Article (Scientific journals)
Inferring biological networks with output kernel trees
Geurts, Pierre; Touleimat, Nizar; Dutreix, Marie et al.
2007In BMC Bioinformatics, 8 (Suppl. 2), p. 4
Peer Reviewed verified by ORBi
 

Files


Full Text
geurts-bmc2007-1.pdf
Publisher postprint (478.38 kB)
Download

All documents in ORBi are protected by a user license.

Send to



Details



Keywords :
Systems biology; Bioinformatics; Machine learning
Abstract :
[en] Background: Elucidating biological networks between proteins appears nowadays as one of the most important challenges in systems biology. Computational approaches to this problem are important to complement high-throughput technologies and to help biologists in designing new experiments. In this work, we focus on the completion of a biological network from various sources of experimental data. Results: We propose a new machine learning approach for the supervised inference of biological networks, which is based on a kernelization of the output space of regression trees. It inherits several features of tree-based algorithms such as interpretability, robustness to irrelevant variables, and input scalability. We applied this method to the inference of two kinds of networks in the yeast S. cerevisiae: a protein-protein interaction network and an enzyme network. In both cases, we obtained results competitive with existing approaches. We also show that our method provides relevant insights on input data regarding their potential relationship with the existence of interactions. Furthermore, we confirm the biological validity of our predictions in the context of an analysis of gene expression data. Conclusion: Output kernel tree based methods provide an efficient tool for the inference of biological networks from experimental data. Their simplicity and interpretability should make them of great value for biologists.
Disciplines :
Microbiology
Biochemistry, biophysics & molecular biology
Biotechnology
Author, co-author :
Geurts, Pierre ;  Université de Liège - ULiège > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Systèmes et modélisation
Touleimat, Nizar;  Université d'Evry > IBISC FRE CNRS 2873
Dutreix, Marie;  Institut Curie (France)
d'Alche-Buc, Florence;  Université d'Evry > IBISC FRE CNRS 2871
Language :
English
Title :
Inferring biological networks with output kernel trees
Publication date :
03 May 2007
Journal title :
BMC Bioinformatics
eISSN :
1471-2105
Publisher :
Biomed Central Ltd, London, United Kingdom
Volume :
8
Issue :
Suppl. 2
Pages :
S4
Peer reviewed :
Peer Reviewed verified by ORBi
Available on ORBi :
since 13 August 2009

Statistics


Number of views
139 (30 by ULiège)
Number of downloads
150 (7 by ULiège)

Scopus citations®
 
28
Scopus citations®
without self-citations
22
OpenCitations
 
17

Bibliography


Similar publications



Contact ORBi