Unlocking Multimodal Protein Language Models at Inference Time

Abstract:Multimodal protein language models (pLMs) learn joint protein sequence-structure distributions, and their generation performance should also depend critically on inference-time sampling strategies. Yet prior work has focused more on model training than on how inference-time strategies behave. In this paper, we establish a three-stage investigation framework to empirically study the inference design space of multimodal pLMs across three representative pLMs and four fundamental tasks. We evaluate vanilla sampling, task-specific classifier-free guidance, and reward-guided beam search on multimodal pLMs, corresponding to controls over sampling distributions, per-step logits, and parallel trajectories. Throughout the complementary advancements centered on exploration-exploitation trade-off, we (1) reveal the suboptimality of default inference protocols and identify task-oriented sampling preferences; (2) observe substantial quantitative gains across tasks, consistently boosting the upper bound performance of multimodal pLMs without updating model parameters; (3) derive conclusions about base models that differ from prior consensus.

Computational Engineering, Finance, and Science (cs.CE); Artificial Intelligence (cs.AI)

arXiv:2608.25855 [cs.CE]

(or arXiv:2608.25855v1 [cs.CE] for this version)

https://doi.org/10.48550/arXiv.2608.25855 Focus to learn more arXiv-issued DOI via DataCite

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