@inproceedings{ibtehaz-kihara-2026-protein,
    title = "Protein-{STORY}: Semantic Text-Oriented Representation Yields biologically meaningful Protein embeddings",
    author = "Ibtehaz, Nabil  and
      Kihara, Daisuke",
    editor = "Liakata, Maria  and
      Moreira, Viviane P.  and
      Zhang, Jiajun  and
      Jurgens, David",
    booktitle = "Proceedings of the 64th Annual Meeting of the {A}ssociation for {C}omputational {L}inguistics (Volume 2: Short Papers)",
    month = jul,
    year = "2026",
    address = "San Diego, California, United States",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/ingest-acl/2026.acl-short.73/",
    pages = "883--897",
    ISBN = "979-8-89176-391-3",
    abstract = "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."
}