A new approach for interpreting Random Forest models and its application to the biology of ageing

Bioinformatics. 2018 Jul 15;34(14):2449-2456. doi: 10.1093/bioinformatics/bty087.

Abstract

Motivation: This work uses the Random Forest (RF) classification algorithm to predict if a gene is over-expressed, under-expressed or has no change in expression with age in the brain. RFs have high predictive power, and RF models can be interpreted using a feature (variable) importance measure. However, current feature importance measures evaluate a feature as a whole (all feature values). We show that, for a popular type of biological data (Gene Ontology-based), usually only one value of a feature is particularly important for classification and the interpretation of the RF model. Hence, we propose a new algorithm for identifying the most important and most informative feature values in an RF model.

Results: The new feature importance measure identified highly relevant Gene Ontology terms for the aforementioned gene classification task, producing a feature ranking that is much more informative to biologists than an alternative, state-of-the-art feature importance measure.

Availability and implementation: The dataset and source codes used in this paper are available as 'Supplementary Material' and the description of the data can be found at: https://fabiofabris.github.io/bioinfo2018/web/.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aging / genetics*
  • Animals
  • Brain / metabolism*
  • Computational Biology / methods*
  • Gene Expression Regulation*
  • Gene Ontology
  • Humans
  • Machine Learning
  • Software*