Cited by 320Genomics and Chromatin DynamicsRNA Research and SplicingBioinformatics and Genomic Networks

Iterative random forests to discover predictive and stable high-order interactions

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Basu, Sumanta, Kumbier, Karl, Brown, James B., Yu, Bin·2018·Proceedings of the National Academy of Sciences

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Abstract

Significance: We developed a predictive, stable, and interpretable tool: the iterative random forest algorithm (iRF). iRF discovers high-order interactions among biomolecules with the same order of computational cost as random forests. We demonstrate the efficacy of iRF by finding known and promising interactions among biomolecules, of up to fifth and sixth order, in two data examples in transcriptional regulation and alternative splicing.

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  1. [47]Hallmann RS Schneeweiss LG Correa E Zamora J 1998 Fine needle aspiration biopsy of thymic carcinoid tumor: A case with immunocytochemical correlation Acta Cytol 42 1042 1043 9684600

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Authors
Basu, S., Kumbier, K., Brown, J. B., & Yu, B.
Affiliations
  • Cornell University (US)
  • University of California, Berkeley (US)
  • Lawrence Berkeley National Laboratory (US)
Corresponding author
  • Brown, James B.
  • Yu, Bin
Venue
Proceedings of the National Academy of Sciences
Published
2018-01-19
Volume
115
Issue
8
Pages
1943-1948
ISSN
  • 0027-8424 (ISSN-L)
  • 1091-6490
OpenAlex
W2731142262
Cited by
317
References
80
Citations by year
2026: 24 · 2025: 32 · 2024: 39 · 2023: 51 · 2022: 48 · 2021: 42 · 2020: 46 · 2019: 20 · 2018: 12 · 2017: 3
FWCI
10.76
Type
journal article
Language
en
Open access
Locations
  • Proceedings of the National Academy of Sciences (publishedVersion, cc-by-nc-nd)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • arXiv (Cornell University) (submittedVersion)
  • eScholarship (California Digital Library) (submittedVersion)
  • OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
  • arXiv (Cornell University)
Funders
  • HHS | NIH | National Human Genome Research Institute (U01HG007031, R00 HG006698)
  • DOD | United States Army | RDECOM | Army Research Office (W911NF1710005)
  • DOD | United States Navy | Office of Naval Research (N00014-16-1- 2664)
  • U.S. Department of Energy (DOE DE-AC02-05CH11231, DE-SC0017069)
  • National Science Foundation (CCF-0939370)
  • HHS | NIH |U.S. National Library of Medicine (T32LM012417)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
Keywords
higher-order interactions, epistasis, H3K36me3, epigenetic interactions
MeSH terms
Algorithms, Animals, Drosophila, Models, Genetic, Alternative Splicing, Gene Expression Regulation, Developmental, Computational Biology, Gene Regulatory Networks, Genome-Wide Association Study

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