Immunogenicity Prediction with Dual Attention Enables Vaccine Target Selection

Song Li, Yang Tan, Song Ke, Liang Hong, Bingxin Zhou

Keywords: protein language model, protein representation learning, immunogenicity prediction

TL;DR: We propose a protocol for deep learning-based immunogenicity prediction, covering dataset preparation, model construction, and evaluation through quantitative assessments and post-hoc analysis.

Abstract:

Immunogenicity prediction is a central topic in reverse vaccinology for finding candidate vaccines that can trigger protective immune responses. Existing approaches typically rely on highly compressed features and simple model architectures, leading to limited prediction accuracy and poor generalizability. To address these challenges, we introduce VenusVaccine, a novel deep learning solution with a dual attention mechanism that integrates pre-trained latent vector representations of protein sequences and structures. We also compile the most comprehensive immunogenicity dataset to date, encompassing over 7000 antigen sequences, structures, and immunogenicity labels from bacteria, viruses, and tumors. Extensive experiments demonstrate that VenusVaccine outperforms existing methods across a wide range of evaluation metrics. Furthermore, we establish a post-hoc validation protocol to assess the practical significance of deep learning models in tackling vaccine design challenges. Our work provides an effective tool for vaccine design and sets valuable benchmarks for future research. The implementation is at \url{https://github.com/songleee/VenusVaccine}.

Primary Area: applications to physical sciences (physics, chemistry, biology, etc.)

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Submission Number: 2576