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HEMDAG: Hierarchical Ensemble Methods for Directed Acyclic Graphs

An implementation of several Hierarchical Ensemble Methods (HEMs) for Directed Acyclic Graphs (DAGs). 'HEMDAG' package: 1) reconciles flat predictions with the topology of the ontology; 2) can enhance the predictions of virtually any flat learning methods by taking into account the hierarchical relationships between ontology classes; 3) provides biologically meaningful predictions that always obey the true-path-rule, the biological and logical rule that governs the internal coherence of biomedical ontologies; 4) is specifically designed for exploiting the hierarchical relationships of DAG-structured taxonomies, such as the Human Phenotype Ontology (HPO) or the Gene Ontology (GO), but can be safely applied to tree-structured taxonomies as well (as FunCat), since trees are DAGs; 5) scales nicely both in terms of the complexity of the taxonomy and in the cardinality of the examples; 6) provides several utility functions to process and analyze graphs; 7) provides several performance metrics to evaluate HEMs algorithms. (Marco Notaro, Max Schubach, Peter N. Robinson and Giorgio Valentini (2017) <doi:10.1186/s12859-017-1854-y>).

Version: 2.7.4
Depends: R (≥ 2.10)
Imports: graph, RBGL, precrec, preprocessCore, methods, plyr, foreach, doParallel, parallel
Suggests: Rgraphviz, testthat
Published: 2021-02-12
DOI: 10.32614/CRAN.package.HEMDAG
Author: Marco Notaro ORCID iD [aut, cre], Alessandro Petrini ORCID iD [ctb], Giorgio Valentini ORCID iD [aut]
Maintainer: Marco Notaro <marco.notaro at unimi.it>
BugReports: https://github.com/marconotaro/hemdag/issues
License: GPL (≥ 3)
URL: https://hemdag.readthedocs.io https://github.com/marconotaro/hemdag https://anaconda.org/bioconda/r-hemdag
NeedsCompilation: yes
Citation: HEMDAG citation info
Materials: NEWS
CRAN checks: HEMDAG results

Documentation:

Reference manual: HEMDAG.pdf

Downloads:

Package source: HEMDAG_2.7.4.tar.gz
Windows binaries: r-devel: HEMDAG_2.7.4.zip, r-release: HEMDAG_2.7.4.zip, r-oldrel: HEMDAG_2.7.4.zip
macOS binaries: r-release (arm64): HEMDAG_2.7.4.tgz, r-oldrel (arm64): HEMDAG_2.7.4.tgz, r-release (x86_64): HEMDAG_2.7.4.tgz, r-oldrel (x86_64): HEMDAG_2.7.4.tgz
Old sources: HEMDAG archive

Linking:

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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.