A Fast Reconstruction Algorithm for Gene Networks

Details A Fast Reconstruction Algorithm for Gene Networks A Fast Reconstruction Algorithm for Gene Networks

2004-01-30

arxiv.org/abs/q-bio/0401044v1

Biology

Quantitative Biology

Quantitative Methods

12 pages, 3 figures

Scientific paper

This paper deals with gene networks whose dynamics is assumed to be generated by a continuous-time, linear, time invariant, finite dimensional system (LTI) at steady state. In particular, we deal with the problem of network reconstruction in the typical practical situation in which the number of available data is largely insufficient to uniquely determine the network. In order to try to remove this ambiguity, we will exploit the biologically a priori assumption of network sparseness, and propose a new algorithm for network reconstruction having a very low computational complexity (linear in the number of genes) so to be able to deal also with very large networks (say, thousands of genes). Its performances are also tested both on artificial data (generated with linear models) and on real data obtained by Gardner et al. from the SOS pathway in Escherichia coli.

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