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:2609.00073v1 Announce Type: new
Abstract: Malaria remains a significant global health burden, necessitating continuous research efforts to understand its complex molecular mechanisms, epidemiol...
By V. S. Anoop, Devika N
arXiv:2608. 19201v1 Announce Type: cross Abstract: Bioinformatics software and databases are essential components of modern life science research, yet their mentions in the scientific literature are often inconsistent and difficult to systematically identify at scale.
By Hao Xuan, Rithvij Pasupuleti, Ben Liu, Haishuo Sun, Jun Zhang, Zijun Yao, Cuncong Zhong
arXiv:2604. 25374v2 Announce Type: replace-cross Abstract: Background: Dutch medical corpora are scarce, limiting NLP development.
By B. van Es
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
arXiv:2608. 04144v1 Announce Type: cross Abstract: Biomedical entity linking grounds mentions in clinical and scientific text to entities in a curated knowledge base (KB) with ontological structure, which supports downstream applications such as literature-scale information extraction and patient-record normalization.
By Yicheng Tao, Jie Liu
The paper introduces a unified framework for aligning biomedical text with knowledge graphs using a lightweight projection learned via contrastive learning, keeping the text encoder and KG embedding model frozen. It evaluates six design choices—text encoder, KG embedding, projection head, triple composition, training direction, and hard‑negative sampling—on a newly created CTD‑Align corpus of 22K chemical‑gene interaction pairs linked to PubMed passages. The study finds that triple composition and training direction have the largest impact, while simpler linear projections over concatenated subject, predicate, and object embeddings yield the best performance.
By Artem Bisliouk, Elizaveta Nosova, Heiko Paulheim, Andreea Iana, Rita T. Sousa
arXiv:2607. 05644v1 Announce Type: cross Abstract: Natural language processing (NLP) is a common method for supplying data to clinical research and decision making by extracting information from electronic medical records.
By Olga V. Patterson, Brett South, T. Elizabeth Workman, Scott L DuVall
arXiv:2606. 15155v1 Announce Type: new Abstract: Knowledge graphs (KGs) have emerged as a promising solution for integrating and reasoning over complex biomedical and clinical data in healthcare.
By Haniye Sherafatmandjoo, Mohammad Akbari, Zahed Rahmati
arXiv:2607. 11464v1 Announce Type: cross Abstract: Retrieval-Augmented Generation (RAG) addresses the limitations of Large Language Models (LLMs) when providing responses to domain-specific questions.
By Marlena Fl\"uh, Soo-Yon Kim, Carolin Victoria Schneider, Sandra Geisler
arXiv:2608.28329v1 Announce Type: cross
Abstract: Medical question answering (QA) systems have become crucial tools for providing reliable health information. But they remain very unexplored for low-...
By Rowzatul Zannat, Abdullah Al Shafi, K. M. Azharul Hasan, Atia Shahnaz Ipa
arXiv:2606. 19852v1 Announce Type: cross Abstract: Information extraction from pathology reports is essential for cancer staging, tumor registry population.
By Aman Pathak, Cheng Peng, Mengxian Lyu, Ziyi Chen, Reema Solan, Sankalp Talankar, Yasir Khan, Hiren Mehta, Aokun Chen, Yi Guo, Yonghui Wu