The article proposes a framework called quantitative evidence mining to transform biomedical findings into structured, context-rich evidence units. It outlines core elements such as claim, measured entity, value, comparator, population, conditions, temporal context, uncertainty, provenance, validation, and expert review. The authors present an eight-stage reference architecture and emphasize that plausibility should remain multidimensional rather than collapsed into a single truth label, linking extraction to evidence synthesis for applications like clinical trials, biomarker research, and knowledge-graph construction.
By Negin Sadat Babaiha, Stefan Geissler, Marie-Christine Simon, Martin Hofmann-Apitius, Marc Jacobs
arXiv:2608.03154v2 Announce Type: replace
Abstract: Biomedical relation extraction (BioRE) supports knowledge graph construction and hypothesis generation. In real-world settings, most candidate enti...
By Shufan Ming, Yikun Han, Gibong Hong, Rui Zhang, Halil Kilicoglu
OptimusKG is a multimodal biomedical labeled property graph that integrates structured and semi‑structured resources to preserve detailed, type‑specific metadata across molecular, anatomical, clinical, and environmental domains. The graph contains nearly 191,000 nodes, over 21.8 million edges, and more than 67 million property instances derived from 18 ontologies, with a top‑level schema that enforces node and edge constraints while retaining granular provenance. Validation using the PaperQA3 agent found that 70.0% of sampled edges are supported by literature evidence, and the graph offers a standardized resource for machine learning, knowledge‑grounded retrieval, and hypothesis generation in biomedical research.
By Lucas Vittor, Ayush Noori, I\~naki Arango, Joaqu\'in Polonuer, Sam Rodriques, Andrew White, David A. Clifton, Marinka Zitnik
LingShu is a large-scale, symptom‑centric knowledge graph that bridges Traditional Chinese Medicine (TCM) and modern biomedicine. It contains 17.33 million entity records and 39.47 million relation records, combining 17.19 million semantic triples with 22.29 million contextualized quadruples to encode conditional medical associations. The graph integrates data from electronic medical records, TCM texts, biomedical ontologies, and curated knowledge bases, and is supported by a web platform offering visualization, reasoning, and evidence‑grounded question answering.
By Rui Hua, Zixin Shu, Kai Chang, Dengying Yan, Jianan Xia, Hui Zhu, Shujie Song, Shurui Yang, Tongxin Wang, Yue Yin, Yu Wei, Lijuan Pei, Yunhui Hu, Hao Xu, Mingzhong Xiao, Xiaodong Li, Haibin Yu, Runshun Zhang, Wenjia Wang, Baoyan Liu, Xuezhong Zhou
arXiv:2607. 22592v1 Announce Type: new Abstract: Graph-based retrieval-augmented generation (GraphRAG) grounds answers in structured knowledge, but current systems extract entities and relationships exhaustively, producing graphs whose size and construction cost scale with corpus length rather than with the reasoning a query requires.
By Marc Saouda (Boston Consulting Group), Rajprakash Bale (Boston Consulting Group), Eren Aldis (Boston Consulting Group), Cloves Almeida (Boston Consulting Group)
The paper introduces ReSemReason, a framework for biomedical multi-hop question answering that addresses the reachable-but-invalid problem—where correct answers are retrieved but lack valid evidential support. ReSemReason aligns question-induced relation schemas with graph search and employs relation-conditioned attention and uncertainty-weighted priors to improve both answer ranking and evidence quality. Experiments on BioHopR, PrimeKGQA, and MedReason demonstrate enhanced answer-set quality and provide analyses distinguishing endpoint correctness from evidential support.
By Ziyang Ling, Ziyi Chen, Ronald X. Xu, Mingzhai Sun
arXiv:2607. 21859v2 Announce Type: replace Abstract: Constructing causal directed acyclic graphs (DAGs) is a core step in biomedical causal analysis, yet it remains a largely manual process.
By Yi-han Sheu, Michael R. Steigman, Yu Zhou, Bo Wang, Fan-Yu Yen, Jordan W. Smoller
The paper introduces Clinical Graph-JEPA, a framework for building and refining predictive patient-state knowledge graphs from clinical records. It combines multi-agent relation proposal, ontology-aware normalization, deterministic evidence scoring, and JEPA-based latent refinement to construct evidence-scored graphs from MIMIC-IV data and recover missing clinical relations. Experiments show that injecting discharge-note representations into note-grounded entities boosts leave-one-out MRR by 31% relative improvement.
By Kushagra Yadav, Nalin Prabhath, Amit Lamba, Goeun Han, Yining Mao
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
The paper introduces a configurable semantic chunking framework for biomedical information extraction in retrieval‑augmented generation systems. It replaces the fixed‑size chunking stage of BioMedRAG with entity‑preserving windows, trigger‑centered chunking, proposition‑first extraction, tiered trigger prioritization, and hierarchical relation resolution, while keeping the rest of the pipeline unchanged. Experiments on relation extraction benchmarks (GM‑CIHT, DDI, ChemProt) and adverse event classification (ADE) show that the hybrid configuration boosts performance on datasets with explicit relation cues, achieving 82.6% F1 on GM‑CIHT compared to 74.2% with the baseline.
By Riya Ahuja (Institute of Data Science in Biomedicine, TU Braunschweig, Braunschweig, Germany, Braunschweig Integrated Centre of Systems Biology, TU Braunschweig, Braunschweig, Germany), Tim Kacprowski (Institute of Data Science in Biomedicine, TU Braunschweig, Braunschweig, Germany, Braunschweig Integrated Centre of Systems Biology, TU Braunschweig, Braunschweig, Germany), Roya Shiasi Sardoabi (Institute of Data Science in Biomedicine, TU Braunschweig, Braunschweig, Germany, Braunschweig Integrated Centre of Systems Biology, TU Braunschweig, Braunschweig, Germany)
arXiv:2606. 29876v1 Announce Type: cross Abstract: Modern large language models (LLMs) reach 60-70% diagnostic accuracy on complex clinical case benchmarks, but accuracy alone cannot distinguish stable clinically-grounded reasoning from pattern matching.
By Nisarg A. Patel (University of California, San Francisco)
arXiv:2606. 08093v1 Announce Type: new Abstract: Pathology is the cornerstone of modern medicine, where accurate decision-making relies heavily on evidence-based practices.
By Zhe Xu, Zhengyu Zhang, Zhiyuan Cai, Jiahao Xu, Yijie Lin, Ziyi Liu, Junlin Hou, Hongyi Wang, Yuxiang Nie, Ling Liang, Yihui Wang, Yingxue Xu, Ronald Cheong Kin Chan, Li Liang, Hao Chen