5 papers
ProbeID: Verifying MCP Tool Identity for LLM Agents under Registry Drift
Guanxing Chen, Sining Zhang, Haohuai He +3
Agents select tools by copyable descriptions, which cannot establish which implementation runs. ProbeID compares canonicalized responses to schema-valid probes with a trusted admis…
CADS: Measuring the Incremental Contribution of LLM Proposers in Sequential Biological Screens
Guanxing Chen, Nihui Shao, Haohuai He +3
Large language models are increasingly used to guide sequential biological screens, yet standard evaluations rely on raw hit counts that conflate a proposer's value with the discov…
PharmAgent: Constraint-Aware Search with Frozen Language Models for Molecular Optimization
Nihui Shao, Guanxing Chen, Jilong Shi +6
Molecular optimization must improve target activity and satisfy developability constraints within limited evaluation budgets. Classical methods require tailored rules or training t…
PertMind: Eliciting Emergent Biological Reasoning in LLM via Reinforcement Learning on Cellular Perturbation Data
Zhenchao Tang, Xiaogang Xu, Tianxu Lv +16
Large language models can describe mechanisms, yet scalable post-training still depends on costly, manually curated biological reasoning traces. Here we show that cellular perturba…
Aligning LLMs with Biomedical Knowledge using Balanced Fine-Tuning
Zhenchao Tang, Fang Wang, Haohuai He +13
Engineering LLMs to accelerate life sciences research requires a robust alignment with biomedical knowledge. We observe that biomedical text exhibits a fundamentally different unce…