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:2609.00228v1 Announce Type: new
Abstract: Scientific domain entity linking (EL) differs from general domain EL because mentions and entity names often lack lexical overlap. Another challenge is...
By Md Rasel Khondokar, Qiao Qiao, Farjana Sultana Samia, Nhat Le, Yuepei Li, Qi Li
BioELX is a retrieve‑rerank framework for cross‑lingual biomedical entity linking that tackles two key problems: the English‑biased UMLS alias training data and the degradation caused by naïvely adding context. It fine‑tunes SapBERT_multi with Wikidata‑derived cross‑lingual alias supervision to create shared concept neighborhoods, and then reranks candidates using pretrained LLMs with mention‑anchored prompting to focus on the target mention. Experiments demonstrate state‑of‑the‑art performance on four benchmarks, improving Recall@1 by 4.8–18.2 percentage points without task‑specific annotations.
By Yi Wang, Corina Dima, Liangyu Zhong, Steffen Staab
arXiv:2506. 02212v2 Announce Type: replace-cross Abstract: Natural Language Processing (NLP) has transformed various fields beyond linguistics by applying techniques originally developed for human language to the analysis of biological sequences.
By Ella Rannon, David Burstein
FlyAOC is a benchmark that tests AI agents on end‑to‑end ontology curation of Drosophila scientific literature. Given a gene symbol, a brief description, a large paper corpus, and ontology resources, agents must search for evidence and produce structured annotations such as function terms, expression patterns, and historical synonyms. The benchmark contains 7,397 expert‑curated annotations across 100 genes and evaluates different agent harnesses, revealing system‑level failure modes that single‑task evaluations miss.
By Xingjian Zhang, Sophia Moylan, Ziyang Xiong, Qiaozhu Mei, Yichen Luo, Jiaqi W. Ma
The article presents a new semantic model for representing scientific evidence, specifically tailored to genetics, that extends existing standards by adding fine‑grained, domain‑specific structure. It aligns with FHIR Evidence and SEPIO, incorporates a compact vocabulary validated by SHACL, and was tested in a human‑AI annotation pilot on six genetics papers, producing 28 evidence items and 95 source‑anchored assertions. The authors argue that this model advances trustworthy, AI‑ready infrastructure for variant interpretation by providing a reference data model and validation schema for genetic evidence.
By Michael Bouzinier, Dmitry Etin
arXiv:2609.35549v2 Announce Type: replace
Abstract: Rare-disease diagnosis is a long-tail reasoning problem: phenotypes are incomplete, individual disorders are sparsely documented, and relevant evid...
By Bo Zhang, Yuchen Wang, Dongbai Li, Matthew Yu Heng Wong, Qingkai Zeng, Lijun Wang, Tien-Yin Wong, Peng Cui, Tianyu Liu
arXiv:2601. 12805v4 Announce Type: replace-cross Abstract: Large language models (LLMs) have shown growing promise in biomedical research, particularly for knowledge-driven interpretation tasks.
By Xiaohan Huang, Meng Xiao, Chuan Qin, Qingqing Long, Jinmiao Chen, Yuanchun Zhou, Hengshu Zhu
BELXTR is a new biomedical entity linking model that uses a multi‑vector (late interaction) architecture to preserve token‑level matching information, unlike traditional embedding‑based approaches that compress mentions into a single vector. By extending the XTR model with a task‑specific training objective and active query expansion, BELXTR achieves state‑of‑the‑art performance on half of ten evaluated corpora, with an average 5‑percentage‑point gain in recall@1. The model shows especially strong results on cross‑species gene disambiguation, outperforming an LLM‑powered retrieve‑and‑rerank pipeline and approaching a specialized rule‑based system.
By Samuele Garda, Ulf Leser
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
The paper introduces EGT-KG, an evidence‑grounded typed knowledge graph retrieval framework designed to enhance scientific question answering with small language models (SLMs). It compares three QA settings—standard Retrieval‑Augmented Generation (RAG) and two EGT‑KG variants (automatically generated and expert‑defined relation schemas)—using a six‑dimensional evaluation on a biopolymer‑bound soil composite literature benchmark. Results show that both EGT‑KG variants outperform vanilla RAG, with the llama3:8b model achieving a final score of 70.37 (+14.67%) and 68.82 (+12.14%) for the AS and ES variants, respectively.
By Muran Yu, Jiechao Gao, Yuandong Pan, Barney H. Miao, Andrew C. Lesh, Kincho H. Law, Jie Wang, Michael D. Lepech
R2VC is a modular fact‑checking system that separates retrieval, reasoning, verification, and confidence calibration. It uses hybrid sparse‑plus‑dense Wikipedia retrieval, a fine‑tuned generator for structured verdicts, an NLI cross‑encoder for selecting evidence‑based candidates, and a lightweight calibrator for confidence and abstention. On the FEVER benchmark, R2VC improves accuracy by 13.74% over a baseline and shows that verifier‑based candidate selection and calibration are key contributors to performance.
By Dhruv Dixit, Paritosh Pandey