A memetic inference method for gene regulatory networks based on S-Systems

• Published in: Proceedings of the 2004 Congress on Evolutionary Computation (IEEE Cat. No.04TH8753) Vol. 1; pp. 152 - 157 Vol.1
• Main Authors: Spieth, C., Streichert, F., Speer, N., Zell, A.
• Format: Conference Proceeding
• Language: English
• Published: Piscataway NJ IEEE 2004
• Subjects: Applied sciences; Artificial intelligence; Bioinformatics; Biological system modeling; Biological systems; Computer science; control theory; systems; DNA; Exact sciences and technology; Gene expression; Mathematical model; Probes; Proteins; Semiconductor device measurement; Systems biology; Genetic algorithm; Process planning; Evolutionary algorithm; DNA chip; Observation data; Inference; Topology; Gene expression; Bioinformatics; Modeling; Optimization; Quantitative analysis
• DOI: 10.1109/CEC.2004.1330851
• ISBN: 9780780385153; 0780385152

In this paper, we address the problem of finding gene regulatory networks from experimental DNA microarray data. As underlying mathematical model we used S-Systems, a quantitative model, which recently has found increased attention in the literature. Due to the complexity of the inference problem some researchers suggested evolutionary algorithms for this purpose. We introduce enhancements to this optimization process to infer the parameters of sparsely connected non-linear systems given by the observed data more reliably and precisely. Due to the limited number of available data the inferring problem is under-determined and ambiguous. Further on, the problem often is multi-modal and therefore appropriate optimization strategies become necessary. In this paper, we propose a new method, which evolves the topology as well as the parameters of the mathematical model to find the correct network. This method is compared to standard algorithms found in the literature.