EPIC: Event Prototyping via Information Constrained graph learning for personalized cancer driver gene prediction

Precision oncology relies on accurately distinguishing patient-specific driver mutations from the vast background of passenger alterations. While graph-based computational methods have emerged as powerful tools for this task, they often struggle to preserve the distinct genomic context of individual mutations within complex biological networks. Consequently, subtle patient-specific driver signals are frequently obscured by dominant topological patterns, critically impeding the identification of individualized oncogenic events essential for personalized cancer therapy.

To address this, we propose EPIC, a novel framework for Event Prototyping via Information Constrained Graph Learning. Unlike traditional node-centric approaches, EPIC redefines driver prediction as a metric learning task in an event embedding space. We introduce an information-constrained learning strategy that imposes explicit geometric constraints on feature variance, effectively preventing feature collapse and ensuring that low-frequency driver signals are distinctively preserved. Experiments on large-scale cancer cohorts demonstrate that EPIC significantly outperforms established baselines. Notably, the model prioritizes low-frequency driver variants typically overlooked by population-based methods, mapping them to critical oncogenic mechanisms associated with drug resistance and metastasis. Furthermore, clinical actionability analysis confirms that EPIC substantially expands the patient population eligible for targeted therapies. EPIC provides a robust and context-aware solution for personalized cancer driver discovery, bridging the gap between genomic data and actionable therapeutic insights.

The source code and datasets are available at https://github.com/spcho-dev/EPIC.