Visible neural networks for multi-omics integration: a critical review.

ABSTRACT:

Background

Biomarker discovery and drug response prediction are central to personalized medicine, driving demand for predictive models that also offer biological insights. Biologically informed neural networks (BINNs), also referred to as visible neural networks (VNNs), have recently emerged as a solution to this goal. BINNs or VNNs are neural networks whose inter-layer connections are constrained based on prior knowledge from gene ontologies and pathway databases. These sparse models enhance interpretability by embedding prior knowledge into their architecture, ideally reducing the space of learnable functions to those that are biologically meaningful.

Methods

This systematic review-the first of its kind-identified 86 recent papers implementing BINNs/VNNs. We analyzed these

SUBMITTER: Selby DA 

PROVIDER: S-EPMC12310660 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature