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:2608. 07437v1 Announce Type: new Abstract: Reliable hypothesis testing is the foundation of many empirical scientific claims.
By Jiacheng Miao, Jin Mu, Guanhua Chen, James Zou
arXiv:2606. 01042v1 Announce Type: cross Abstract: Perturbation experiments are central to understanding cellular mechanisms, but remain costly and sparse, motivating prediction of gene expression responses for unobserved conditions.
By Xinyu Yuan, Xixian Liu, Jianan Zhao, Yashi Zhang, Hongyu Guo, Jian Tang
arXiv:2510. 17532v2 Announce Type: replace-cross Abstract: Predicting cancer treatment outcomes requires models that are both accurate and interpretable, particularly in the presence of heterogeneous clinical data.
By Raghu Vamshi Hemadri, Geetha Krishna Guruju, Kristi Topollai, Anna Ewa Choromanska
The study evaluates whether biological reasoning models actually use their biological inputs by testing six models on DNA, protein, and single‑cell tasks. By perturbing one biological input while keeping others fixed, the authors find that many models (e.g., Evo2, ESM3, BioReason, BioReason‑Pro) rely primarily on textual information, with minimal impact from the biological representations. In contrast, models like ChatNT, Prot2Text‑V2, CellWhisperer, and Cell2Sentence‑Scale show greater dependence on their biological inputs, yet overall accuracy gains do not consistently reflect increased biological input contribution.
By Ada Fang, Nikitha Thoduguli, Lukas Fesser, Hanlin Zhang, Sham M. Kakade, Marinka Zitnik
ForeSCITE is a framework that uses large language models to analyze temporal patterns in biomedical conclusions. It clusters published conclusions, estimates a direction that separates earlier from more recent findings within each cluster, and projects conclusion embeddings along these directions. The projected coordinates are decoded into natural‑language hypotheses, and retrospective evaluations show that ForeSCITE expands semantic coverage, introduces novel biomedical entity pairs, and identifies plausible CAR‑T hypotheses that experts deem biologically relevant.
By Chia-Hsuan Chang, Brian Ondov, Jiang Lv, Lan Jiang, Yunmai Wang, Haerin Song, Xueqing Peng, Qiaozhu Mei, Xiaolei Su, Hua Xu