Unlocking Multimodal Protein Language Models at Inference Time

2026-08-26

AI Summary

本文研究了多模态蛋白质语言模型在推理时的采样策略问题，通过三种方法优化了模型性能，无需更新模型参数。

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.

Problem

• multimodal protein language models
• inference-time sampling strategies
• generation performance

Innovation

• multimodal protein language models
• inference-time sampling strategies
• classifier-free guidance
• reward-guided beam search