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