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Graph Neural Networks for Modeling Biological Regulatory Networks with Stochasticity

Jincheng Zhang
Aug 2026 · Zenodo (CERN European Organization for Nuclear Research)
Gene Regulatory Network Analysis

Abstract

Biological regulatory networks (BRNs) govern cellular processes with inherent stochasticity, reflecting the probabilistic nature of gene expression and protein interactions. Traditional Graph Neural Networks (GNNs) often treat these networks as deterministic, leading to inaccurate representations and predictions. This work proposes a novel framework for modeling BRNs that explicitly incorporates stochasticity. We introduce probabilistic layers within a GNN architecture to represent the uncertainty in network dynamics, drawing inspiration from stochastic differential equations (SDEs). These layers allow the GNN to learn and propagate probabilistic information, capturing the random fluctuations observed in biological systems. Our approach provides a more realistic and robust model of BRNs, offering potential improvements in predicting network behavior and identifying key regulatory nodes. The core claim is to develop GNN architectures that can explicitly model the stochastic nature of biological regulatory networks, accounting for the inherent randomness in gene expression and protein interactions. The core mechanism involves introducing probabilistic layers within the GNN to represent the uncertainty in the network's dynamics, incorporating elements of stochastic differential equations. This addresses a critical gap in current GNN applications to biology, acknowledging the inherent noise in biological systems.

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