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HEMDAG: Hierarchical Ensemble Methods for Directed Acyclic Graphs
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README.md

Brief Description

HEMDAG library:

  • implements several Hierarchical Ensemble Methods (HEMs) for Directed Acyclic Graphs (DAGs);
  • can be used to reconcile flat predictions by considering the topology of the ontology;
  • provides biologically consistent predictions according to the hierarchical nature of the ontology classes;
  • 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 (e.g. FunCat), since trees are DAGs;
  • scales nicely both in terms of the complexity of the taxonomy and in the cardinality of the examples;
  • provides several utility functions to process and analyze graphs;
  • provides several performance metrics to evaluate HEMs algorithms.

Documentation

Please get a look to the documentation to know how to download, install and make experiments with the HEMDAG package.

Cite HEMDAG

If you use HEMDAG, please cite our BMC Bioinformatics article:

M. Notaro, M. Schubach, P. N. Robinson, and G Valentini. 
Prediction of Human Phenotype Ontology terms by means of hierarchical ensemble methods.
BMC Bioinformatics, 18(1):449, 2017
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