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A novel one-class classification approach to accurately predict disease-gene association in acute myeloid leukemia cancer

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  • Akram Vasighizaker
  • Alok Sharma
  • Abdollah Dehzangi

Abstract

Disease causing gene identification is considered as an important step towards drug design and drug discovery. In disease gene identification and classification, the main aim is to identify disease genes while identifying non-disease genes are of less or no significant. Hence, this task can be defined as a one-class classification problem. Existing machine learning methods typically take into consideration known disease genes as positive training set and unknown genes as negative samples to build a binary-class classification model. Here we propose a new One-class Classification Support Vector Machines (OCSVM) method to precisely classify candidate disease genes. Our aim is to build a model that concentrate its focus on detecting known disease-causing gene to increase sensitivity and precision. We investigate the impact of our proposed model using a benchmark consisting of the gene expression dataset for Acute Myeloid Leukemia (AML) cancer. Compared with the traditional methods, our experimental result shows the superiority of our proposed method in terms of precision, recall, and F-measure to detect disease causing genes for AML. OCSVM codes and our extracted AML benchmark are publicly available at: https://github.com/imandehzangi/OCSVM.

Suggested Citation

  • Akram Vasighizaker & Alok Sharma & Abdollah Dehzangi, 2019. "A novel one-class classification approach to accurately predict disease-gene association in acute myeloid leukemia cancer," PLOS ONE, Public Library of Science, vol. 14(12), pages 1-12, December.
  • Handle: RePEc:plo:pone00:0226115
    DOI: 10.1371/journal.pone.0226115
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    References listed on IDEAS

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    1. U Martin Singh-Blom & Nagarajan Natarajan & Ambuj Tewari & John O Woods & Inderjit S Dhillon & Edward M Marcotte, 2013. "Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses," PLOS ONE, Public Library of Science, vol. 8(5), pages 1-17, May.
    2. Muhammad Asif & Hugo F M C M Martiniano & Astrid M Vicente & Francisco M Couto, 2018. "Identifying disease genes using machine learning and gene functional similarities, assessed through Gene Ontology," PLOS ONE, Public Library of Science, vol. 13(12), pages 1-15, December.
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