Using Deep Learning with Position Specific Scoring Matrices to Identify Efflux Proteins in Membrane and Transport Proteins

Semmy Wellem Taju, Nguyen Quoc Khanh Le, Yu Yen Ou

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

2 Citations (Scopus)

Abstract

In several years, deep learning is a new area of machine learning field, which is the motivation of developing machine learning near to artificial intelligent. The neural networks belongs to deep learning are progressively important ideas in a variety of fields with great performance. Accordingly, utilization of deep learning in bioinformatics to enhance performance is very important. Convolutional neural networks is a network of deep learning which is claimed to be the best model to solve the problem of object recognition and detection utilizing GPU computing. In this study, we try to use CNN to identify efflux proteins in membrane and transport proteins, which is a famous problem in bioinformatics field. We construct the CNN from PSSM profiles with CUDA and Keras package based on Theano backend. Finally this approach achieved a significant improvement after we compare with the previous paper on efflux proteins. The proposed method can serve as an effective tool for identifying efflux proteins and can help biologists understand the functions of the efflux proteins. Moreover this study provides a basis for further research that can enrich a field of applying deep learning in bioinformatics.

Original languageEnglish
Title of host publicationProceedings - 2016 IEEE 16th International Conference on Bioinformatics and Bioengineering, BIBE 2016
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages101-108
Number of pages8
ISBN (Electronic)9781509038336
DOIs
Publication statusPublished - Dec 16 2016
Externally publishedYes
Event16th IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2016 - Taichung, Taiwan
Duration: Oct 31 2016Nov 2 2016

Publication series

NameProceedings - 2016 IEEE 16th International Conference on Bioinformatics and Bioengineering, BIBE 2016

Conference

Conference16th IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2016
CountryTaiwan
CityTaichung
Period10/31/1611/2/16

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Keywords

  • Convolutional neural network
  • Deep learning
  • Efflux
  • Position specific scoring matrices
  • Proteins

ASJC Scopus subject areas

  • Biotechnology
  • Genetics
  • Bioengineering
  • Biomedical Engineering
  • Health Informatics

Cite this

Taju, S. W., Le, N. Q. K., & Ou, Y. Y. (2016). Using Deep Learning with Position Specific Scoring Matrices to Identify Efflux Proteins in Membrane and Transport Proteins. In Proceedings - 2016 IEEE 16th International Conference on Bioinformatics and Bioengineering, BIBE 2016 (pp. 101-108). [7789966] (Proceedings - 2016 IEEE 16th International Conference on Bioinformatics and Bioengineering, BIBE 2016). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBE.2016.69