Genetic programming-based approach to elucidate biochemical interaction networks from data

Manoj Kandpal, Chakravarthy Mynampati Kalyan, Lakshminarayanan Samavedham

Research output: Contribution to journalArticlepeer-review

7 Scopus citations

Abstract

Biochemical systems are characterised by cyclic/reversible reciprocal actions, non-linear interactions and a mixed relationship structures (linear and non-linear; static and dynamic). Deciphering the architecture of such systems using measured data to provide quantitative information regarding the nature of relationships that exist between the measured variables is a challenging proposition. Causality detection is one of the methodologies that are applied to elucidate biochemical networks from such data. Autoregressive-based modelling approach such as granger causality, partial directed coherence, directed transfer function and canonical variate analysis have been applied on different systems for deciphering such interactions, but with limited success. In this study, the authors propose a genetic programming-based causality detection (GPCD) methodology which blends evolutionary computation-based procedures along with parameter estimation methods to derive a mathematical model of the system. Application of the GPCD methodology on five data sets that contained the different challenges mentioned above indicated that GPCD performs better than the other methods in uncovering the exact structure with less false positives. On a glycolysis data set, GPCD was able to fill the 'interaction gaps' which were missed by other methods.

Original languageEnglish (US)
Pages (from-to)18-25
Number of pages8
JournalIET Systems Biology
Volume7
Issue number1
DOIs
StatePublished - Dec 1 2013

ASJC Scopus subject areas

  • Biotechnology
  • Modeling and Simulation
  • Molecular Biology
  • Genetics
  • Cell Biology

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