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Briefings in Bioinformatics Advance Access published online on February 27, 2006
Briefings in Bioinformatics, doi:10.1093/bib/bbk007
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© The Author 2006. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org
Received July 29, 2005
Accepted October 21, 2005

Original Article

Machine learning in bioinformatics

Pedro Larrañaga *, Borja Calvo, Roberto Santana, Concha Bielza, Josu Galdiano, Iñaki Inza, José A. Lozano, Rubén Armañanzas, Guzmán Santafé, Aritz Perez, and Victor Robles

* To whom correspondence should be addressed.
Pedro Larrañaga, E-mail: pedro.larranaga{at}ehu.es


  Abstract

This article reviews machine learning methods for bioinformatics. It presents modelling methods, such as supervised classification, clustering and probabilistic graphical models for knowledge discovery, as well as deterministic and stochastic heuristics for optimization. Applications in genomics, proteomics, systems biology, evolution and text mining are also shown.

Keywords: machine learning; bioinformatics; supervised classification; clustering; probabilistic graphical models; optimisation; heuristic; genomics; proteomics; microarray; system biology; evolution; text mining.

Pedro Larrañaga is Professor of Computer Science and Artificial Intelligence at the University of the Basque Country. He received MS degree in mathematics from the University of Valladolid in 1981, and PhD in computer science from the University of the Basque Country in 1995. He has published over 40 refereed journal papers. His main research interests are in the areas of evolutionary computation, machine learning, probabilistic graphical models and bioinformatics.

Borja Calvo received MS in Biochemistry in 1999 and Bachelor degree in Computer Science in 2004, both from the University of the Basque Country. Currently he is a PhD student at the University of the Basque Country and a member of the Intelligent Systems Group. His research interests include machine learning methods applied to bioinformatics.

Roberto Santana received PhD in Mathematics from the University of Havana in 2005. At present, he is at the University of the Basque Country as a member of the Intelligent Systems Group. His research interests include estimation of distribution algorithms and bioinformatics.

Concha Bielza received her MS degree in Mathematics in 1989 from Complutense University, Madrid, and PhD in Computer Science in 1996 from Technical University of Madrid, Madrid. She is an Associate Professor of Statistics and Operation Research in the School of Computer Science at Madrid Technical University. Her research interests are primarily in the areas of probabilistic graphical models, decision analysis, metaheuristics for optimization, data mining, classification models and real applications. Her research has appeared in journals like Management Science, Computers and Operations Research, Statistics and Computing, Naval Research Logistics, Journal of the Operational Research Society and as chapters of many books.

Josu Galdiano is currently doing his MS in Computer Science at the University of the Basque Country. His research interests include machine learning methods applied to bioinformatics.

Iñaki Inza is a Lecturer at the Intelligent Systems Group of the University of the Basque Country. His research interests include data mining and search heuristics in general, with special focus on probabilistic graphical models and bioinformatic applications.

José A. Lozano received his BS degrees in Mathematics and Computer Science and the PhD degree from the University of the Basque Country, Spain in 1991, 1992 and 1998, respectively. Since 1999, he has been an Associate Professor of Computer Science at the University of the Basque Country. He has edited three books and has published over 25 refereed journal papers. His main research interests are evolutionary computation, machine learning, probabilistic graphical models and bioinformatics.

Rubén Armañanzas received his MS in Computer Science from the University of the Basque Country in 2004. At present, he is a PhD student and member of the Intelligent Systems Group. His research interests include feature selection, computational biology and bioinformatics.

Guzmán Santafé received his MS in Computer Science from the University of the Basque Country in 2002. At present, he is a PhD student at the University of the Basque Country and member of the Intelligent Systems Group. His research interests include machine learning techniques applied to bioinformatics.

Aritz Pérez received her Computer Science degree from the University of the Basque Country. He is currently pursuing PhD in Computer Science in the Department of Computer Science and Artificial Intelligence. His research interests include machine learning, data mining and bioinformatics. Currently, he is working on supervised classification using Bayesian networks, variable selection and density estimation, focused for continuous domains.

Victor Robles received the MS degree in Computer Engineering and PhD from the Universidad Politécnica de Madrid, in 1998 and 2003, respectively. During 2004, he was a postdoctoral researcher at Harvard Medical School. He is currently an associate professor in the Department of Computer Systems Architecture and Technology at the Universidad Politécnica de Madrid. His research interests include bioinformatics, data mining and optimization. Dr Robles has been involved in the organization of several workshops and publications, as well as in several books on proceedings.


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