Feature Extraction Using a Mutually-Competitive Autoencoder for Protein Function Prediction

Lester James Miranda, Takayuki Furuzuki

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Learning new representations from data has been effective in predicting protein functions. However, common techniques tend to extract features irrelevant to the classification task. We propose an autoencoder network that selectively extracts features to produce meaningful representations. By increasing the activation of neurons kept by a winner-take-all operation, hidden units compete to form a subset that encodes relevant features, a process dubbed as mutual competition. We test this method on protein benchmarks, evaluating feature score distribution and classification performance. Results show that the autoencoder extracted features relevant to the classification task, and significantly outperformed other techniques in literature based on non-parameteric statistical tests. This demonstrates that adding competition between neurons encodes meaningful features, further improving the prediction of protein functions.

Original languageEnglish
Title of host publicationProceedings - 2018 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2018
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages1337-1342
Number of pages6
ISBN (Electronic)9781538666500
DOIs
Publication statusPublished - 2019 Jan 16
Event2018 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2018 - Miyazaki, Japan
Duration: 2018 Oct 72018 Oct 10

Publication series

NameProceedings - 2018 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2018

Conference

Conference2018 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2018
CountryJapan
CityMiyazaki
Period18/10/718/10/10

Fingerprint

Feature extraction
Proteins
Neurons
Benchmarking
Statistical tests
Chemical activation
Learning
Prediction
Protein
Neuron
Activation
Benchmark
Test methods
Winner-take-all

Keywords

  • autoencoder
  • bioinformatics
  • machine learning
  • neural networks

ASJC Scopus subject areas

  • Information Systems
  • Information Systems and Management
  • Health Informatics
  • Artificial Intelligence
  • Computer Networks and Communications
  • Human-Computer Interaction

Cite this

Miranda, L. J., & Furuzuki, T. (2019). Feature Extraction Using a Mutually-Competitive Autoencoder for Protein Function Prediction. In Proceedings - 2018 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2018 (pp. 1337-1342). [8616230] (Proceedings - 2018 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2018). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/SMC.2018.00234

Feature Extraction Using a Mutually-Competitive Autoencoder for Protein Function Prediction. / Miranda, Lester James; Furuzuki, Takayuki.

Proceedings - 2018 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2018. Institute of Electrical and Electronics Engineers Inc., 2019. p. 1337-1342 8616230 (Proceedings - 2018 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2018).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Miranda, LJ & Furuzuki, T 2019, Feature Extraction Using a Mutually-Competitive Autoencoder for Protein Function Prediction. in Proceedings - 2018 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2018., 8616230, Proceedings - 2018 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2018, Institute of Electrical and Electronics Engineers Inc., pp. 1337-1342, 2018 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2018, Miyazaki, Japan, 18/10/7. https://doi.org/10.1109/SMC.2018.00234
Miranda LJ, Furuzuki T. Feature Extraction Using a Mutually-Competitive Autoencoder for Protein Function Prediction. In Proceedings - 2018 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2018. Institute of Electrical and Electronics Engineers Inc. 2019. p. 1337-1342. 8616230. (Proceedings - 2018 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2018). https://doi.org/10.1109/SMC.2018.00234
Miranda, Lester James ; Furuzuki, Takayuki. / Feature Extraction Using a Mutually-Competitive Autoencoder for Protein Function Prediction. Proceedings - 2018 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2018. Institute of Electrical and Electronics Engineers Inc., 2019. pp. 1337-1342 (Proceedings - 2018 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2018).
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