BioMTAN: A Biological Knowledge-Guided Multi-Task Attention Network for Co-Enhanced Cancer Diagnosis and Prognosis

With the advancement of precision medicine, gene expression data have become a crucial tool in both cancer diagnosis and prognosis for different cancer types. The incorporation of biological pathways as prior knowledge has gained increasing interest in tackling the difficulties of high dimensionality and noisy information within gene expression data. However, most existing approaches guided by biological pathways ignore the intrinsic link between diagnostic and prognostic tasks in cancer research. They fail to capitalize on the potential of leveraging shared biological information from both tasks to enhance gene pathway representations. To this end, we introduce the Biological Knowledge-guided Multi-task Attention Network (BioMTAN), a novel multi-task learning framework designed for simultaneous prediction of molecular subtypes and survival risk. Specifically, we compile tailored knowledge collections that comprise multiple pathways for the two tasks, model them as unique subgraphs and use a multi-level information fusion strategy to provide a wealth of biological insights. Moreover, we develop a Multi-task Attention Module, which extracts essential global information functioning as the key and value by interacting with biological pathways from different collections, and utilizes task-specific local information as the query, efficiently decoding task-awareness feature for each task and facilitating communication across tasks within cancer diagnosis and prognosis. Extensive validation on the public The Cancer Genome Atlas (TCGA) datasets confirms the enhanced performance of BioMTAN and highlights the significant pathways in each task, underscoring its potential as an instrumental asset in precision oncology.