Inverse Potts model improves accuracy of phylogenetic profiling

Tsukasa Fukunaga*, Wataru Iwasaki

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

Motivation: Phylogenetic profiling is a powerful computational method for revealing the functions of function-unknown genes. Although conventional similarity metrics in phylogenetic profiling achieved high prediction accuracy, they have two estimation biases: an evolutionary bias and a spurious correlation bias. While previous studies reduced the evolutionary bias by considering a phylogenetic tree, few studies have analyzed the spurious correlation bias. Results: To reduce the spurious correlation bias, we developed metrics based on the inverse Potts model (IPM) for phylogenetic profiling. We also developed a metric based on both the IPM and a phylogenetic tree. In an empirical dataset analysis, we demonstrated that these IPM-based metrics improved the prediction performance of phylogenetic profiling. In addition, we found that the integration of several metrics, including the IPM-based metrics, had superior performance to a single metric.

Original languageEnglish
Pages (from-to)1794-1800
Number of pages7
JournalBioinformatics
Volume38
Issue number7
DOIs
Publication statusPublished - 2022 Apr 1
Externally publishedYes

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Fingerprint

Dive into the research topics of 'Inverse Potts model improves accuracy of phylogenetic profiling'. Together they form a unique fingerprint.

Cite this