Decoding cell signaling via optimal transport and information theory

Abstract

Cellular signal processing performs reliably despite molecular noise. Mutual information (MI) is widely used to quantify signaling fidelity, capturing how well outputs discriminate input states. However, it fails to capture whether the output preserves the statistical structure of the input, a property crucial in morphogen patterning and dose-dependent signaling. To address this gap, we introduce the 2-Wasserstein (2-WD) distance, which provides a geometric basis for comparing input and output distributions. We define MI as informational fidelity (INF) and the inverse of the 2-WD as geometric fidelity (GMF). Applying this dual-fidelity framework to canonical regulatory motifs under Gaussian channel approximation reveals topology-dependent trade-offs: coherent feed-forward loops can perform well in both dimensions, whereas feedback architectures reduce INF to enhance GMF. Experimental analysis of tumor necrosis factor signaling reveals dual-fidelity behavior qualitatively consistent with feedback regulation. RAS-MAPK data analysis further shows that jointly considering INF and GMF better characterizes intracellular signal relay than INF alone. Our results thus indicate that these signaling behaviors are not fully characterized by MI alone; instead, distributional correspondence provides a complementary dimension of signaling fidelity. Our study provides a practical framework for analyzing natural networks and guiding the design of task-specific synthetic circuits.