A Deep Learning Approach Based on Stacked Denoising Autoencoders for Protein Function Prediction

Lester James Miranda, Takayuki Furuzuki

研究成果: Conference contribution

1 引用 (Scopus)

抄録

Predicting protein functions is a fundamental task with applications in medicine and healthcare. However, the accelerating pace of protein-discovery renders slow and expensive biochemical techniques unsustainable. Machine learning is suitable for such data-intensive task, but the presence of noise in protein datasets adds another level of difficulty. Hence, we propose a deep learning system based on a stacked denoising autoencoder that extracts robust features to improve predictive performance. We then feed the resulting features to a multilabel support-vector machine for classification. We evaluated on two protein benchmarks, and experimental results show that our system consistently produced the best performance against techniques that do not have a denoising or feature learning capability. This research demonstrates that learning robust representations from raw data can benefit the process of predicting protein functions.

元の言語English
ホスト出版物のタイトルProceedings - 2018 IEEE 42nd Annual Computer Software and Applications Conference, COMPSAC 2018
編集者Chung-Horng Lung, Thomas Conte, Ling Liu, Toyokazu Akiyama, Kamrul Hasan, Edmundo Tovar, Hiroki Takakura, William Claycomb, Stelvio Cimato, Ji-Jiang Yang, Zhiyong Zhang, Sheikh Iqbal Ahamed, Sorel Reisman, Claudio Demartini, Motonori Nakamura
出版者IEEE Computer Society
ページ480-485
ページ数6
1
ISBN(電子版)9781538626665
DOI
出版物ステータスPublished - 2018 6 8
イベント42nd IEEE Computer Software and Applications Conference, COMPSAC 2018 - Tokyo, Japan
継続期間: 2018 7 232018 7 27

Other

Other42nd IEEE Computer Software and Applications Conference, COMPSAC 2018
Japan
Tokyo
期間18/7/2318/7/27

Fingerprint

Proteins
Learning systems
Medicine
Support vector machines
Deep learning

Keywords

    ASJC Scopus subject areas

    • Software
    • Computer Science Applications

    これを引用

    Miranda, L. J., & Furuzuki, T. (2018). A Deep Learning Approach Based on Stacked Denoising Autoencoders for Protein Function Prediction. : C-H. Lung, T. Conte, L. Liu, T. Akiyama, K. Hasan, E. Tovar, H. Takakura, W. Claycomb, S. Cimato, J-J. Yang, Z. Zhang, S. I. Ahamed, S. Reisman, C. Demartini, ... M. Nakamura (版), Proceedings - 2018 IEEE 42nd Annual Computer Software and Applications Conference, COMPSAC 2018 (巻 1, pp. 480-485). [8377699] IEEE Computer Society. https://doi.org/10.1109/COMPSAC.2018.00074

    A Deep Learning Approach Based on Stacked Denoising Autoencoders for Protein Function Prediction. / Miranda, Lester James; Furuzuki, Takayuki.

    Proceedings - 2018 IEEE 42nd Annual Computer Software and Applications Conference, COMPSAC 2018. 版 / Chung-Horng Lung; Thomas Conte; Ling Liu; Toyokazu Akiyama; Kamrul Hasan; Edmundo Tovar; Hiroki Takakura; William Claycomb; Stelvio Cimato; Ji-Jiang Yang; Zhiyong Zhang; Sheikh Iqbal Ahamed; Sorel Reisman; Claudio Demartini; Motonori Nakamura. 巻 1 IEEE Computer Society, 2018. p. 480-485 8377699.

    研究成果: Conference contribution

    Miranda, LJ & Furuzuki, T 2018, A Deep Learning Approach Based on Stacked Denoising Autoencoders for Protein Function Prediction. : C-H Lung, T Conte, L Liu, T Akiyama, K Hasan, E Tovar, H Takakura, W Claycomb, S Cimato, J-J Yang, Z Zhang, SI Ahamed, S Reisman, C Demartini & M Nakamura (版), Proceedings - 2018 IEEE 42nd Annual Computer Software and Applications Conference, COMPSAC 2018. 巻. 1, 8377699, IEEE Computer Society, pp. 480-485, 42nd IEEE Computer Software and Applications Conference, COMPSAC 2018, Tokyo, Japan, 18/7/23. https://doi.org/10.1109/COMPSAC.2018.00074
    Miranda LJ, Furuzuki T. A Deep Learning Approach Based on Stacked Denoising Autoencoders for Protein Function Prediction. : Lung C-H, Conte T, Liu L, Akiyama T, Hasan K, Tovar E, Takakura H, Claycomb W, Cimato S, Yang J-J, Zhang Z, Ahamed SI, Reisman S, Demartini C, Nakamura M, 編集者, Proceedings - 2018 IEEE 42nd Annual Computer Software and Applications Conference, COMPSAC 2018. 巻 1. IEEE Computer Society. 2018. p. 480-485. 8377699 https://doi.org/10.1109/COMPSAC.2018.00074
    Miranda, Lester James ; Furuzuki, Takayuki. / A Deep Learning Approach Based on Stacked Denoising Autoencoders for Protein Function Prediction. Proceedings - 2018 IEEE 42nd Annual Computer Software and Applications Conference, COMPSAC 2018. 編集者 / Chung-Horng Lung ; Thomas Conte ; Ling Liu ; Toyokazu Akiyama ; Kamrul Hasan ; Edmundo Tovar ; Hiroki Takakura ; William Claycomb ; Stelvio Cimato ; Ji-Jiang Yang ; Zhiyong Zhang ; Sheikh Iqbal Ahamed ; Sorel Reisman ; Claudio Demartini ; Motonori Nakamura. 巻 1 IEEE Computer Society, 2018. pp. 480-485
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