The paper introduces MITE, a method that transforms biomedical named entity recognition (BioNER) into a structure‑to‑structure generation task by encoding instructions and outputs in multiple programming languages (Python, C++, Java). This approach provides structurally diverse supervision without extra biomedical knowledge, and during inference it aggregates predictions via entity‑level voting to reduce language‑specific variance. Experiments on six BioNER datasets show that MITE outperforms BERT‑based and LLM‑based baselines and generalizes well across datasets.
By Songtao Li, Yijia Zhang, Jianyuan Yuan, Shidi Zhang, Fengyu Zhang, Hongfei Lin
arXiv:2510. 17064v4 Announce Type: replace Abstract: Single-cell RNA sequencing has transformed our ability to identify diverse cell types and their transcriptomic signatures.
By Rongbin Li, Wenbo Chen, Zhao Li, Rodrigo Munoz-Castaneda, Jinbo Li, Neha S. Maurya, Arnav Solanki, Huan He, Hanwen Xing, Meaghan Ramlakhan, Zachary Wise, Nelson Johansen, Zhuhao Wu, Hua Xu, Michael Hawrylycz, W. Jim Zheng
arXiv:2608.20887v1 Announce Type: cross
Abstract: Automatic Medical Coding (AMC), which assigns standardized International Classification of Diseases (ICD) codes to clinical notes, is essential for m...
By Xubin Chen, Yipeng Zhou, Wen Sun, Chengkai Huang, Xiaoming Fu, Quan Z. Sheng
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
arXiv:2608. 14228v1 Announce Type: new Abstract: Life science knowledge graphs make large collections of structured data available through SPARQL, but each resource uses its own schema, identifiers, and links.
By Yiming Zhang, Koji Tsuda
arXiv:2603. 11872v3 Announce Type: replace-cross Abstract: Translating single-cell RNA sequencing (scRNA-seq) data into mechanistic biological hypotheses remains a critical bottleneck, as agentic AI systems lack direct access to transcriptomic representations while expression foundation models remain opaque to natural language.
By Omar Coser
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
arXiv:2607. 08803v1 Announce Type: cross Abstract: The push toward large language models for biology (BioLM) has created a need for training corpora that can endow models with a genuine understanding of biology.
By Hyunjin Seo, Hyeon Hwang, Gyubok Lee, Jay Shin, Jimin Park, Taesoo Kim, Sanghoon Lee, Hongjoon Ahn, Sungjun Han, Sangwon Jung
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
arXiv:2605. 07022v3 Announce Type: replace Abstract: Manually curated biomedical repositories -- spanning bioactivity, genomics, and chemistry -- are expensive to maintain, lag behind primary literature, and discard experimental context, obscuring nuances needed to assess data correctness and coverage.
By Haydn Jones, Yimeng Zeng, Alden Rose, Li S. Yifei, Yining Huang, Kaiwen Wu, Jiaming Liang, Maggie Ziyu Huan, Yoseph Barash, Cesar de la Fuente-Nunez, Osbert Bastani, Zachary Ives, Mark Yatskar, Jacob R. Gardner
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:2608.28974v1 Announce Type: new
Abstract: Clinically relevant oncology information is distributed across heterogeneous, longitudinal documentation, creating substantial abstraction burden and r...
By Daniel Kang, Michelle Hu, Soorya Ram Shimgekar, Shayan Vassef, Yufan Wang, Anit Kumar Sahu, Munmun De Choudhury, Vedant Das Swain, Christian Poellabauer, Li Yan Khor, Koustuv Saha, Robert Wojciechowski, Elliot Kidd, Piyum Zonooz, Navin Kumar