Data-driven graph reconstruction using compressive sensing

Young Hwan Chang, Claire Tomlin

Research output: Contribution to journalConference article

10 Scopus citations

Abstract

Modeling of biological signal pathways forms the basis of systems biology. Also, network models have been important representations of biological signal pathways. In many biological signal pathways, the underlying networks over which the propagations spread are unobserved so inferring network structures from observed data is an important procedure to study the biological systems. In this paper, we focus on protein regulatory networks which are sparse and where the time series measurements of protein dynamics are available. We propose a method based on compressive sensing (CS) for reconstructing a sparse network structure based on limited time-series gene expression data without any a priori information. We present a set of numerical examples to demonstrate the method. We discuss issues of coherence in the data set, and we demonstrate that incoherence in the sensing matrix can be used as a performance metric and a guideline for designing effective experiments.

Original languageEnglish (US)
Article number6426447
Pages (from-to)1035-1040
Number of pages6
JournalProceedings of the IEEE Conference on Decision and Control
DOIs
StatePublished - Dec 1 2012
Event51st IEEE Conference on Decision and Control, CDC 2012 - Maui, HI, United States
Duration: Dec 10 2012Dec 13 2012

ASJC Scopus subject areas

  • Control and Systems Engineering
  • Modeling and Simulation
  • Control and Optimization

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