Abstract:In multi-modal biomedical research, integrating high-dimensional genomic data with clinical baselines is essential for precision medicine. However, standard deep neural network approaches often entangle these modalities, obscuring the specific predictive impact of genetic features and leading to possibly suboptimal predictive performance. Motivated by the landmark METABRIC cohort primary breast tumors study, we propose the Stein-Encoder, a white-box supervised framework designed to isolate the genetic signal driving clinical outcomes conditional on nuisance covariates. By leveraging Stein's method and residualization techniques, our approach constructs an interpretable single index that summarizes relevant biological heterogeneity while flexibly incorporating clinical factors and can be used to improve downstream prediction. We establish theoretical guarantees for identification, consistency and efficiency improvement. Applied to the METABRIC cohort, the Stein-Encoder outperforms unsupervised benchmarks in predictive accuracy. Crucially, it achieves structural disentanglement by revealing response-specific biological mechanisms: we find that tumor size is driven primarily by mitotic networks, whereas prognostic indices rely on a distinct proliferation-versus-immune axis. This work contributes a unified, computationally efficient framework that bridges statistical rigor with the representational power of neural networks, enabling interpretable, task-specific and efficient compression of multi-modal health data for a wide range of precision medicine applications, beyond biomarker discovery.
| Subjects: | Applications (stat.AP); Methodology (stat.ME); Machine Learning (stat.ML) |
| Cite as: | arXiv:2605.25734 [stat.AP] |
| (or arXiv:2605.25734v1 [stat.AP] for this version) | |
| https://doi.org/10.48550/arXiv.2605.25734 arXiv-issued DOI via DataCite (pending registration) |
From: Jiarui Zhang [view email]
[v1]
Mon, 25 May 2026 11:43:09 UTC (142 KB)
此内容由惯性聚合(RSS阅读器)自动聚合整理，仅供阅读参考。 原文来自 — 版权归原作者所有。