Scientific reasoning models for biology combine language models with foundation models trained on multimodal biological data, including DNA, RNA, and proteins. These models are built through post-training, yet how each stage shapes reasoning and generalization remains poorly understood.
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. 26119v1 Announce Type: new Abstract: Large reasoning models trained via reinforcement learning (RL) have been increasingly shown to outperform their supervised fine-tuned (SFT) counterparts on mathematical reasoning tasks; Yet the mechanistic basis for this advantage remains unclear.
By Antyabha Rahman, Akshaj Gurugubelli, Omar Ankit, Kevin Zhu, Aishwarya Balwani
arXiv:2607. 16097v1 Announce Type: cross Abstract: Reinforcement learning (RL) has become central to improving large language models (LLMs) on complex reasoning tasks, yet RL post-training is largely studied in isolation from the pretraining that precedes it.
By Jingyan Shen, Ang Li, Salman Rahman, Yifan Sun, Micah Goldblum, Matus Telgarsky, Pavel Izmailov
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. 00531v1 Announce Type: cross Abstract: Scientific reasoning is an increasingly important capability of large language models, yet improving the robustness and efficiency of training such reasoning remains a key open challenge.
By Xuefeng Liu, Mingxuan Cao, Qinan Huang, Thomas Brettin, Rick Stevens, Le Cong