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Open Access Highly Accessed Research article

Reverse engineering a gene network using an asynchronous parallel evolution strategy

Luke Jostins12 and Johannes Jaeger13*

Author Affiliations

1 Laboratory for Development & Evolution, University Museum of Zoology, Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK

2 Wellcome Trust Sanger Institute, Hinxton, UK

3 EMBL/CRG Systems Biology Research Unit, Centre de Regulació Genòmica (CRG), Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain

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BMC Systems Biology 2010, 4:17  doi:10.1186/1752-0509-4-17

Published: 2 March 2010

Abstract

Background

The use of reverse engineering methods to infer gene regulatory networks by fitting mathematical models to gene expression data is becoming increasingly popular and successful. However, increasing model complexity means that more powerful global optimisation techniques are required for model fitting. The parallel Lam Simulated Annealing (pLSA) algorithm has been used in such approaches, but recent research has shown that island Evolutionary Strategies can produce faster, more reliable results. However, no parallel island Evolutionary Strategy (piES) has yet been demonstrated to be effective for this task.

Results

Here, we present synchronous and asynchronous versions of the piES algorithm, and apply them to a real reverse engineering problem: inferring parameters in the gap gene network. We find that the asynchronous piES exhibits very little communication overhead, and shows significant speed-up for up to 50 nodes: the piES running on 50 nodes is nearly 10 times faster than the best serial algorithm. We compare the asynchronous piES to pLSA on the same test problem, measuring the time required to reach particular levels of residual error, and show that it shows much faster convergence than pLSA across all optimisation conditions tested.

Conclusions

Our results demonstrate that the piES is consistently faster and more reliable than the pLSA algorithm on this problem, and scales better with increasing numbers of nodes. In addition, the piES is especially well suited to further improvements and adaptations: Firstly, the algorithm's fast initial descent speed and high reliability make it a good candidate for being used as part of a global/local search hybrid algorithm. Secondly, it has the potential to be used as part of a hierarchical evolutionary algorithm, which takes advantage of modern multi-core computing architectures.