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Unlocking Multimodal Protein Language Models at Inference Time

Research Bioinformatics AI

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TL;DR - This paper systematically studies inference-time sampling for multimodal protein language models across three models and four tasks. It finds that task-tailored inference strategies can substantially improve generation quality without updating model parameters.

  • Compares vanilla sampling, task-specific classifier-free guidance, and reward-guided beam search.
  • Examines three levels of inference control: sampling distributions, per-step logits, and parallel generation trajectories.
  • Shows that default inference protocols are often suboptimal and that preferred exploration-exploitation trade-offs vary by task.
  • Reports consistent quantitative gains that raise model performance ceilings and challenge prior conclusions about the underlying models.

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Unlocking Multimodal Protein Language Models at Inference Time

arXiv cs.CE Yi Zhou, Qipeng Wang, Yunqing Liu, Jun Xia, Qing Li, Wenqi Fan 2026-08-26 arXiv:2608.25855
Public signals Semantic Scholar citations 0 · Semantic Scholar influential citations 0
Providers: Hugging Face · N/A OpenAlex · N/A Publisher · N/A Semantic Scholar · Citations 0 · Influential citations 0 X · N/A Fetched 2026-09-24 14:33:04.394285 UTC

TL;DR - This paper systematically studies inference-time sampling for multimodal protein language models across three models and four tasks. It finds that task-tailored inference strategies can substantially improve generation quality without updating model parameters.

  • Compares vanilla sampling, task-specific classifier-free guidance, and reward-guided beam search.
  • Examines three levels of inference control: sampling distributions, per-step logits, and parallel generation trajectories.
  • Shows that default inference protocols are often suboptimal and that preferred exploration-exploitation trade-offs vary by task.
  • Reports consistent quantitative gains that raise model performance ceilings and challenge prior conclusions about the underlying models.
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