package de.lmu.ifi.dbs.elki.algorithm.statistics; /* This file is part of ELKI: Environment for Developing KDD-Applications Supported by Index-Structures Copyright (C) 2015 Ludwig-Maximilians-Universität München Lehr- und Forschungseinheit für Datenbanksysteme ELKI Development Team This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see . */ import java.util.ArrayList; import java.util.Collection; import de.lmu.ifi.dbs.elki.algorithm.AbstractDistanceBasedAlgorithm; import de.lmu.ifi.dbs.elki.algorithm.clustering.trivial.ByLabelOrAllInOneClustering; import de.lmu.ifi.dbs.elki.data.Cluster; import de.lmu.ifi.dbs.elki.data.DoubleVector; import de.lmu.ifi.dbs.elki.data.model.Model; import de.lmu.ifi.dbs.elki.data.type.TypeInformation; import de.lmu.ifi.dbs.elki.data.type.TypeUtil; import de.lmu.ifi.dbs.elki.database.Database; import de.lmu.ifi.dbs.elki.database.ids.DBIDIter; import de.lmu.ifi.dbs.elki.database.ids.KNNList; import de.lmu.ifi.dbs.elki.database.query.distance.DistanceQuery; import de.lmu.ifi.dbs.elki.database.query.knn.KNNQuery; import de.lmu.ifi.dbs.elki.database.relation.Relation; import de.lmu.ifi.dbs.elki.distance.distancefunction.DistanceFunction; import de.lmu.ifi.dbs.elki.evaluation.scores.ROCEvaluation; import de.lmu.ifi.dbs.elki.logging.Logging; import de.lmu.ifi.dbs.elki.logging.progress.FiniteProgress; import de.lmu.ifi.dbs.elki.math.MeanVariance; import de.lmu.ifi.dbs.elki.result.CollectionResult; import de.lmu.ifi.dbs.elki.result.HistogramResult; import de.lmu.ifi.dbs.elki.utilities.datastructures.histogram.DoubleStaticHistogram; import de.lmu.ifi.dbs.elki.utilities.documentation.Description; import de.lmu.ifi.dbs.elki.utilities.documentation.Title; import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID; import de.lmu.ifi.dbs.elki.utilities.optionhandling.constraints.CommonConstraints; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; /** * Evaluate a distance function with respect to kNN queries. For each point, the * neighbors are sorted by distance, then the ROC AUC is computed. A score of 1 * means that the distance function provides a perfect ordering of relevant * neighbors first, then irrelevant neighbors. A value of 0.5 can be obtained by * random sorting. A value of 0 means the distance function is inverted, i.e. a * similarity. * * TODO: Add sampling * * @author Erich Schubert * @since 0.2 * @param Object type */ @Title("Ranking Quality Histogram") @Description("Evaluates the effectiveness of a distance function via the obtained rankings.") public class RankingQualityHistogram extends AbstractDistanceBasedAlgorithm> { /** * The logger for this class. */ private static final Logging LOG = Logging.getLogger(RankingQualityHistogram.class); /** * Number of bins to use. */ protected int numbins = 100; /** * Constructor. * * @param distanceFunction Distance function to evaluate * @param numbins Number of bins */ public RankingQualityHistogram(DistanceFunction distanceFunction, int numbins) { super(distanceFunction); this.numbins = numbins; } /** * Process a database * * @param database Database to process * @param relation Relation to process * @return Histogram of ranking qualities */ public HistogramResult run(Database database, Relation relation) { final DistanceQuery distanceQuery = database.getDistanceQuery(relation, getDistanceFunction()); final KNNQuery knnQuery = database.getKNNQuery(distanceQuery, relation.size()); if(LOG.isVerbose()) { LOG.verbose("Preprocessing clusters..."); } // Cluster by labels Collection> split = (new ByLabelOrAllInOneClustering()).run(database).getAllClusters(); DoubleStaticHistogram hist = new DoubleStaticHistogram(numbins, 0.0, 1.0); if(LOG.isVerbose()) { LOG.verbose("Processing points..."); } FiniteProgress progress = LOG.isVerbose() ? new FiniteProgress("Computing ROC AUC values", relation.size(), LOG) : null; MeanVariance mv = new MeanVariance(); // sort neighbors for(Cluster clus : split) { for(DBIDIter iter = clus.getIDs().iter(); iter.valid(); iter.advance()) { KNNList knn = knnQuery.getKNNForDBID(iter, relation.size()); double result = new ROCEvaluation().evaluate(clus, knn); mv.put(result); hist.increment(result, 1. / relation.size()); LOG.incrementProcessed(progress); } } LOG.ensureCompleted(progress); // Transform Histogram into a Double Vector array. Collection res = new ArrayList<>(relation.size()); for(DoubleStaticHistogram.Iter iter = hist.iter(); iter.valid(); iter.advance()) { DoubleVector row = new DoubleVector(new double[] { iter.getCenter(), iter.getValue() }); res.add(row); } HistogramResult result = new HistogramResult<>("Ranking Quality Histogram", "ranking-histogram", res); result.addHeader("Mean: " + mv.getMean() + " Variance: " + mv.getSampleVariance()); return result; } @Override public TypeInformation[] getInputTypeRestriction() { return TypeUtil.array(getDistanceFunction().getInputTypeRestriction()); } @Override protected Logging getLogger() { return LOG; } /** * Parameterization class. * * @author Erich Schubert * * @apiviz.exclude * * @param Object type */ public static class Parameterizer extends AbstractDistanceBasedAlgorithm.Parameterizer { /** * Option to configure the number of bins to use. */ public static final OptionID HISTOGRAM_BINS_ID = new OptionID("rankqual.bins", "Number of bins to use in the histogram"); /** * Number of bins. */ protected int numbins = 20; @Override protected void makeOptions(Parameterization config) { super.makeOptions(config); final IntParameter param = new IntParameter(HISTOGRAM_BINS_ID, 100); param.addConstraint(CommonConstraints.GREATER_THAN_ONE_INT); if(config.grab(param)) { numbins = param.getValue(); } } @Override protected RankingQualityHistogram makeInstance() { return new RankingQualityHistogram<>(distanceFunction, numbins); } } }