6 Scopus citations

Abstract

Heterogeneous ensembles are an effective approach in scenarios where the ideal data type and/or individual predictor are unclear for a given problem. These ensembles have shown promise for protein function prediction (PFP), but their ability to improve PFP at a large scale is unclear. The overall goal of this study is to critically assess this ability of a variety of heterogeneous ensemble methods across a multitude of functional terms, proteins and organisms. Our results show that these methods, especially Stacking using Logistic Regression, indeed produce more accurate predictions for a variety of Gene Ontology terms differing in size and specificity. To enable the application of these methods to other related problems, we have publicly shared the HPC-enabled code underlying this work as LargeGOPred (https://github.com/GauravPandeyLab/LargeGOPred).

Original languageEnglish
Article number1577
JournalF1000Research
Volume7
DOIs
StatePublished - 2018

Keywords

  • Protein function prediction heterogeneous ensembles machine learning high-performance computing performance evaluation

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