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Committee-Based Active Learning to Select Negative Examples for Predicting Protein Functions

  • Marco Frasca
  • Maryam Sepehri
  • Alessandro Petrini
  • Giuliano Grossi
  • Giorgio ValentiniEmail author
Conference paper
  • 59 Downloads
Part of the Lecture Notes in Computer Science book series (LNCS, volume 11925)

Abstract

The Automated Functional Prediction (AFP) of proteins became a challenging problem in bioinformatics and biomedicine aiming at handling and interpreting the extremely large-sized proteomes of several eukaryotic organisms. A central issue in AFP is the absence in public repositories for protein functions, e.g. the Gene Ontology (GO), of well defined sets of negative examples to learn accurate classifiers for AFP. In this paper we investigate the Query by Committee paradigm of active learning to select the negatives most informative for the classifier and the protein function to be inferred. We validated our approach in predicting the Gene Ontology function for the S.cerevisiae proteins.

Keywords

Query By Committee Active learning Protein function prediction 

Notes

Acknowledgments

This work was supported by the grant title Machine learning algorithms to handle label imbalance in biomedical taxonomies, code PSR2017\(\_\)DIP\(\_\)010\(\_\)MFRAS, Università degli Studi di Milano.

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Copyright information

© Springer Nature Switzerland AG 2020

Authors and Affiliations

  • Marco Frasca
    • 1
  • Maryam Sepehri
    • 1
  • Alessandro Petrini
    • 1
  • Giuliano Grossi
    • 1
  • Giorgio Valentini
    • 1
    Email author
  1. 1.Dipartimento di InformaticaUniversità degli Studi di MilanoMilanItaly

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