Proposal ofapplication method of inductive Logic Programming to microarray data

Hiromu Ide, Masakazu Umezawa, Hayato Ohwada

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

Abstract

This paper describing a method of specifying common terms of genes from microarray data in 3 steps. First, we use random forest for extracting disease-related genes and it give each gene variable importance. The higher the variable importance, the more effective feature for classification. We extract genes whose variable importance more than 0 and set them positive samples and the rest set negative samples for ILP. Next, we annotate extracted genes by using Gene Ontology (GO) and use the term as predicate for ILP. Annotation is the process of assigning GO terms to gene products. Finally, we obtain rules about common terms in positive samples by using ILP. ILP is a subfield of machine learning which uses logic programming as a uniform representation technique for examples, background knowledge and hypotheses. ILP learns based on background knowledge. Background knowledge is represented in first-order logic. In the result, we extracted 1051 mRNA as positive samples for ILP from random forest and its F-measure score was 65.1%. We obtained about 4000 terms at each dataset and use them as predicates for ILP. We got eventually some rules about positive samples.

Original languageEnglish
Title of host publicationProceedings of the 8th International Conference on Computational Systems-Biology and Bioinformatics, CSBio 2017
PublisherAssociation for Computing Machinery
Pages50-55
Number of pages6
ISBN (Electronic)9781450353502
DOIs
Publication statusPublished - 7 Dec 2017
Event8th International Conference on Computational Systems-Biology and Bioinformatics, CSBio 2017 - Nha Trang, Viet Nam
Duration: 7 Dec 20178 Dec 2017

Publication series

NameACM International Conference Proceeding Series

Conference

Conference8th International Conference on Computational Systems-Biology and Bioinformatics, CSBio 2017
CountryViet Nam
CityNha Trang
Period7/12/178/12/17

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Keywords

  • Annotation
  • Bioinformatics
  • ILP
  • Machine learning
  • Random forest

Cite this

Ide, H., Umezawa, M., & Ohwada, H. (2017). Proposal ofapplication method of inductive Logic Programming to microarray data. In Proceedings of the 8th International Conference on Computational Systems-Biology and Bioinformatics, CSBio 2017 (pp. 50-55). (ACM International Conference Proceeding Series). Association for Computing Machinery. https://doi.org/10.1145/3156346.3156356