Multi-objective model optimization for inferring gene regulatory networks

With the invention of microarray technology, researchers are able to measure the expression levels of ten thousands of genes in parallel at various time points of a biological process. The investigation of gene regulatory networks has become one of the major topics in Systems Biology. In this paper we address the problem of finding gene regulatory networks from experimental DNA microarray data. We suggest to use a multi-objective evolutionary algorithm to identify the parameters of a non-linear system given by the observed data. Currently, only limited information on gene regulatory pathways is available in Systems Biology. Not only the actual parameters of the examined system are unknown, also the connectivity of the components is a priori not known. However, this number is crucial for the inference process. Therefore, we propose a method, which uses the connectivity as an optimization objective in addition to the data dissimilarity (relative standard error - RSE) between experimental and simulated data.