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
The paper introduces HypoKG, a unified biochemical knowledge graph built from KEGG, Rhea, and UniProt, and uses it to benchmark 13,200 biomedical hypotheses generated by six large language models (LLMs). By varying the biological information provided—source enzyme only, full biological path, or source and disease endpoint—the study finds that LLMs produce higher-scoring hypotheses when given minimal information, but these are less evidence‑grounded. When supplied with the full biological path, the models generate hypotheses that align more closely with known mechanistic relationships, a phenomenon the authors term evidence‑disciplined reasoning, which is confirmed by shuffling intermediate path steps.
"whyItMatters":"The study demonstrates that knowledge graphs can both uncover novel disease–enzyme pairs and guide LLMs to reason more accurately from evidence, improving the reliability of AI‑generated biomedical hypotheses."
By Dominic Okonkwo, Adetayo Okunoye, Ismailcem Budak Arpinar
arXiv:2606. 01682v1 Announce Type: cross Abstract: Selecting the best response from multiple small-model samples using a stronger scorer is a simple inference-time strategy, but fails when the small model has already committed to incorrect reasoning paths.
By Atoosa Chegini, Soheil Feizi
arXiv:2610. 02191v1 Announce Type: new Abstract: While Large Language Models (LLMs) have demonstrated striking capabilities on frontier mathematical problems, it remains unclear whether they possess the structural mathematical understanding underlying their solutions.
By Shuo Xing, Zilin Dai, Chengyuan Qian, Fangzhou Lin, Wenjing Chen, Ping He, Pan Lu, Alvaro Velasquez, Mohit Bansal, Zhengzhong Tu
arXiv:2608.31068v1 Announce Type: new
Abstract: When a large language model fails a reasoning task, it is often assumed to lack the underlying capability. However, this conflates a genuine absence of...
By Qiyao Yan, Chenpeng Wang, Liangming Pan
arXiv:2606. 26797v1 Announce Type: new Abstract: Supervised fine-tuning (SFT) on a small, high-quality set of long reasoning traces is an effective approach for eliciting strong reasoning capabilities in Large Language Models (LLMs).
By Hongyi Henry Jin, Wenhan Yang, Meysam Ghaffari, Carlos Morato, Baharan Mirzasoleiman