EvidenceNet is a disease‑specific dataset that transforms full‑text biomedical literature into structured evidence records and graph representations, preserving study design, provenance, and quantitative support. Using an LLM‑assisted pipeline, it extracts experimentally grounded findings, normalizes entities, scores evidence quality, and links related records via typed semantic relations. The released subsets—EvidenceNet‑HCC and EvidenceNet‑CRC—contain thousands of evidence records and richly connected graphs, with high extraction and relation‑type accuracy, enabling retrieval‑augmented question answering and graph‑based tasks such as link prediction and target prioritization.
By Chang Zong, Jinyu Chen, Sicheng Lv, Si-tu Xue, Huilin Zheng, Jian Wan, Lei Zhang
arXiv:2606. 15412v1 Announce Type: cross Abstract: Biomedical relation extraction (BioRE) is a key step in transforming biomedical literature into structured knowledge.
By Jakob Mraz, Toma\v{z} Curk, Bla\v{z} Zupan
CONSISTRE is a consistency‑aware framework for document‑level relation extraction that tackles contradictions in large language model predictions. It offers two tracks: an inference‑time track that refines black‑box LLM outputs through constraint‑aware prompting, verification, and self‑reflection, and a training‑time track that distills consistency knowledge into smaller open‑source models via supervised fine‑tuning and reinforcement learning. Experiments on DocRED show both tracks outperform baselines, with the inference‑time track matching competitive F1 scores and the training‑time track narrowing the performance gap to proprietary LLMs while reducing inference cost.
By Mingxuan Sun
Document-level relation extraction (DocRE) aims to extract relations among multiple entities across extended contexts while maintaining consistency across predicted triples. Although large language models (LLMs) show remarkable reasoning capabilities in information extraction, their predictions are typically generated independently for each candidate triple and may violate fundamental relational constraints such as transitivity, symmetry, and functional uniqueness, leading to contradictory and unreliable outputs.
The paper presents an automated framework for building ontology networks by discovering typed semantic links between concepts across domains. It uses domain‑adapted DistilBERT embeddings, clustering to prune candidates, and GPT‑4o for generating interpretable relationships, reducing 800k raw pairs to 95k high‑quality candidates. Human validation on 429 links shows an 80.19% precision and 0.890 F1, outperforming five similarity‑based baselines and demonstrating the need for LLM reasoning in ontology link construction.
By Nouha Hayouni, Sheeba Samuel, Alsayed Algergawy
arXiv:2511.21075v4 Announce Type: replace-cross
Abstract: Engineering LLMs to accelerate life sciences research requires a robust alignment with biomedical knowledge. We observe that biomedical text...
By Zhenchao Tang, Fang Wang, Haohuai He, Jiale Zhou, Tianxu Lv, Jun Zhu, Shouzhi Chen, Minghao Yang, Yu Wang, Jiayang Wu, Yidong Song, Yaokun Li, Jiehui Huang, Jun Zhou, Bing He, Jianhua Yao
The paper introduces BioCheck Agent, an LLM-based system that generates structured biomedical fact‑checking reports using agentic search and a reinforcement‑learning framework called EG‑GRPO. Unlike prior methods that output only supported or refuted labels, BioCheck Agent synthesizes conclusions with retrieved evidence from PubMed, employing advanced Boolean search operators. Experiments show that, compared to the base Qwen3.5‑4B model, BioCheck Agent improves label prediction accuracy on SciFact by 9.95 %, raises evidence quality by 3.7 %, and reduces hallucinations by 19.63 %.
By Jiongxiao Wang, Dingli Ma, Chaoqun Ni
The paper introduces OmicsBench, a new reasoning benchmark for multi‑omics sequences that includes 1,160 expert‑validated questions across DNA regulation, RNA processing, and protein function tasks, requiring traceable evidence chains. Evaluation of 17 large language models shows that scientific LLMs, while more accurate in classification, often lack valid evidence, suggesting shortcut learning. To address this, the authors propose tool‑augmented on‑policy distillation (TA‑OPD), a post‑training method that improves both evidence grounding and predictive performance across five Qwen3.5 models of varying sizes.
By Jie Ying, Zhefan Wang, Zihong Chen, Zhengqing Li, Jinzhe Li, Gang Li, Jian Liu, Fang Hu, Tao Luo, Zhonghang Yuan, Wanli Ouyang, Stan Z. Li, Fan Yang, Nanqing Dong
MedRAGChecker is a claim-level verification framework designed for biomedical retrieval‑augmented generation (RAG). It decomposes generated answers into atomic claims and assesses each claim’s support by combining evidence‑grounded natural language inference with biomedical knowledge‑graph consistency signals. The aggregated claim decisions provide diagnostics that distinguish retrieval and generation failures, such as faithfulness, under‑evidence, contradiction, and safety‑critical errors, and the system is distilled into compact models for scalable evaluation.
By Yuelyu Ji, Min Gu Kwak, Hang Zhang, Xizhi Wu, Chenyu Li, Yanshan Wang
arXiv:2603.08166v2 Announce Type: replace
Abstract: Automated Drug Combination Extraction (DCE) from large-scale biomedical literature is crucial for advancing precision medicine and pharmacological...
By Zhijun Wang, Ling Luo, Dinghao Pan, Huan Zhuang, Lejing Yu, Yuanyuan Sun, Hongfei Lin
arXiv:2607. 20163v1 Announce Type: cross Abstract: The rapid growth of biomedical knowledge has made the validation of automatically generated biological annotations a major bottleneck in biomedical curation.
By Emanuele Cavalleri, Miad Alavinezhad, Dario Malchiodi, Marco Mesiti
arXiv:2609.08174v1 Announce Type: new
Abstract: We introduce OntologyBench, a tiered biomedical retrieval benchmark comprising 471,854 training and 125,744 evaluation query-document relevance pairs a...
By Xiao Yu Cindy Zhang, Wyeth Wasserman, Jian Zhu