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Author

Alex Aliper

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Preprint Jul 2026

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints

A clear pattern is revealed in LLM spatial capabilities: while they still lag behind state-of-the-art approaches, they are promising and can handle multiple spatial constraints simultaneously, enabling scaling to heterogeneous setups.

Thomas MacDougall, Maksim Kuznetsov, Roman Schutski et al. · 0 citations
#artificial intelligence Preprint Aug 2026

Training Chemical Plausibility-Aware Large Language Models for Single-Step Retrosynthesis

Single-step retrosynthesis is a central component of computer-aided synthesis planning, yet its intrinsically one-to-many nature is poorly captured by single-answer evaluation and benchmarking protocols. To address this, we introduce Top-K prompting as a robust training and inference paradigm to better capture diverse, plausible reaction predictions. We compile CREED-CCV-2+USPTO-XL, an ultra-large-scale dataset of ~45.6 million verified reactions to train the C3LM (Chemistry Constraint-Consistent Language Model). By integrating fine-tuning with ChemCensor-based and novelty-oriented rewards, our model achieves state-of-the-art performance on the OOD URSA-expert-2026 benchmark. Further analysis of reaction uniqueness shows that LLMs and conventional models explore complementary reaction spaces, motivating ensemble-based retrosynthesis systems. Overall, our results establish Top-K, plausibility-aware training as a practical new direction for robust future LLM-based synthesis planning.

B. Zagribelnyy, Ivan D. Ilin, N. Bondarev et al. · 0 citations