NEWS.md

In HEMDAG: Hierarchical Ensemble Methods for Directed Acyclic Graphs

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

HEMDAG documentation built on Feb. 12, 2021, 5:13 p.m.