A unified approach to reverse engineering and data selection for unique network identification

TL;DR

This paper introduces a unified algebraic approach to determine minimal data sets for uniquely identifying both unsigned and signed network wiring diagrams in discrete systems, enhancing computational efficiency and addressing longstanding open problems.

Contribution

It develops a unified algebraic framework that encodes unsigned and signed network information, enabling efficient data selection for unique network identification.

Findings

Identifies data sets that uniquely determine network wiring diagrams.

Provides an algebraic encoding for both unsigned and signed diagrams.

Offers computational advantages over separate studies of unsigned and signed cases.

Abstract

Due to cost concerns, it is optimal to gain insight into the connectivity of biological and other networks using as few experiments as possible. Data selection for unique network connectivity identification has been an open problem since the introduction of algebraic methods for reverse engineering for almost two decades. In this manuscript we determine what data sets uniquely identify the unsigned wiring diagram corresponding to a system that is discrete in time and space. Furthermore, we answer the question of uniqueness for signed wiring diagrams for Boolean networks. Computationally, unsigned and signed wiring diagrams have been studied separately, and in this manuscript we also show that there exists an ideal capable of encoding both unsigned and signed information. This provides a unified approach to studying reverse engineering that also gives significant computational benefits.