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Abstract
In the human proteome, about 5’000 proteins lack experimentally validated functional information. In this work we propose to tackle the problem of human protein function prediction by three distinct supervised learning schemes: one-versus-all classification; tournament learning; multi-label learning. Target values of supervised learning models are represented by the nodes of a subset of the Gene Ontology, which is widely used as a benchmark for functional prediction. With an independent dataset including very difficult cases the recall measure reached a reasonable performance for the first 50 ranked predictions, on average; however, average precision was quite low.
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Authors and Affiliations
CALIPHO Group, Swiss Institute of Bioinformartics, Rue Michel Servet 1, 1211, Geneva 4, Switzerland
Guido Bologna, Lydie Lane & Amos Bairoch
Swiss-Prot Group, Swiss Institute of Bioinformartics, Rue Michel Servet 1, 1211, Geneva 4, Switzerland
Anne-Lise Veuthey
Vital-IT Group, Swiss Institute of Bioinformartics, Quartier Sorge, Genopode, 1015, Switzerland
Marco Pagni
Department of Structural Biology and Bioinformatics, University of Geneva, Rue Michel Servet 1, 1211, Geneva 4, Switzerland
Lydie Lane & Amos Bairoch
- Guido Bologna
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- Anne-Lise Veuthey
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- Marco Pagni
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- Lydie Lane
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- Amos Bairoch
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Editors and Affiliations
Departamento de Electrónica, Tecnología de Computadoras y Proyectos, Universidad Politécnica de Cartagena, Pl. Hospital, 1, 30201,, Cartagena, Spain
José Manuel Ferrández
Departamento de Inteligencia Artificial, Universidad Nacional de Educación a Distancia, E.T.S. de Ingeniería Informática, Juan del Rosal, 16, 28040, Madrid, Spain
José Ramón Álvarez Sánchez
Dapartamento de Inteligencia Artificial, Universidad Nacional de Educación a Distancia, E.T.S. de Ingeniería Informática, Juan del Rosal, 16, 28040, Madrid, Spain
Félix de la Paz
Universidad Politécnica de Cartagena, Departamento de Electrónica, Tecnología de Computadoras y Proyectos, Pl. Hospital, 1, 30201, Cartagena
F. Javier Toledo
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Bologna, G., Veuthey, AL., Pagni, M., Lane, L., Bairoch, A. (2011). A Preliminary Study on the Prediction of Human Protein Functions. In: Ferrández, J.M., Álvarez Sánchez, J.R., de la Paz, F., Toledo, F.J. (eds) Foundations on Natural and Artificial Computation. IWINAC 2011. Lecture Notes in Computer Science, vol 6686. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-21344-1_35
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