Article (Scientific journals)
Classifying pairs with trees for supervised biological network inference
Schrynemackers, Marie; Wehenkel, Louis; Madan Babu, Mohan et al.
2015In Molecular Biosystems, 11 (8), p. 2116-2125
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Keywords :
Network inference; Machine learning; Decision trees
Abstract :
[en] Networks are ubiquitous in biology, and computational approaches have been largely investigated for their inference. In particular, supervised machine learning methods can be used to complete a partially known network by integrating various measurements. Two main supervised frameworks have been proposed: the local approach, which trains a separate model for each network node, and the global approach, which trains a single model over pairs of nodes. Here, we systematically investigate, theoretically and empirically, the exploitation of tree-based ensemble methods in the context of these two approaches for biological network inference. We first formalize the problem of network inference as a classification of pairs, unifying in the process homogeneous and bipartite graphs and discussing two main sampling schemes. We then present the global and the local approaches, extending the latter for the prediction of interactions between two unseen network nodes, and discuss their specializations to tree-based ensemble methods, highlighting their interpretability and drawing links with clustering techniques. Extensive computational experiments are carried out with these methods on various biological networks that clearly highlight that these methods are competitive with existing methods.
Disciplines :
Engineering, computing & technology: Multidisciplinary, general & others
Author, co-author :
Schrynemackers, Marie ;  Université de Liège - ULiège > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Dép. d'électric., électron. et informat. (Inst.Montefiore)
Wehenkel, Louis  ;  Université de Liège - ULiège > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Systèmes et modélisation
Madan Babu, Mohan
Geurts, Pierre  ;  Université de Liège - ULiège > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Algorith. des syst. en interaction avec le monde physique
Language :
English
Title :
Classifying pairs with trees for supervised biological network inference
Publication date :
11 May 2015
Journal title :
Molecular Biosystems
ISSN :
1742-206X
eISSN :
1742-2051
Publisher :
Royal Society of Chemistry, United Kingdom
Volume :
11
Issue :
8
Pages :
2116-2125
Peer reviewed :
Peer Reviewed verified by ORBi
Available on ORBi :
since 29 September 2014

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