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HEMDAG 2.7.4

Changes

• remove extra input parameter f.criterion from tpr.dag.cv, tpr.dag.holdout, find.best.f and compute.fmax: type of F-measure used to select the best F-measure is always the harmonic mean between the average precision and recall (f.criterion="F") and never the F-measure computed as average across examples (f.criterion="avF");
• fix a minor bug in tpr.dag.holdout;
• add warning checks in tpr.dag.cv and tpr.dag.holdout;
• improve some test cases and manual;

HEMDAG 2.7.3

New Features

• add build.scores.matrix.from.list;
• add build.scores.matrix.from.tupla;
• add several test cases;

Changes

• streamline and lighten HEMDAG’s hierarchical functions (namespace clearer and lighter);
• rename the following functions:
  • htd-dag:
    • Do.HTD –> htd.vanilla;
    • Do.HTD.holdout –> htd.holdout;
  • obozinski heuristic methods:
    • heuristic.max –> obozinski.max;
    • heuristic.and –> obozinski.and;
    • heuristic.or –> obozinski.or;
    • Do.heuristic.methods –> obozinski.methods;
    • Do.heuristic.methods.holdout –> obozinski.holdout;
  • gpav:
    • GPAV –> gpav;
    • GPAV.over.examples –> gpav.over.examples;
    • GPAV.parallel –> gpav.parallel;
    • Do.GPAV –> gpav.vanilla;
    • Do.GPAV.holdout –> gpav.holdout;
  • tpr-dag:
    • TPR.DAG –> tpr.dag;
    • Do.TPR.DAG –> tpr.dag.cv;
    • Do.TPR.DAG.holdout –> tpr.dag.holdout;
  • utility functions:
    • get.parents –> build.parents;
    • get.parents.top.down –> build.parents.top.down;
    • get.parents.bottom.up –> build.parents.bottom.up;
    • get.parents.topological.sorting –> build.parents.topological.sorting;
    • get.children.top.down –> build.children.top.down;
    • get.children.bottom.up –> build.children.bottom.up;
    • check.DAG.integrity –> check.dag.integrity;
    • do.subgraph –> build.subgraph;
    • do.submatrix –> build.submatrix;
    • do.stratified.cv.data.single.class –> stratified.cv.data.single.class;
    • do.stratified.cv.data.over.classes –> stratified.cv.data.over.classes;
    • do.unstratified.cv.data –> unstratified.cv.data;
    • do.edges.from.HPO.obo –> build.edges.from.hpo.obo;
  • performance metrics:
    • AUPRC.single.class –> auprc.single.class;
    • AUPRC.single.over.classes –> auprc.single.over.classes;
    • AUROC.single.class –> auroc.single.class;
    • AUROC.single.over.classes –> auroc.single.over.classes;
    • compute.Fmeasure.multilabel –> compute.fmax;
• remove the following functions (no more needed):
  • Do.flat.scores.normalization;
  • Do.full.annotation.matrix;
• improve manual;
• make HEMDAG’s documentation clearer and less redundant;

HEMDAG 2.6.1

Changes

• fix stringsAsFactors issue – link;

HEMDAG 2.6.0

Changes

• fix NAMESPACE notes in CRAN checks;
• add link to the GitHub repository obogaf::parser;
• adjust link to read the docs;

HEMDAG 2.5.9

New Features

• add build.consistent.graph;

Changes

• add some warning checks in functions that compute performance metrics;
• improve some graph utility functions;
• improve manual;
• improve tutorial on read the docs – link;
• make namespace clearer;
• fix minor bugs;
• remove defunct functions;

HEMDAG 2.4.8

Changes

• fix a minor bug in Do.GPAV.holdout;
• improve package description;

HEMDAG 2.4.7

New Features

• fix degenerate case in precision.at.all.recall.levels.single.class (labels are all negatives/positives);
• fix degenerate case in precision.at.given.recall.levels.over.classes (labels in a fold are all negatives/positives);
• fix degenerate case in do.stratified.cv.data.single.class (sampling of the labels with just one positive/negative);
• add input variable compute.performance to the following high level functions:
  • Do.TPR.DAG and Do.TPR.DAG.holdout;
  • Do.HTD and Do.HTD.holdout;
  • Do.GPAV and Do.GPAV.holdout;
  • Do.heuristic.methods and Do.heuristic.methods.holdout;

Changes

• improve manual;

HEMDAG 2.3.6

New Features

• add lexicographical.topological.sort;

Changes

• fix minor bugs;
• improve manual;

HEMDAG 2.2.5

New Features

• precision-recall performance computed through precrec package:
  • add precision.at.all.recall.levels.single.class;
  • PXR.at.multiple.recall.levels.over.classes –> precision.at.given.recall.levels.over.classes;
• improve IO functions: the extension of the input or output file can be or plain text (.txt) or compressed (.gz);

Changes

• fix minor bugs;
• improve manual;

HEMDAG 2.2.4

Changes

• fix CRAN Package Check Results: remove unneeded header and define from GPAV C++ source code

HEMDAG 2.2.3

New Features

• add GPAV algorithm (Burdakov et al., Journal of Computational Mathematics, 2006 – link);
• Embed GPAV algorithm in the top-down step of the functions TPR.DAG, Do.TPR.DAG and Do.TPR.DAG.holdout;
• Some functions have been defunct. To know the defunct functions just typing in the R environment: help("HEMDAG-defunct");

Changes

• improve manual;

AUTHOR

• add Alessandro Petrini as author for his contribution in writing the C++ code of GPAV algorithm;

HEMDAG 2.1.3

Changes

• various fixes from 2.1.2

HEMDAG 2.1.2

New Features

• improve performance metrics:
  • add compute.Fmeasure.multilabel;
  • add PXR.at.multiple.recall.levels.over.classes;
  • all the performance metrics (AUPRC, AUROC, FMM, PXR) can be computed either one-shot or averaged across folds;
• improve the high-level hierarchical ensemble functions:
  • embed the new performance metric functions;
  • add the parameter metric: maximization by FMAX or PRC (see manual for further details);
  • add some checkers (warning/stop messages) to make the library more user-friendly;

Changes

• improve manual;

HEMDAG 2.0.1

Changes

• fix bug in do.stratified.cv.data.single.class;

HEMDAG 2.0.0

New Features

• add TPR-DAG: function gathering several hierarchical ensemble variants;

• add Do.TPR.DAG: high-level function to run TPR-DAG cross-validated experiments;

• add Do.TPR.DAG.holdout: high-level functions to run TPR-DAG holdout experiments;

• The following TPR-DAG and DESCENS high-level functions were remove:

  • Do.tpr.threshold.free;
  • Do.tpr.threshold.cv;
  • Do.tpr.weighted.threshold.free.cv;
  • Do.tpr.weighted.threshold.cv;
  • Do.descens.threshold.free;
  • Do.descens.threshold.cv;
  • Do.descens.weighted.threshold.free.cv;
  • Do.descens.tau.cv;
  • Do.descens.weighted.threshold.cv;
  • Do.tpr.threshold.free.holdout;
  • Do.tpr.threshold.holdout;
  • Do.tpr.weighted.threshold.free.holdout;
  • Do.tpr.weighted.threshold.holdout;
  • Do.descens.threshold.free.holdout;
  • Do.descens.threshold.holdout;
  • Do.descens.weighted.threshold.free.holdout;
  • Do.descens.tau.holdout;
  • Do.descens.weighted.threshold.holdout;

NOTE: all the removed functions can be run opportunely by setting the input parameters of the new high-level function Do.TPR.DAG (for cross-validated experiments) and Do.TPR.DAG.holdout (for hold-out experiments);

Changes

• improve manual;

HEMDAG 1.1.1

New Features

• add DESCENS algorithm;
• add Heuristic Methods Max, And, Or (Obozinski et al., Genome Biology, 2008 – link);
• add tupla.matrix function;

Changes

• improve manual;
• add link to the GitHub repository HPOparser (note: from version 2.6.0 HPOparser was changed in obogaf::parser);
• add CITATION file;

HEMDAG 1.0.0

Package Genesis

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.