← 研踪 PaperTrailACL Anthology · ACL 2026:acl:2026.acl-short.73 · 记录 #1
Protein-STORY: Semantic Text-Oriented Representation Yields biologically meaningful Protein embeddings
来源日期（仅到月份） 2026-07
来源记录日期 2026-07
雷达观测 2026-11-01 21:44
摘要
Unsupervised representation learning using masked language modeling on the language of life has transformed protein research, enabling the analysis of a protein universe that is expanding at an exponential pace. However, most current models rely solely on sequence data, overlooking decades of expert-curated biological knowledge stored in natural language. While recent multimodal and knowledge-graph-based approaches attempt to bridge this gap, they often rely on shallow functional labels that lack the contextual depth of full textual narratives. We present Protein-STORY, a general pipeline that synthesizes protein embeddings from diverse, multi-source text descriptions. At the core of our approach is a novel network architecture designed for the semantic compression of multi document embeddings, which integrates high-fidelity functional and structural insights into a unified representation. Our experiments demonstrate that Protein-STORY produces biologically meaningful embeddings (r \approx 0.75) that outperform existing models on diverse downstream tasks (+2 pts F1 in function prediction). Furthermore, by projecting the story of a protein into a natural language semantic space, our model enables effective zero-shot text-prompted protein search.
论文发现出处
这些页面提供论文线索，不代表同行评审或质量认证。
观测到的版本
平台记录号代表本站观测到的元数据变化，不是作者修订号。来源日期仅到月份或年份时，按该月或该年首日存档。
记录 #1 · 2026-07 · 最新观测版本
Protein-STORY: Semantic Text-Oriented Representation Yields biologically meaningful Protein embeddings
Unsupervised representation learning using masked language modeling on the language of life has transformed protein research, enabling the analysis of a protein universe that is expanding at an exponential pace. However, most current models rely solely on sequence data, overlooking decades of expert-curated biological knowledge stored in natural language. While recent multimodal and knowledge-graph-based approaches attempt to bridge this gap, they often rely on shallow functional labels that lack the contextual depth of full textual narratives. We present Protein-STORY, a general pipeline that synthesizes protein embeddings from diverse, multi-source text descriptions. At the core of our approach is a novel network architecture designed for the semantic compression of multi document embeddings, which integrates high-fidelity functional and structural insights into a unified representation. Our experiments demonstrate that Protein-STORY produces biologically meaningful embeddings (r \approx 0.75) that outperform existing models on diverse downstream tasks (+2 pts F1 in function prediction). Furthermore, by projecting the story of a protein into a natural language semantic space, our model enables effective zero-shot text-prompted protein search.
查看此版本解读 →查看此版本原文 ↗