Closed-Loop Molecular Inverse Design with Semantic LLM Surrogates

arXiv:2608.22967v3 Announce Type: replace Abstract: Practical molecular inverse design is rarely a one-shot generation problem; it often involves enriching a pool of molecules that match a desired property profile under a limited oracle budget. Bayesian optimization (BO) offers a natural framework for this setting, with standard Gaussian-process (GP) surrogates operating in continuous embedding spaces. We propose LoopMol, a closed-loop framework whose large language model (LLM) surrogate reasons directly over task instructions, SMILES-level optimization histories, and oracle feedback. At each iteration, the surrogate selects informative reference molecules under an exploration--exploitation principle, optionally with a concise guidance sentence. These outputs condition the next generation round and yield an inspectable optimization trace. Experiments on six drug and material tasks across three Llamole backbones show that the LLM-based variant improves over one-shot generation and is competitive with or stronger than GP-based BO. They also reveal a domain-dependent interface: reference-only conditioning performs better on binary drug tasks, while adding a concise guidance sentence generally benefits continuous material tasks.