The gene expression matrix: towards the extraction of genetic network architectures
Proceedings of the second world congress on Nonlinear analysts: part 3
IPCAT '97 Proceedings of the second international workshop on Information processing in cell and tissues
Swarm intelligence: from natural to artificial systems
Swarm intelligence: from natural to artificial systems
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
EA'09 Proceedings of the 9th international conference on Artificial evolution
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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In this paper, we address the problem of reverse-engineering a gene regulatory network from gene expression time series. We approach the problem by implementing an ant system to generate candidate network structures. The quality of a candidate structure is evaluated using a particle swarm optimization algorithm that tunes the parameters of the corresponding model, by minimizing the error between the actual time series and the trained model's output. We extend this approach by incorporating domain-specific heuristics to the ant system, as a mechanism that has the potential to bias the pheromone amplification effect towards biologically plausible relationships. We apply the method to a subset of genes from a real world data set and report on the results.