Oracle-Budgeted Molecular Optimization with Short-Term Graph Memory

Molecular optimization in drug discovery, materials design, and catalysis requires searching vast chemical spaces under tight evaluation budgets, since high-fidelity oracles and experimental measurements are costly. The practical impact of an optimization method therefore hinges on its sample efficiency: how few evaluations it needs to find strong candidates. We introduce Sample Efficient Generative Optimization (SEGO), a framework for Bayesian optimization on adaptively generated molecules. In SEGO, a probabilistic surrogate model forms a hypothesis about where hits lie in chemical space, a generative model is steered to propose candidates in that region, the most promising candidate is selected via an acquisition function, and the resulting oracle call is used both to sharpen the surrogate and to anchor the generator in real reward. SEGO attains state-of-the-art performance on the practical molecular optimization (PMO) benchmark using only one tenth of the oracle calls consumed by other methods, and on a multiparameter docking task it reaches ten hits in roughly half the oracle calls of existing approaches. These gains move molecular optimization closer to campaigns driven by direct experimental feedback.

Oracle-limited molecular optimization gives reward only after a complete molecule is generated, while each rollout requires many local next-token decisions. This delayed-feedback interface makes molecular policy optimization myopic: an optimizer can learn that a molecule was good without knowing which intermediate actions made it good. We introduce Q-Steer, a rollout-time action-value steering primitive for molecular language models. Q-Steer uses an offline-trained and frozen prefix-action value scorer, PAVS-Q, that estimates the downstream reward of taking a candidate next token under a partial SMILES prefix, then adds a normalized value bonus to sampling logits. The optimizer update rule and online oracle budget are unchanged; the claim is fixed-online-oracle performance, not equal total compute. On PMO23 with a fixed 10,000-call online budget, complete factorial studies across two molecular language-model backbones and four optimizers show that Q-Steer improves mean valid-unique score in all eight backbone-optimizer cells, with positive macro mean-score gains between +0.033 and +0.049 and 18-20 task wins per cell. Mechanism controls show that action identity matters: prefix-broadcast values are nearly neutral, while shuffled action values harm performance. These results support Q-Steer as a reusable rollout-time action-value wrapper that improves average molecular optimization reward across optimizer families and policy backbones without changing the online oracle budget.

Identifying high-utility candidates from massive discrete spaces under expensive evaluations is a recurring challenge across the sciences, with structure-based drug discovery as a prominent example. While surrogate-based optimization can increase sample efficiency by reducing the number of expensive evaluations, modern molecular libraries have reached billions to trillions of compounds, making full-library surrogate inference itself a major computational bottleneck. We introduce BOBa, a bandit-guided surrogate optimization framework that eliminates full-library inference by adaptively allocating computation across partitions of the action space. By treating partitions as arms in a multi-armed bandit, BOBa concentrates inference and evaluations on empirically promising partitions while maintaining principled exploration. Experiments on real-world synthesis-on-demand libraries demonstrate that optimism-under-uncertainty bandits, combined with meaningful action space partitioning, are essential for effective allocation of inference and evaluations. Our findings reveal a tunable tradeoff between screening performance and surrogate inference cost, which supports practical optimization over current libraries, and establishes a viable route to ultra-large library virtual screening.