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/*******************************************************************************
* Copyright (c) 2015-2018 Skymind, Inc.
*
* This program and the accompanying materials are made available under the
* terms of the Apache License, Version 2.0 which is available at
* https://www.apache.org/licenses/LICENSE-2.0.
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
* WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
* License for the specific language governing permissions and limitations
* under the License.
*
* SPDX-License-Identifier: Apache-2.0
******************************************************************************/
package org.nd4j.evaluation.classification;
import lombok.EqualsAndHashCode;
import lombok.Getter;
import lombok.val;
import org.nd4j.base.Preconditions;
import org.nd4j.evaluation.BaseEvaluation;
import org.nd4j.evaluation.IMetric;
import org.nd4j.evaluation.classification.Evaluation.Metric;
import org.nd4j.evaluation.curves.Histogram;
import org.nd4j.evaluation.curves.ReliabilityDiagram;
import org.nd4j.linalg.api.buffer.DataType;
import org.nd4j.linalg.api.ndarray.INDArray;
import org.nd4j.linalg.api.ops.impl.reduce.longer.MatchCondition;
import org.nd4j.linalg.api.ops.impl.transforms.any.IsMax;
import org.nd4j.linalg.factory.Nd4j;
import org.nd4j.linalg.indexing.conditions.Conditions;
import org.nd4j.linalg.lossfunctions.LossUtil;
import org.nd4j.linalg.ops.transforms.Transforms;
import org.nd4j.linalg.primitives.Triple;
import org.nd4j.serde.jackson.shaded.NDArrayDeSerializer;
import org.nd4j.serde.jackson.shaded.NDArraySerializer;
import org.nd4j.serde.jackson.shaded.NDArrayTextDeSerializer;
import org.nd4j.serde.jackson.shaded.NDArrayTextSerializer;
import org.nd4j.shade.jackson.annotation.JsonProperty;
import org.nd4j.shade.jackson.databind.annotation.JsonDeserialize;
import org.nd4j.shade.jackson.databind.annotation.JsonSerialize;
import java.io.Serializable;
import java.util.List;
/**
* EvaluationCalibration is an evaluation class designed to analyze the calibration of a classifier.
* It provides a number of tools for this purpose:
* - Counts of the number of labels and predictions for each class
* - Reliability diagram (or reliability curve)
* - Residual plot (histogram)
* - Histograms of probabilities, including probabilities for each class separately
*
* References:
* - Reliability diagram: see for example Niculescu-Mizil and Caruana 2005, Predicting Good Probabilities With
* Supervised Learning
* - Residual plot: see Wallace and Dahabreh 2012, Class Probability Estimates are Unreliable for Imbalanced Data
* (and How to Fix Them)
*
*
* @author Alex Black
*/
@Getter
@EqualsAndHashCode
public class EvaluationCalibration extends BaseEvaluation {
public static final int DEFAULT_RELIABILITY_DIAG_NUM_BINS = 10;
public static final int DEFAULT_HISTOGRAM_NUM_BINS = 50;
private final int reliabilityDiagNumBins;
private final int histogramNumBins;
private final boolean excludeEmptyBins;
@EqualsAndHashCode.Exclude //Exclude axis: otherwise 2 Evaluation instances could contain identical stats and fail equality
protected int axis = 1;
@JsonSerialize(using = NDArraySerializer.class)
@JsonDeserialize(using = NDArrayDeSerializer.class)
private INDArray rDiagBinPosCount;
@JsonSerialize(using = NDArraySerializer.class)
@JsonDeserialize(using = NDArrayDeSerializer.class)
private INDArray rDiagBinTotalCount;
@JsonSerialize(using = NDArraySerializer.class)
@JsonDeserialize(using = NDArrayDeSerializer.class)
private INDArray rDiagBinSumPredictions;
@JsonSerialize(using = NDArrayTextSerializer.class)
@JsonDeserialize(using = NDArrayTextDeSerializer.class)
private INDArray labelCountsEachClass;
@JsonSerialize(using = NDArrayTextSerializer.class)
@JsonDeserialize(using = NDArrayTextDeSerializer.class)
private INDArray predictionCountsEachClass;
@JsonSerialize(using = NDArrayTextSerializer.class)
@JsonDeserialize(using = NDArrayTextDeSerializer.class)
private INDArray residualPlotOverall;
@JsonSerialize(using = NDArraySerializer.class)
@JsonDeserialize(using = NDArrayDeSerializer.class)
private INDArray residualPlotByLabelClass;
@JsonSerialize(using = NDArrayTextSerializer.class)
@JsonDeserialize(using = NDArrayTextDeSerializer.class)
private INDArray probHistogramOverall; //Simple histogram over all probabilities
@JsonSerialize(using = NDArraySerializer.class)
@JsonDeserialize(using = NDArrayDeSerializer.class)
private INDArray probHistogramByLabelClass; //Histogram - for each label class separately
protected EvaluationCalibration(int axis, int reliabilityDiagNumBins, int histogramNumBins, boolean excludeEmptyBins) {
this.axis = axis;
this.reliabilityDiagNumBins = reliabilityDiagNumBins;
this.histogramNumBins = histogramNumBins;
this.excludeEmptyBins = excludeEmptyBins;
}
/**
* Create an EvaluationCalibration instance with the default number of bins
*/
public EvaluationCalibration() {
this(DEFAULT_RELIABILITY_DIAG_NUM_BINS, DEFAULT_HISTOGRAM_NUM_BINS, true);
}
/**
* Create an EvaluationCalibration instance with the specified number of bins
*
* @param reliabilityDiagNumBins Number of bins for the reliability diagram (usually 10)
* @param histogramNumBins Number of bins for the histograms
*/
public EvaluationCalibration(int reliabilityDiagNumBins, int histogramNumBins) {
this(reliabilityDiagNumBins, histogramNumBins, true);
}
/**
* Create an EvaluationCalibration instance with the specified number of bins
*
* @param reliabilityDiagNumBins Number of bins for the reliability diagram (usually 10)
* @param histogramNumBins Number of bins for the histograms
* @param excludeEmptyBins For the reliability diagram, whether empty bins should be excluded
*/
public EvaluationCalibration(@JsonProperty("reliabilityDiagNumBins") int reliabilityDiagNumBins,
@JsonProperty("histogramNumBins") int histogramNumBins,
@JsonProperty("excludeEmptyBins") boolean excludeEmptyBins) {
this.reliabilityDiagNumBins = reliabilityDiagNumBins;
this.histogramNumBins = histogramNumBins;
this.excludeEmptyBins = excludeEmptyBins;
}
/**
* Set the axis for evaluation - this is the dimension along which the probability (and label classes) are present.
* For DL4J, this can be left as the default setting (axis = 1).
* Axis should be set as follows:
* For 2D (OutputLayer), shape [minibatch, numClasses] - axis = 1
* For 3D, RNNs/CNN1D (DL4J RnnOutputLayer), NCW format, shape [minibatch, numClasses, sequenceLength] - axis = 1
* For 3D, RNNs/CNN1D (DL4J RnnOutputLayer), NWC format, shape [minibatch, sequenceLength, numClasses] - axis = 2
* For 4D, CNN2D (DL4J CnnLossLayer), NCHW format, shape [minibatch, channels, height, width] - axis = 1
* For 4D, CNN2D, NHWC format, shape [minibatch, height, width, channels] - axis = 3
*
* @param axis Axis to use for evaluation
*/
public void setAxis(int axis){
this.axis = axis;
}
/**
* Get the axis - see {@link #setAxis(int)} for details
*/
public int getAxis(){
return axis;
}
@Override
public void eval(INDArray labels, INDArray predictions, INDArray mask) {
Triple triple = BaseEvaluation.reshapeAndExtractNotMasked(labels, predictions, mask, axis);
if(triple == null){
//All values masked out; no-op
return;
}
INDArray labels2d = triple.getFirst();
INDArray predictions2d = triple.getSecond();
INDArray maskArray = triple.getThird();
Preconditions.checkState(maskArray == null, "Per-output masking for EvaluationCalibration is not supported");
//Stats for the reliability diagram: one reliability diagram for each class
// For each bin, we need: (a) the number of positive cases AND total cases, (b) the average probability
val nClasses = labels2d.size(1);
if (rDiagBinPosCount == null) {
DataType dt = DataType.DOUBLE;
//Initialize
rDiagBinPosCount = Nd4j.create(DataType.LONG, reliabilityDiagNumBins, nClasses);
rDiagBinTotalCount = Nd4j.create(DataType.LONG, reliabilityDiagNumBins, nClasses);
rDiagBinSumPredictions = Nd4j.create(dt, reliabilityDiagNumBins, nClasses);
labelCountsEachClass = Nd4j.create(DataType.LONG, 1, nClasses);
predictionCountsEachClass = Nd4j.create(DataType.LONG, 1, nClasses);
residualPlotOverall = Nd4j.create(dt, 1, histogramNumBins);
residualPlotByLabelClass = Nd4j.create(dt, histogramNumBins, nClasses);
probHistogramOverall = Nd4j.create(dt, 1, histogramNumBins);
probHistogramByLabelClass = Nd4j.create(dt, histogramNumBins, nClasses);
}
//First: loop over classes, determine positive count and total count - for each bin
double histogramBinSize = 1.0 / histogramNumBins;
double reliabilityBinSize = 1.0 / reliabilityDiagNumBins;
INDArray p = predictions2d;
INDArray l = labels2d;
if (maskArray != null) {
//2 options: per-output masking, or
if (maskArray.isColumnVectorOrScalar()) {
//Per-example masking
l = l.mulColumnVector(maskArray);
} else {
l = l.mul(maskArray);
}
}
for (int j = 0; j < reliabilityDiagNumBins; j++) {
INDArray geqBinLower = p.gte(j * reliabilityBinSize).castTo(predictions2d.dataType());
INDArray ltBinUpper;
if (j == reliabilityDiagNumBins - 1) {
//Handle edge case
ltBinUpper = p.lte(1.0).castTo(predictions2d.dataType());
} else {
ltBinUpper = p.lt((j + 1) * reliabilityBinSize).castTo(predictions2d.dataType());
}
//Calculate bit-mask over each entry - whether that entry is in the current bin or not
INDArray currBinBitMask = geqBinLower.muli(ltBinUpper);
if (maskArray != null) {
if (maskArray.isColumnVectorOrScalar()) {
currBinBitMask.muliColumnVector(maskArray);
} else {
currBinBitMask.muli(maskArray);
}
}
INDArray isPosLabelForBin = l.mul(currBinBitMask);
INDArray maskedProbs = predictions2d.mul(currBinBitMask);
INDArray numPredictionsCurrBin = currBinBitMask.sum(0);
rDiagBinSumPredictions.getRow(j).addi(maskedProbs.sum(0).castTo(rDiagBinSumPredictions.dataType()));
rDiagBinPosCount.getRow(j).addi(isPosLabelForBin.sum(0).castTo(rDiagBinPosCount.dataType()));
rDiagBinTotalCount.getRow(j).addi(numPredictionsCurrBin.castTo(rDiagBinTotalCount.dataType()));
}
//Second, we want histograms of:
//(a) Distribution of label classes: label counts for each class
//(b) Distribution of prediction classes: prediction counts for each class
//(c) residual plots, for each class - (i) all instances, (ii) positive instances only, (iii) negative only
//(d) Histograms of probabilities, for each class
labelCountsEachClass.addi(labels2d.sum(0).castTo(labelCountsEachClass.dataType()));
//For prediction counts: do an IsMax op, but we need to take masking into account...
INDArray isPredictedClass = Nd4j.getExecutioner().exec(new IsMax(p, p.ulike(), 1))[0];
if (maskArray != null) {
LossUtil.applyMask(isPredictedClass, maskArray);
}
predictionCountsEachClass.addi(isPredictedClass.sum(0).castTo(predictionCountsEachClass.dataType()));
//Residual plots: want histogram of |labels - predicted prob|
//ND4J's histogram op: dynamically calculates the bin positions, which is not what I want here...
INDArray labelsSubPredicted = labels2d.sub(predictions2d);
INDArray maskedProbs = predictions2d.dup();
Transforms.abs(labelsSubPredicted, false);
//if masking: replace entries with < 0 to effectively remove them
if (maskArray != null) {
//Assume per-example masking
INDArray newMask = maskArray.mul(-10);
labelsSubPredicted.addiColumnVector(newMask);
maskedProbs.addiColumnVector(newMask);
}
for (int j = 0; j < histogramNumBins; j++) {
INDArray geqBinLower = labelsSubPredicted.gte(j * histogramBinSize).castTo(predictions2d.dataType());
INDArray ltBinUpper;
INDArray geqBinLowerProbs = maskedProbs.gte(j * histogramBinSize).castTo(predictions2d.dataType());
INDArray ltBinUpperProbs;
if (j == histogramNumBins - 1) {
//Handle edge case
ltBinUpper = labelsSubPredicted.lte(1.0).castTo(predictions2d.dataType());
ltBinUpperProbs = maskedProbs.lte(1.0).castTo(predictions2d.dataType());
} else {
ltBinUpper = labelsSubPredicted.lt((j + 1) * histogramBinSize).castTo(predictions2d.dataType());
ltBinUpperProbs = maskedProbs.lt((j + 1) * histogramBinSize).castTo(predictions2d.dataType());
}
INDArray currBinBitMask = geqBinLower.muli(ltBinUpper);
INDArray currBinBitMaskProbs = geqBinLowerProbs.muli(ltBinUpperProbs);
int newTotalCount = residualPlotOverall.getInt(0, j) + currBinBitMask.sumNumber().intValue();
residualPlotOverall.putScalar(0, j, newTotalCount);
//Counts for positive class only: values are in the current bin AND it's a positive label
INDArray isPosLabelForBin = l.mul(currBinBitMask);
residualPlotByLabelClass.getRow(j).addi(isPosLabelForBin.sum(0).castTo(residualPlotByLabelClass.dataType()));
int probNewTotalCount = probHistogramOverall.getInt(0, j) + currBinBitMaskProbs.sumNumber().intValue();
probHistogramOverall.putScalar(0, j, probNewTotalCount);
INDArray isPosLabelForBinProbs = l.mul(currBinBitMaskProbs);
INDArray temp = isPosLabelForBinProbs.sum(0);
probHistogramByLabelClass.getRow(j).addi(temp.castTo(probHistogramByLabelClass.dataType()));
}
}
@Override
public void eval(INDArray labels, INDArray networkPredictions) {
eval(labels, networkPredictions, (INDArray) null);
}
@Override
public void eval(INDArray labels, INDArray networkPredictions, INDArray maskArray, List recordMetaData) {
throw new UnsupportedOperationException("Not yet implemented");
}
@Override
public void merge(EvaluationCalibration other) {
if (reliabilityDiagNumBins != other.reliabilityDiagNumBins) {
throw new UnsupportedOperationException(
"Cannot merge EvaluationCalibration instances with different numbers of bins");
}
if (other.rDiagBinPosCount == null) {
return;
}
if (rDiagBinPosCount == null) {
this.rDiagBinPosCount = other.rDiagBinPosCount;
this.rDiagBinTotalCount = other.rDiagBinTotalCount;
this.rDiagBinSumPredictions = other.rDiagBinSumPredictions;
}
this.rDiagBinPosCount.addi(other.rDiagBinPosCount);
this.rDiagBinTotalCount.addi(other.rDiagBinTotalCount);
this.rDiagBinSumPredictions.addi(other.rDiagBinSumPredictions);
}
@Override
public void reset() {
rDiagBinPosCount = null;
rDiagBinTotalCount = null;
rDiagBinSumPredictions = null;
}
@Override
public String stats() {
return "EvaluationCalibration(nBins=" + reliabilityDiagNumBins + ")";
}
public int numClasses() {
if (rDiagBinTotalCount == null) {
return -1;
}
return (int) rDiagBinTotalCount.size(1);
}
/**
* Get the reliability diagram for the specified class
*
* @param classIdx Index of the class to get the reliability diagram for
*/
public ReliabilityDiagram getReliabilityDiagram(int classIdx) {
Preconditions.checkState(rDiagBinPosCount != null, "Unable to get reliability diagram: no evaluation has been performed (no data)");
INDArray totalCountBins = rDiagBinTotalCount.getColumn(classIdx);
INDArray countPositiveBins = rDiagBinPosCount.getColumn(classIdx);
double[] meanPredictionBins = rDiagBinSumPredictions.getColumn(classIdx).castTo(DataType.DOUBLE)
.div(totalCountBins.castTo(DataType.DOUBLE)).data().asDouble();
double[] fracPositives = countPositiveBins.castTo(DataType.DOUBLE).div(totalCountBins.castTo(DataType.DOUBLE)).data().asDouble();
if (excludeEmptyBins) {
val condition = new MatchCondition(totalCountBins, Conditions.equals(0));
int numZeroBins = Nd4j.getExecutioner().exec(condition).getInt(0);
if (numZeroBins != 0) {
double[] mpb = meanPredictionBins;
double[] fp = fracPositives;
meanPredictionBins = new double[(int) (totalCountBins.length() - numZeroBins)];
fracPositives = new double[meanPredictionBins.length];
int j = 0;
for (int i = 0; i < mpb.length; i++) {
if (totalCountBins.getDouble(i) != 0) {
meanPredictionBins[j] = mpb[i];
fracPositives[j] = fp[i];
j++;
}
}
}
}
String title = "Reliability Diagram: Class " + classIdx;
return new ReliabilityDiagram(title, meanPredictionBins, fracPositives);
}
/**
* @return The number of observed labels for each class. For N classes, be returned array is of length N, with
* out[i] being the number of labels of class i
*/
public int[] getLabelCountsEachClass() {
return labelCountsEachClass == null ? null : labelCountsEachClass.data().asInt();
}
/**
* @return The number of network predictions for each class. For N classes, be returned array is of length N, with
* out[i] being the number of predicted values (max probability) for class i
*/
public int[] getPredictionCountsEachClass() {
return predictionCountsEachClass == null ? null : predictionCountsEachClass.data().asInt();
}
/**
* Get the residual plot for all classes combined. The residual plot is defined as a histogram of
* |label_i - prob(class_i | input)| for all classes i and examples.
* In general, small residuals indicate a superior classifier to large residuals.
*
* @return Residual plot (histogram) - all predictions/classes
*/
public Histogram getResidualPlotAllClasses() {
String title = "Residual Plot - All Predictions and Classes";
int[] counts = residualPlotOverall.data().asInt();
return new Histogram(title, 0.0, 1.0, counts);
}
/**
* Get the residual plot, only for examples of the specified class.. The residual plot is defined as a histogram of
* |label_i - prob(class_i | input)| for all and examples; for this particular method, only predictions where
* i == labelClassIdx are included.
* In general, small residuals indicate a superior classifier to large residuals.
*
* @param labelClassIdx Index of the class to get the residual plot for
* @return Residual plot (histogram) - all predictions/classes
*/
public Histogram getResidualPlot(int labelClassIdx) {
Preconditions.checkState(rDiagBinPosCount != null, "Unable to get residual plot: no evaluation has been performed (no data)");
String title = "Residual Plot - Predictions for Label Class " + labelClassIdx;
int[] counts = residualPlotByLabelClass.getColumn(labelClassIdx).dup().data().asInt();
return new Histogram(title, 0.0, 1.0, counts);
}
/**
* Return a probability histogram for all predictions/classes.
*
* @return Probability histogram
*/
public Histogram getProbabilityHistogramAllClasses() {
String title = "Network Probabilities Histogram - All Predictions and Classes";
int[] counts = probHistogramOverall.data().asInt();
return new Histogram(title, 0.0, 1.0, counts);
}
/**
* Return a probability histogram of the specified label class index. That is, for label class index i,
* a histogram of P(class_i | input) is returned, only for those examples that are labelled as class i.
*
* @param labelClassIdx Index of the label class to get the histogram for
* @return Probability histogram
*/
public Histogram getProbabilityHistogram(int labelClassIdx) {
Preconditions.checkState(rDiagBinPosCount != null, "Unable to get probability histogram: no evaluation has been performed (no data)");
String title = "Network Probabilities Histogram - P(class " + labelClassIdx + ") - Data Labelled Class "
+ labelClassIdx + " Only";
int[] counts = probHistogramByLabelClass.getColumn(labelClassIdx).dup().data().asInt();
return new Histogram(title, 0.0, 1.0, counts);
}
public static EvaluationCalibration fromJson(String json){
return fromJson(json, EvaluationCalibration.class);
}
@Override
public double getValue(IMetric metric){
throw new IllegalStateException("Can't get value for non-calibration Metric " + metric);
}
@Override
public EvaluationCalibration newInstance() {
return new EvaluationCalibration(axis, reliabilityDiagNumBins, histogramNumBins, excludeEmptyBins);
}
}
