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
arXiv:2607. 10296v1 Announce Type: new Abstract: Reasoning failures in large language models (LLMs) are usually evaluated from final answers, but a wrong answer does not reveal why the model failed.
By Dongxu Zhang, Yiding Sun, Zihao Guo, Xiangyang Yang, Kai Tang, Lin Chen, Cheng Tan, Jihua Zhu
The study evaluates whether a portfolio of compact, semantically named descriptor blocks can match the performance of a 2048‑dimensional CheMeleon embedding in low‑data molecular assays. Using a fixed 11‑dimensional physicochemical base and greedily adding provenance‑screened blocks, the portfolio achieves a mean test AUC of 0.762 across nine ADME/Tox assays, comparable to CheMeleon’s 0.764 and better than Mordred’s 0.756. The results meet a predeclared pooled parity threshold but not all per‑assay thresholds, and further analysis confirms the competitiveness of the auditable representation while highlighting unresolved assay‑level differences.
By Yiqi Yao, Miquel Duran-Frigola
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). However, existing methods for curating high-quality SFT data rely heavily on strong reasoning models to filter examples based on diversity and difficulty, making the curation process costly while often yielding suboptimal data quality.
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
arXiv:2607. 09999v1 Announce Type: cross Abstract: We show that post-training quantization can silently alter how large language models reason even when task accuracy is preserved.
By Renuka Oladri, Mohan Vamsi Varadaraju Priya, Jerry Wu
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. PRM guided search avoids this by scoring candidate continuations during generation, but requires a reward model trained with step-level labels.