Automated Classification of Homeostasis Structure in Input-Output Networks

TL;DR

This paper introduces a Python algorithm that automates the detection of homeostasis mechanisms in biological input-output networks based solely on their connectivity, enabling analysis of complex systems beyond small or simple networks.

Contribution

We develop a scalable, automated method to identify homeostasis subnetworks from network topology, extending theoretical frameworks to multi-input biological systems.

Findings

Successfully applied to various biological network examples

Able to handle large and complex networks

Identifies all relevant homeostasis mechanisms

Abstract

Homeostasis is widely observed in biological systems and refers to their ability to maintain an output quantity approximately constant despite variations in external disturbances. Mathematically, homeostasis can be formulated through an input-output function mapping an external parameter to an output variable. Infinitesimal homeostasis occurs at isolated points where the derivative of this input-output function vanishes, allowing tools from singularity theory and combinatorial matrix theory to characterize homeostatic mechanisms in terms of network topology. However, the required combinatorial enumeration becomes increasingly intractable as network size grows, and the reliance on advanced graph-theoretic concepts limits accessibility and practical use in biological applications. To overcome these limitations, we develop a Python-based algorithm that automates the identification of homeostasis subnetworks and their associated homeostasis conditions directly from network topology. Given an input-output network specified solely by its connectivity structure and designated input and output nodes, the algorithm identifies the relevant graph-theoretical structures and enumerates all homeostatic mechanisms. We demonstrate its applicability across a range of biological examples, including small and large networks, networks with single or multiple input nodes or parameters, and cases where input and output coincide. This wide applicability stems from our extension of the theoretical framework from single-input-single-output networks to networks with multiple input nodes through an augmented single-input-node representation. The resulting computational framework provides a scalable and systematic approach to classifying homeostatic mechanisms in complex biological networks, facilitating the application of advanced mathematical theory to a broad range of biological systems.