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A Preliminary Study on the Prediction of Human Protein Functions

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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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Author information

Authors and Affiliations

  1. CALIPHO Group, Swiss Institute of Bioinformartics, Rue Michel Servet 1, 1211, Geneva 4, Switzerland

    Guido Bologna, Lydie Lane & Amos Bairoch

  2. Swiss-Prot Group, Swiss Institute of Bioinformartics, Rue Michel Servet 1, 1211, Geneva 4, Switzerland

    Anne-Lise Veuthey

  3. Vital-IT Group, Swiss Institute of Bioinformartics, Quartier Sorge, Genopode, 1015, Switzerland

    Marco Pagni

  4. Department of Structural Biology and Bioinformatics, University of Geneva, Rue Michel Servet 1, 1211, Geneva 4, Switzerland

    Lydie Lane & Amos Bairoch

Authors
  1. Guido Bologna

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  2. Anne-Lise Veuthey

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  3. Marco Pagni

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  4. Lydie Lane

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  5. Amos Bairoch

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Editor information

Editors and Affiliations

  1. Departamento de Electrónica, Tecnología de Computadoras y Proyectos, Universidad Politécnica de Cartagena, Pl. Hospital, 1, 30201,, Cartagena, Spain

    José Manuel Ferrández

  2. 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

  3. 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

  4. Universidad Politécnica de Cartagena, Departamento de Electrónica, Tecnología de Computadoras y Proyectos, Pl. Hospital, 1, 30201, Cartagena

    F. Javier Toledo

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© 2011 Springer-Verlag Berlin Heidelberg

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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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