence-only, with mean gains of 7.2--33.4 points in incorrect-only (IC') and 3.6--14.4 points in incorrect-first conflicting (ICC') conditions across 75%, 50%, and 25% coverage. These results show that conflicting biomedical evidence is both an uncertainty and robustness problem and motivate evaluation and abstention methods that explicitly account for evidence disagreement.
May 12, 2026cs.CL

MedHopQA: A Disease-Centered Multi-Hop Reasoning Benchmark and Evaluation Framework for LLM-Based Biomedical Question Answering

Evaluating large language models (LLMs) in the biomedical domain requires benchmarks that can distinguish reasoning from pattern matching and remain discriminative as model capabilities improve. Existing biomedical question answering (QA) benchmarks are limited in this respect. Multiple-choice formats can allow models to succeed through answer elimination rather than inference, while widely circulated exam-style datasets are increasingly vulnerable to performance saturation and training data contamination. Multi-hop reasoning, defined as the ability to integrate information across multiple sources to derive an answer, is central to clinically meaningful tasks such as diagnostic support, literature-based discovery, and hypothesis generation, yet remains underrepresented in current biomedical QA benchmarks. MedHopQA is a disease-centered multi-hop reasoning benchmark consisting of 1,000 expert-curated question-answer pairs introduced as a shared task at BioCreative IX. Each question requires synthesis of information across two distinct Wikipedia articles, and answers are provided in an open-ended free-text format. Gold annotations are augmented with ontology-grounded synonym sets from MONDO, NCBI Gene, and NCBI Taxonomy to support both lexical and concept-level evaluation. MedHopQA was constructed through a structured process combining human annotation, triage, iterative verification, and LLM-as-a-judge validation. To reduce leaderboard gaming and contamination risk, the 1,000 scored questions are embedded within a publicly downloadable set of 10,000 questions, with answers withheld, on a CodaBench leaderboard. MedHopQA provides both a benchmark and a reusable framework for constructing future biomedical QA datasets that prioritize compositional reasoning, saturation resistance, and contamination resistance as core design constraints.
May 12, 2026cs.CL

Overview of the MedHopQA track at BioCreative IX: track description, participation and evaluation of systems for multi-hop medical question answering

Multi-hop question answering (QA) remains a significant challenge in the biomedical domain, requiring systems to integrate information across multiple sources to answer complex questions. To address this problem, the BioCreative IX MedHopQA shared task was designed to benchmark in multi-hop reasoning for large language models (LLMs). We developed a novel dataset of 1,000 challenging QA pairs spanning diseases, genes, and chemicals, with particular emphasis on rare diseases. Each question was constructed to require two-hop reasoning through the integration of information from two distinct Wikipedia pages. The challenge attracted 48 submissions from 13 teams. Systems were evaluated using both surface string comparison and conceptual accuracy (MedCPT score). The results showed a substantial performance gap between baseline LLMs and enhanced systems. The top-ranked submission achieved an 89.30% F1 score on the MedCPT metric and an 87.30% exact match (EM) score, compared with 67.40% and 60.20%, respectively, for the zero-shot baseline. A central finding of the challenge was that retrieval-augmented generation (RAG) and related retrieval-based strategies were critical for strong performance. In addition, concept-level evaluation improved answer assessment when correct responses differed in surface form. The MedHopQA dataset is publicly available to support continued progress in this important area. Challenge materials: https://www.ncbi.nlm.nih.gov/research/bionlp/medhopqa and benchmark https://www.codabench.org/competitions/7609/
May 5, 2026cs.IR

Evaluating Advanced Prompting on Gemini Flash for Multi-Hop Biomedical QA

The MedHopQA challenge presents a critical test for Large Language Models (LLMs): complex, multi-hop reasoning in the high-stakes biomedical domain. This paper details our direct API-based evaluation of Google's Gemini Flash models, focusing on the impact of advanced prompt engineering. We designed a sophisticated, multi-component prompt for Gemini 2.0 Flash that combined role-playing, explicit multi-shot Chain-of-Thought (CoT) examples, and detailed formatting rules. Our best run, using this complex prompt, achieved a Concept Level Score of 0.720. This result dramatically outperformed a baseline prompt which scored only 0.565. Remarkably, this performance on the efficient Gemini 2.0 Flash was almost identical to the result from the next-generation Gemini 2.5 Flash. Our findings demonstrate that sophisticated prompt design is a critical factor for unlocking the full reasoning capabilities of modern LLMs.
May 4, 2026cs.CL

Benchmarking Retrieval Strategies for Biomedical Retrieval-Augmented Generation: A Controlled Empirical Study

Retrieval-Augmented Generation (RAG) offers a well-established path to grounding large language model (LLM) outputs in external knowledge, yet the question of which retrieval strategy works best in a high-stakes domain such as biomedicine has not received the controlled, multi-metric treatment it deserves. This paper presents a systematic empirical comparison of five retrieval strategies -- Dense Vector Search, Hybrid BM25 + Dense retrieval, Cross-Encoder Reranking, Multi-Query Expansion, and Maximal Marginal Relevance (MMR) -- within a biomedical question-answering RAG pipeline. All strategies share a fixed generation model (GPT-4o-mini), a common vector store (ChromaDB), and OpenAI's text-embedding-3-small embeddings, ensuring that observed differences are attributable to retrieval alone. Evaluation is conducted on 250 question-answer pairs drawn from a preprocessed subset of the BioASQ benchmark (rag-mini-bioasq) using four DeepEval metrics: contextual precision, contextual recall, faithfulness, and answer relevancy, each reported with 95% confidence intervals. A no-context ablation is included as a lower bound. Cross-Encoder Reranking achieves the best composite score (0.827) and highest contextual precision (0.852), confirming that query-document interaction yields measurable retrieval gains. Multi-Query Expansion, despite its recall-oriented design, produces the weakest contextual precision (0.671), suggesting naive query diversification introduces retrieval noise. MMR sacrifices answer relevancy for diversity, while the Dense baseline (composite 0.822) falls within 0.005 points of the top strategy. All RAG conditions dramatically outperform the no-context ablation on answer relevancy (0.658-0.701 vs. 0.287), confirming the practical value of retrieval. The full pipeline, hyperparameters, and evaluation code are publicly available.
Apr 28, 2026cs.CL

BioGraphletQA: Knowledge-Anchored Generation of Complex QA Datasets

This paper presents a principled and scalable framework for systematically generating complex Question Answering (QA) data. In the core of this framework is a graphlet-anchored generation process, where small subgraphs from a Knowledge Graph (KG) are used in a structured prompt to control the complexity and ensure the factual grounding of questions generated by Large Language Models. The first instantiation of this framework is BioGraphletQA, a new biomedical KGQA dataset of 119,856 QA pairs. Each entry is grounded in a graphlet of up to five nodes from the OREGANO KG, with most of the pairs being enriched with relevant document snippets from PubMed. We start by demonstrating the framework's value and the dataset's quality through evaluation by a domain expert on 106 QA pairs, confirming the high scientific validity and complexity of the generated data. Secondly, we establish its practical utility by showing that augmenting downstream benchmarks with our data improves accuracy on PubMedQA from 49.2% to 68.5% in a low-resource setting, and on MedQA from a 41.4% baseline to 44.8% in a full-resource setting. Our framework provides a robust and generalizable solution for creating critical resources to advance complex QA tasks, including MCQA and KGQA. All resources supporting this work, including the dataset (https://zenodo.org/records/17381119) and framework code (https://github.com/ieeta-pt/BioGraphletQA), are publicly available to facilitate use, reproducibility and extension.
Apr 18, 2026cs.AI

If Only My CGM Could Speak: A Privacy-Preserving Agent for Question Answering over Continuous Glucose Data

Continuous glucose monitors (CGMs) used in diabetes care collect rich personal health data that could improve day-to-day self-management. However, current patient platforms only offer static summaries which do not support inquisitive user queries. Large language models (LLMs) could enable free-form inquiries about continuous glucose data, but deploying them over sensitive health records raises privacy and accuracy concerns. In this paper, we present CGM-Agent, a privacy-preserving framework for question answering over personal glucose data. In our design, the LLM serves purely as a reasoning engine that selects analytical functions. All computation occurs locally, and personal health data never leaves the user's device. For evaluation, we construct a benchmark of 4,180 questions combining parameterized question templates with real user queries and ground truth derived from deterministic program execution. Evaluating 6 leading LLMs, we find that top models achieve 94% value accuracy on synthetic queries and 88% on ambiguous real-world queries. Errors stem primarily from intent and temporal ambiguity rather than computational failures. Additionally, lightweight models achieve competitive performance in our agent design, suggesting opportunities for low-cost deployment. We release our code and benchmark to support future work on trustworthy health agents.
Apr 16, 2026cs.AI

DeepER-Med: Advancing Deep Evidence-Based Research in Medicine Through Agentic AI

Trustworthiness and transparency are essential for the clinical adoption of artificial intelligence (AI) in healthcare and biomedical research. Recent deep research systems aim to accelerate evidence-grounded scientific discovery by integrating AI agents with multi-hop information retrieval, reasoning, and synthesis. However, most existing systems lack explicit and inspectable criteria for evidence appraisal, creating a risk of compounding errors and making it difficult for researchers and clinicians to assess the reliability of their outputs. In parallel, current benchmarking approaches rarely evaluate performance on complex, real-world medical questions. Here, we introduce DeepER-Med, a Deep Evidence-based Research framework for Medicine with an agentic AI system. DeepER-Med frames deep medical research as an explicit and inspectable workflow of evidence-based generation, consisting of three modules: research planning, agentic collaboration, and evidence synthesis. To support realistic evaluation, we also present DeepER-MedQA, an evidence-grounded dataset comprising 100 expert-level research questions derived from authentic medical research scenarios and curated by a multidisciplinary panel of 11 biomedical experts. Expert manual evaluation demonstrates that DeepER-Med consistently outperforms widely used production-grade platforms across multiple criteria, including the generation of novel scientific insights. We further demonstrate the practical utility of DeepER-Med through eight real-world clinical cases. Human clinician assessment indicates that DeepER-Med's conclusions align with clinical recommendations in seven cases, highlighting its potential for medical research and decision support.
Jan 6, 2026cs.CL

EpiQAL: Benchmarking Large Language Models in Epidemiological Question Answering and Reasoning

Reliable epidemiological reasoning requires synthesizing study evidence to infer disease burden, transmission dynamics, and intervention effects at the population level. Existing medical question answering benchmarks primarily emphasize clinical knowledge or patient-level reasoning, yet few systematically evaluate evidence-grounded epidemiological inference. We present EpiQAL, to our knowledge the first diagnostic benchmark for epidemiological question answering over research literature, comprising three subsets built from open-access articles across diverse diseases. The three subsets progressively test factual recall, multi-step inference, and conclusion reconstruction under incomplete information, and are constructed through a quality-controlled pipeline combining taxonomy guidance, multi-model verification, and difficulty screening. Experiments on fifteen models spanning open-source and proprietary systems reveal that current LLMs show limited performance on epidemiological reasoning, with multi-step inference posing the greatest challenge. Model rankings shift across subsets, and scale alone does not predict success. Chain-of-Thought prompting benefits multi-step inference but yields mixed results elsewhere. EpiQAL provides fine-grained diagnostic signals for evidence-grounding, inferential reasoning, and conclusion reconstruction.