Supervised reconstruction of biological networks with local models
1Institut de Mathématiques et de Modélisation de Montpellier, UMR CNRS 5149, Equipe de Probabilités et Statistique, Université Montpellier II, CC 051, Place Eugène Bataillon, 34095 Montpellier Cedex 5 and 2Centre for Computational Biology, Ecole des Mines de Paris, 35 rue Saint-Honore, 77305 Fontainebleau Cedex, France
*To whom correspondence should be addressed.
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Abstract |
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Motivation: Inference and reconstruction of biological networks from heterogeneous data is currently an active research subject with several important applications in systems biology. The problem has been attacked from many different points of view with varying degrees of success. In particular, predicting new edges with a reasonable false discovery rate is highly demanded for practical applications, but remains extremely challenging due to the sparsity of the networks of interest.
Results: While most previous approaches based on the partial knowledge of the network to be inferred build global models to predict new edges over the network, we introduce here a novel method which predicts whether there is an edge from a newly added vertex to each of the vertices of a known network using local models. This involves learning individually a certain subnetwork associated with each vertex of the known network, then using the discovered classification rule associated with only that vertex to predict the edge to the new vertex. Excellent experimental results are shown in the case of metabolic and protein–protein interaction network reconstruction from a variety of genomic data.
Availability: An implementation of the proposed algorithm is available upon request from the authors.
Contact: Jean-Philippe.Vert{at}ensmp.fr
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