arXiv:2605.21740v2 Announce Type: replace Abstract: LLM agents have incredible potential for scientific discovery applications. However, the performance of LLM agents on real-world, small molecule drug design (SMDD) tasks across diverse chemistries and targets is unclear. Current evaluation methods are either ad hoc, too simple for real-world discovery, limited in scale, or restricted to single-turn question answering. In effort to standardize the evaluation of LLM agents on small molecule design, we introduce SMDD-Bench, a challenging, multi-turn, long-horizon agentic benchmark consisting of 502 guaranteed-solvable task instances spanning 5 task types: 2D Pharmacophore Identification, Interaction Point Discovery, Scaffold Hopping, Lead Optimization, and Fragment Assembly. SMDD-Bench tasks span a wide region of chemical space and involve 102 unique protein targets. Completely solving the benchmark would require having strong chemical and biological reasoning and 3D intuition, understanding specialized tool use, and displaying planning expertise over a limited number of oracle calls. We benchmark 7 frontier open and closed source LLMs and find even the most performant LLM, GPT5.4, solves only 40.2\% of tasks. We hope SMDD-Bench provides a standardized testbed to invigorate the field towards training and evaluating LLM agents for fully autonomous computational drug design. We host a public leaderboard at smddbench.com .

arXiv:2602.05165v3 Announce Type: replace-cross Abstract: Reinforcement Learning with Verifiable Rewards (RLVR) has proven effective for enhancing the reasoning capabilities of Large Language Models (LLMs). However, dominant approaches like Group Relative Policy Optimization (GRPO) face critical stability challenges: they suffer from high estimator variance under computational constraints (small group sizes) and vanishing gradient signals in saturated failure regimes where all responses yield identical zero rewards. To address this, we propose Empirical Bayes Policy Optimization (EBPO), a novel framework that regularizes local group-based baselines by borrowing strength from the policy's accumulated global statistics. Instead of estimating baselines in isolation, EBPO employs a shrinkage estimator that dynamically balances local group statistics with a global prior updated via Welford's online algorithm. Theoretically, we demonstrate that EBPO guarantees strictly lower Mean Squared Error (MSE), bounded entropy decay, and non-vanishing penalty signals in failure scenarios compared to GRPO. Empirically, EBPO consistently outperforms GRPO and other established baselines across diverse benchmarks, including AIME and OlympiadBench. Notably, EBPO exhibits superior training stability, achieving high-performance gains even with small group sizes, and benefits significantly from difficulty-stratified curriculum learning.