[
https://issues.apache.org/jira/browse/SPARK-19449?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
]
Aseem Bansal updated SPARK-19449:
---------------------------------
Description:
I worked on some code to convert ml package RandomForestClassificationModel to
mllib package RandomForestModel. It was needed because we need to make
predictions on the order of ms. I found that the results are inconsistent
although the underlying DecisionTreeModel are exactly the same.
The below code can be used to reproduce the issue. Can run this as a simple
Java app as long as you have spark dependencies set up properly.
{noformat}
import org.apache.spark.ml.Transformer;
import org.apache.spark.ml.classification.*;
import org.apache.spark.ml.linalg.*;
import org.apache.spark.ml.regression.RandomForestRegressionModel;
import org.apache.spark.mllib.linalg.DenseVector;
import org.apache.spark.mllib.linalg.Vector;
import org.apache.spark.mllib.tree.configuration.Algo;
import org.apache.spark.mllib.tree.model.DecisionTreeModel;
import org.apache.spark.mllib.tree.model.RandomForestModel;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.RowFactory;
import org.apache.spark.sql.SparkSession;
import org.apache.spark.sql.types.DataTypes;
import org.apache.spark.sql.types.Metadata;
import org.apache.spark.sql.types.StructField;
import org.apache.spark.sql.types.StructType;
import scala.Enumeration;
import java.util.ArrayList;
import java.util.List;
import java.util.Random;
abstract class Predictor {
abstract double predict(Vector vector);
}
public class MainConvertModels {
public static final int seed = 42;
public static void main(String[] args) {
int numRows = 1000;
int numFeatures = 3;
int numClasses = 2;
double trainFraction = 0.8;
double testFraction = 0.2;
SparkSession spark = SparkSession.builder()
.appName("conversion app")
.master("local")
.getOrCreate();
// Dataset<Row> data = getData(spark, "libsvm",
"/opt/spark2/data/mllib/sample_libsvm_data.txt");
Dataset<Row> data = getDummyData(spark, numRows, numFeatures,
numClasses);
Dataset<Row>[] splits = data.randomSplit(new double[]{trainFraction,
testFraction}, seed);
Dataset<Row> trainingData = splits[0];
Dataset<Row> testData = splits[1];
testData.cache();
List<Double> labels = getLabels(testData);
List<DenseVector> features = getFeatures(testData);
DecisionTreeClassifier classifier1 = new DecisionTreeClassifier();
DecisionTreeClassificationModel model1 = classifier1.fit(trainingData);
final DecisionTreeModel convertedModel1 =
convertDecisionTreeModel(model1, Algo.Classification());
RandomForestClassifier classifier = new RandomForestClassifier();
RandomForestClassificationModel model2 = classifier.fit(trainingData);
final RandomForestModel convertedModel2 =
convertRandomForestModel(model2);
LogisticRegression lr = new LogisticRegression();
LogisticRegressionModel model3 = lr.fit(trainingData);
final org.apache.spark.mllib.classification.LogisticRegressionModel
convertedModel3 = convertLogisticRegressionModel(model3);
System.out.println(
"****** DecisionTreeClassifier\n" +
"** Original **" + getInfo(model1, testData) + "\n" +
"** New **" + getInfo(new Predictor() {
double predict(Vector vector) {return
convertedModel1.predict(vector);}
}, labels, features) + "\n" +
"\n" +
"****** RandomForestClassifier\n" +
"** Original **" + getInfo(model2, testData) + "\n" +
"** New **" + getInfo(new Predictor() {double
predict(Vector vector) {return convertedModel2.predict(vector);}}, labels,
features) + "\n" +
"\n" +
"****** LogisticRegression\n" +
"** Original **" + getInfo(model3, testData) + "\n" +
"** New **" + getInfo(new Predictor() {double
predict(Vector vector) { return convertedModel3.predict(vector);}}, labels,
features) + "\n" +
"");
}
static Dataset<Row> getData(SparkSession spark, String format, String
location) {
return spark.read()
.format(format)
.load(location);
}
static Dataset<Row> getDummyData(SparkSession spark, int numberRows, int
numberFeatures, int labelUpperBound) {
StructType schema = new StructType(new StructField[]{
new StructField("label", DataTypes.DoubleType, false,
Metadata.empty()),
new StructField("features", new VectorUDT(), false,
Metadata.empty())
});
double[][] vectors = prepareData(numberRows, numberFeatures);
Random random = new Random(seed);
List<Row> dataTest = new ArrayList<>();
for (double[] vector : vectors) {
double label = (double) random.nextInt(2);
dataTest.add(RowFactory.create(label, Vectors.dense(vector)));
}
return spark.createDataFrame(dataTest, schema);
}
static double[][] prepareData(int numRows, int numFeatures) {
Random random = new Random(seed);
double[][] result = new double[numRows][numFeatures];
for (int row = 0; row < numRows; row++) {
for (int feature = 0; feature < numFeatures; feature++) {
result[row][feature] = random.nextDouble();
}
}
return result;
}
static String getInfo(Predictor predictor,
List<Double> labels,
List<DenseVector> features) {
Long startTime = System.currentTimeMillis();
List<Double> predictions = new ArrayList<>();
for (DenseVector feature : features) {
predictions.add(predictor.predict(feature));
}
return getInfo(startTime, labels, predictions);
}
static List<Double> getLabels(Dataset<Row> testData) {
List<Double> labels = new ArrayList<>();
List<DenseVector> vectors = new ArrayList<>();
for (Row row : testData.collectAsList()) {
vectors.add(new DenseVector(((org.apache.spark.ml.linalg.Vector)
row.get(1)).toArray()));
labels.add(row.getDouble(0));
}
return labels;
}
static List<DenseVector> getFeatures(Dataset<Row> testData) {
List<DenseVector> features = new ArrayList<>();
for (Row row : testData.collectAsList()) {
features.add(new DenseVector(((org.apache.spark.ml.linalg.Vector)
row.get(1)).toArray()));
}
return features;
}
static String getInfo(Transformer model, Dataset<Row> testData) {
Dataset<Row> predictions = model.transform(testData);
predictions.cache();
Dataset<Row> correctPredictions = predictions.filter("label ==
prediction");
correctPredictions.cache();
Dataset<Row> incorrectPredictions = predictions.filter("label !=
prediction");
incorrectPredictions.cache();
Long truePositives = correctPredictions.filter("prediction ==
1.0").count();
Long trueNegatives = correctPredictions.filter("prediction ==
0.0").count();
Long falsePositives = incorrectPredictions.filter("prediction ==
1.0").count();
Long falseNegatives = incorrectPredictions.filter("prediction ==
0.0").count();
return getInfo(null, truePositives, trueNegatives, falsePositives,
falseNegatives);
}
static String getInfo(Long startTime, List<Double> labels, List<Double>
predictions) {
Long endTime = System.currentTimeMillis();
if (labels.size() != predictions.size()) {
throw new RuntimeException("labels size is " + labels.size() +
" but predictions size is " + predictions.size());
}
Long truePositives = 0L;
Long trueNegatives = 0L;
Long falsePositives = 0L;
Long falseNegatives = 0L;
for (int i = 0; i < labels.size(); i++) {
double label = labels.get(i);
double prediction = predictions.get(i);
if (label == prediction) {
if (prediction == 1.0) {
truePositives += 1;
} else {
trueNegatives += 1;
}
} else {
if (prediction == 1.0) {
falsePositives += 1;
} else {
falseNegatives += 1;
}
}
}
return getInfo(endTime - startTime, truePositives, trueNegatives,
falsePositives, falseNegatives);
}
static double ratio(Long numerator, Long denominator) {
if (numerator == 0 || denominator == 0) {
return 0;
}
return ((double) numerator) / denominator;
}
static String getInfo(Long timeTakenMilliseconds, Long truePositives, Long
trueNegatives, Long falsePositives,
Long falseNegatives) {
Long testDataCount = truePositives + trueNegatives + falsePositives +
falseNegatives;
double accuracy = ratio(truePositives + trueNegatives, testDataCount);
double precision = ratio(truePositives, truePositives + falsePositives);
double recall = ratio(truePositives, truePositives + falseNegatives);
String last = "";
if (timeTakenMilliseconds != null) {
last = ", Average time taken (ms) " + ratio(timeTakenMilliseconds,
testDataCount);
}
return (
"true positives " + truePositives
+ ", true negatives " + trueNegatives
+ ", false positives " + falsePositives
+ ", false negatives " + falseNegatives
+ ", total " + testDataCount
+ "\n\t accuracy " + accuracy
+ ", precision " + precision
+ ", recall " + recall
+ last
);
}
static DecisionTreeModel
convertDecisionTreeModel(org.apache.spark.ml.tree.DecisionTreeModel model,
Enumeration.Value algo) {
return new DecisionTreeModel(model.rootNode().toOld(1), algo);
}
static RandomForestModel
convertRandomForestModel(org.apache.spark.ml.tree.TreeEnsembleModel model) {
Enumeration.Value algo;
if (model instanceof RandomForestRegressionModel) {
algo = Algo.Regression();
} else {
algo = Algo.Classification();
}
Object[] decisionTreeModels = model.trees();
DecisionTreeModel[] convertedDecisionTreeModels = new
DecisionTreeModel[decisionTreeModels.length];
for (int i = 0; i < decisionTreeModels.length; i++) {
org.apache.spark.ml.tree.DecisionTreeModel originalModel =
(org.apache.spark.ml.tree.DecisionTreeModel) decisionTreeModels[i];
DecisionTreeModel convertedModel =
convertDecisionTreeModel(originalModel, algo);
convertedDecisionTreeModels[i] = convertedModel;
}
RandomForestModel result = new RandomForestModel(algo,
convertedDecisionTreeModels);
return result;
}
static org.apache.spark.mllib.classification.LogisticRegressionModel
convertLogisticRegressionModel(LogisticRegressionModel model) {
org.apache.spark.mllib.classification.LogisticRegressionModel
convertedModel;
try {
convertedModel = new
org.apache.spark.mllib.classification.LogisticRegressionModel(
new DenseVector(model.coefficients().toArray()),
model.intercept(),
model.numFeatures(),
model.numClasses()
);
} catch (Exception e) {
//Should be SparkException but that does not compile.
// Raised when we have Multinomial Linear Regression
// Cannot check as the relevant variable is private
Vector coefficients = matrixToVector(model.coefficientMatrix());
for (double v : coefficients.toArray()) {
System.out.println(v);
}
System.out.println("**********");
for (double v : model.interceptVector().toDense().values()) {
System.out.println(v);
}
convertedModel = new
org.apache.spark.mllib.classification.LogisticRegressionModel(
coefficients,
model.interceptVector().toDense().values()[0], //TODO fix
this.
model.numFeatures(),
model.numClasses()
);
}
convertedModel.setThreshold(model.getThreshold());
return convertedModel;
}
static Vector matrixToVector(Matrix matrix) {
Vector result;
if (matrix instanceof DenseMatrix) {
result = new DenseVector(((DenseMatrix) matrix).values());
} else {
SparseMatrix _matrix = (SparseMatrix) matrix;
result = new org.apache.spark.mllib.linalg.SparseVector(
_matrix.numActives(),
_matrix.rowIndices(),
_matrix.values()
);
}
return result;
}
}
{noformat}
The output looks like the below. In the below the Original refers to ml package
version and New refers to mllib package version.
- I converted the mllib version Decision tree to ml version Decision tree. Gave
both versions same input and I received the exact same output.
- Then converted the mllib version Random Forest to ml version Random Forest
giving both the same underlying Decision trees (using the previoeus conversion
method). Gave both versions same input but I received different output.
{noformat}
****** DecisionTreeClassifier
** Original **true positives 8128, true negatives 1923, false positives 7942,
false negatives 1897, total 19890
accuracy 0.5053293112116641, precision 0.5057871810827629, recall
0.8107730673316709
** New **true positives 8128, true negatives 1923, false positives 7942,
false negatives 1897, total 19890
accuracy 0.5053293112116641, precision 0.5057871810827629, recall
0.8107730673316709, Average time taken (ms) 0.001558572146807441
****** RandomForestClassifier
** Original **true positives 3940, true negatives 5915, false positives 3950,
false negatives 6085, total 19890
accuracy 0.49547511312217196, precision 0.49936628643852976, recall
0.39301745635910224
** New **true positives 2461, true negatives 7350, false positives 2515,
false negatives 7564, total 19890
accuracy 0.4932629462041227, precision 0.4945739549839228, recall
0.2454862842892768, Average time taken (ms) 0.01085972850678733
****** LogisticRegression
** Original **true positives 6728, true negatives 3321, false positives 6544,
false negatives 3297, total 19890
accuracy 0.5052287581699346, precision 0.5069318866787221, recall
0.6711221945137157
** New **true positives 6728, true negatives 3321, false positives 6544,
false negatives 3297, total 19890
accuracy 0.5052287581699346, precision 0.5069318866787221, recall
0.6711221945137157, Average time taken (ms) 0.001558572146807441
{noformat}
was:
I worked on some code to convert ml package RandomForestClassificationModel to
mllib package RandomForestModel. It was needed because we need to make
predictions on the order of ms. I found that the results are inconsistent
although the underlying DecisionTreeModel are exactly the same.
The below code can be used to reproduce the issue.
{noformat}
import org.apache.spark.ml.Transformer;
import org.apache.spark.ml.classification.*;
import org.apache.spark.ml.linalg.*;
import org.apache.spark.ml.regression.RandomForestRegressionModel;
import org.apache.spark.mllib.linalg.DenseVector;
import org.apache.spark.mllib.linalg.Vector;
import org.apache.spark.mllib.tree.configuration.Algo;
import org.apache.spark.mllib.tree.model.DecisionTreeModel;
import org.apache.spark.mllib.tree.model.RandomForestModel;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.RowFactory;
import org.apache.spark.sql.SparkSession;
import org.apache.spark.sql.types.DataTypes;
import org.apache.spark.sql.types.Metadata;
import org.apache.spark.sql.types.StructField;
import org.apache.spark.sql.types.StructType;
import scala.Enumeration;
import java.util.ArrayList;
import java.util.List;
import java.util.Random;
abstract class Predictor {
abstract double predict(Vector vector);
}
public class MainConvertModels {
public static final int seed = 42;
public static void main(String[] args) {
int numRows = 1000;
int numFeatures = 3;
int numClasses = 2;
double trainFraction = 0.8;
double testFraction = 0.2;
SparkSession spark = SparkSession.builder()
.appName("conversion app")
.master("local")
.getOrCreate();
// Dataset<Row> data = getData(spark, "libsvm",
"/opt/spark2/data/mllib/sample_libsvm_data.txt");
Dataset<Row> data = getDummyData(spark, numRows, numFeatures,
numClasses);
Dataset<Row>[] splits = data.randomSplit(new double[]{trainFraction,
testFraction}, seed);
Dataset<Row> trainingData = splits[0];
Dataset<Row> testData = splits[1];
testData.cache();
List<Double> labels = getLabels(testData);
List<DenseVector> features = getFeatures(testData);
DecisionTreeClassifier classifier1 = new DecisionTreeClassifier();
DecisionTreeClassificationModel model1 = classifier1.fit(trainingData);
final DecisionTreeModel convertedModel1 =
convertDecisionTreeModel(model1, Algo.Classification());
RandomForestClassifier classifier = new RandomForestClassifier();
RandomForestClassificationModel model2 = classifier.fit(trainingData);
final RandomForestModel convertedModel2 =
convertRandomForestModel(model2);
LogisticRegression lr = new LogisticRegression();
LogisticRegressionModel model3 = lr.fit(trainingData);
final org.apache.spark.mllib.classification.LogisticRegressionModel
convertedModel3 = convertLogisticRegressionModel(model3);
System.out.println(
"****** DecisionTreeClassifier\n" +
"** Original **" + getInfo(model1, testData) + "\n" +
"** New **" + getInfo(new Predictor() {
double predict(Vector vector) {return
convertedModel1.predict(vector);}
}, labels, features) + "\n" +
"\n" +
"****** RandomForestClassifier\n" +
"** Original **" + getInfo(model2, testData) + "\n" +
"** New **" + getInfo(new Predictor() {double
predict(Vector vector) {return convertedModel2.predict(vector);}}, labels,
features) + "\n" +
"\n" +
"****** LogisticRegression\n" +
"** Original **" + getInfo(model3, testData) + "\n" +
"** New **" + getInfo(new Predictor() {double
predict(Vector vector) { return convertedModel3.predict(vector);}}, labels,
features) + "\n" +
"");
}
static Dataset<Row> getData(SparkSession spark, String format, String
location) {
return spark.read()
.format(format)
.load(location);
}
static Dataset<Row> getDummyData(SparkSession spark, int numberRows, int
numberFeatures, int labelUpperBound) {
StructType schema = new StructType(new StructField[]{
new StructField("label", DataTypes.DoubleType, false,
Metadata.empty()),
new StructField("features", new VectorUDT(), false,
Metadata.empty())
});
double[][] vectors = prepareData(numberRows, numberFeatures);
Random random = new Random(seed);
List<Row> dataTest = new ArrayList<>();
for (double[] vector : vectors) {
double label = (double) random.nextInt(2);
dataTest.add(RowFactory.create(label, Vectors.dense(vector)));
}
return spark.createDataFrame(dataTest, schema);
}
static double[][] prepareData(int numRows, int numFeatures) {
Random random = new Random(seed);
double[][] result = new double[numRows][numFeatures];
for (int row = 0; row < numRows; row++) {
for (int feature = 0; feature < numFeatures; feature++) {
result[row][feature] = random.nextDouble();
}
}
return result;
}
static String getInfo(Predictor predictor,
List<Double> labels,
List<DenseVector> features) {
Long startTime = System.currentTimeMillis();
List<Double> predictions = new ArrayList<>();
for (DenseVector feature : features) {
predictions.add(predictor.predict(feature));
}
return getInfo(startTime, labels, predictions);
}
static List<Double> getLabels(Dataset<Row> testData) {
List<Double> labels = new ArrayList<>();
List<DenseVector> vectors = new ArrayList<>();
for (Row row : testData.collectAsList()) {
vectors.add(new DenseVector(((org.apache.spark.ml.linalg.Vector)
row.get(1)).toArray()));
labels.add(row.getDouble(0));
}
return labels;
}
static List<DenseVector> getFeatures(Dataset<Row> testData) {
List<DenseVector> features = new ArrayList<>();
for (Row row : testData.collectAsList()) {
features.add(new DenseVector(((org.apache.spark.ml.linalg.Vector)
row.get(1)).toArray()));
}
return features;
}
static String getInfo(Transformer model, Dataset<Row> testData) {
Dataset<Row> predictions = model.transform(testData);
predictions.cache();
Dataset<Row> correctPredictions = predictions.filter("label ==
prediction");
correctPredictions.cache();
Dataset<Row> incorrectPredictions = predictions.filter("label !=
prediction");
incorrectPredictions.cache();
Long truePositives = correctPredictions.filter("prediction ==
1.0").count();
Long trueNegatives = correctPredictions.filter("prediction ==
0.0").count();
Long falsePositives = incorrectPredictions.filter("prediction ==
1.0").count();
Long falseNegatives = incorrectPredictions.filter("prediction ==
0.0").count();
return getInfo(null, truePositives, trueNegatives, falsePositives,
falseNegatives);
}
static String getInfo(Long startTime, List<Double> labels, List<Double>
predictions) {
Long endTime = System.currentTimeMillis();
if (labels.size() != predictions.size()) {
throw new RuntimeException("labels size is " + labels.size() +
" but predictions size is " + predictions.size());
}
Long truePositives = 0L;
Long trueNegatives = 0L;
Long falsePositives = 0L;
Long falseNegatives = 0L;
for (int i = 0; i < labels.size(); i++) {
double label = labels.get(i);
double prediction = predictions.get(i);
if (label == prediction) {
if (prediction == 1.0) {
truePositives += 1;
} else {
trueNegatives += 1;
}
} else {
if (prediction == 1.0) {
falsePositives += 1;
} else {
falseNegatives += 1;
}
}
}
return getInfo(endTime - startTime, truePositives, trueNegatives,
falsePositives, falseNegatives);
}
static double ratio(Long numerator, Long denominator) {
if (numerator == 0 || denominator == 0) {
return 0;
}
return ((double) numerator) / denominator;
}
static String getInfo(Long timeTakenMilliseconds, Long truePositives, Long
trueNegatives, Long falsePositives,
Long falseNegatives) {
Long testDataCount = truePositives + trueNegatives + falsePositives +
falseNegatives;
double accuracy = ratio(truePositives + trueNegatives, testDataCount);
double precision = ratio(truePositives, truePositives + falsePositives);
double recall = ratio(truePositives, truePositives + falseNegatives);
String last = "";
if (timeTakenMilliseconds != null) {
last = ", Average time taken (ms) " + ratio(timeTakenMilliseconds,
testDataCount);
}
return (
"true positives " + truePositives
+ ", true negatives " + trueNegatives
+ ", false positives " + falsePositives
+ ", false negatives " + falseNegatives
+ ", total " + testDataCount
+ "\n\t accuracy " + accuracy
+ ", precision " + precision
+ ", recall " + recall
+ last
);
}
static DecisionTreeModel
convertDecisionTreeModel(org.apache.spark.ml.tree.DecisionTreeModel model,
Enumeration.Value algo) {
return new DecisionTreeModel(model.rootNode().toOld(1), algo);
}
static RandomForestModel
convertRandomForestModel(org.apache.spark.ml.tree.TreeEnsembleModel model) {
Enumeration.Value algo;
if (model instanceof RandomForestRegressionModel) {
algo = Algo.Regression();
} else {
algo = Algo.Classification();
}
Object[] decisionTreeModels = model.trees();
DecisionTreeModel[] convertedDecisionTreeModels = new
DecisionTreeModel[decisionTreeModels.length];
for (int i = 0; i < decisionTreeModels.length; i++) {
org.apache.spark.ml.tree.DecisionTreeModel originalModel =
(org.apache.spark.ml.tree.DecisionTreeModel) decisionTreeModels[i];
DecisionTreeModel convertedModel =
convertDecisionTreeModel(originalModel, algo);
convertedDecisionTreeModels[i] = convertedModel;
}
RandomForestModel result = new RandomForestModel(algo,
convertedDecisionTreeModels);
return result;
}
static org.apache.spark.mllib.classification.LogisticRegressionModel
convertLogisticRegressionModel(LogisticRegressionModel model) {
org.apache.spark.mllib.classification.LogisticRegressionModel
convertedModel;
try {
convertedModel = new
org.apache.spark.mllib.classification.LogisticRegressionModel(
new DenseVector(model.coefficients().toArray()),
model.intercept(),
model.numFeatures(),
model.numClasses()
);
} catch (Exception e) {
//Should be SparkException but that does not compile.
// Raised when we have Multinomial Linear Regression
// Cannot check as the relevant variable is private
Vector coefficients = matrixToVector(model.coefficientMatrix());
for (double v : coefficients.toArray()) {
System.out.println(v);
}
System.out.println("**********");
for (double v : model.interceptVector().toDense().values()) {
System.out.println(v);
}
convertedModel = new
org.apache.spark.mllib.classification.LogisticRegressionModel(
coefficients,
model.interceptVector().toDense().values()[0], //TODO fix
this.
model.numFeatures(),
model.numClasses()
);
}
convertedModel.setThreshold(model.getThreshold());
return convertedModel;
}
static Vector matrixToVector(Matrix matrix) {
Vector result;
if (matrix instanceof DenseMatrix) {
result = new DenseVector(((DenseMatrix) matrix).values());
} else {
SparseMatrix _matrix = (SparseMatrix) matrix;
result = new org.apache.spark.mllib.linalg.SparseVector(
_matrix.numActives(),
_matrix.rowIndices(),
_matrix.values()
);
}
return result;
}
}
{noformat}
The output looks like the below. In the below the Original refers to ml package
version and New refers to mllib package version.
- I converted the mllib version Decision tree to ml version Decision tree. Gave
both versions same input and I received the exact same output.
- Then converted the mllib version Random Forest to ml version Random Forest
giving both the same underlying Decision trees (using the previoeus conversion
method). Gave both versions same input but I received different output.
{noformat}
****** DecisionTreeClassifier
** Original **true positives 8128, true negatives 1923, false positives 7942,
false negatives 1897, total 19890
accuracy 0.5053293112116641, precision 0.5057871810827629, recall
0.8107730673316709
** New **true positives 8128, true negatives 1923, false positives 7942,
false negatives 1897, total 19890
accuracy 0.5053293112116641, precision 0.5057871810827629, recall
0.8107730673316709, Average time taken (ms) 0.001558572146807441
****** RandomForestClassifier
** Original **true positives 3940, true negatives 5915, false positives 3950,
false negatives 6085, total 19890
accuracy 0.49547511312217196, precision 0.49936628643852976, recall
0.39301745635910224
** New **true positives 2461, true negatives 7350, false positives 2515,
false negatives 7564, total 19890
accuracy 0.4932629462041227, precision 0.4945739549839228, recall
0.2454862842892768, Average time taken (ms) 0.01085972850678733
****** LogisticRegression
** Original **true positives 6728, true negatives 3321, false positives 6544,
false negatives 3297, total 19890
accuracy 0.5052287581699346, precision 0.5069318866787221, recall
0.6711221945137157
** New **true positives 6728, true negatives 3321, false positives 6544,
false negatives 3297, total 19890
accuracy 0.5052287581699346, precision 0.5069318866787221, recall
0.6711221945137157, Average time taken (ms) 0.001558572146807441
{noformat}
> Inconsistent results between ml package RandomForestClassificationModel and
> mllib package RandomForestModel
> -----------------------------------------------------------------------------------------------------------
>
> Key: SPARK-19449
> URL: https://issues.apache.org/jira/browse/SPARK-19449
> Project: Spark
> Issue Type: Bug
> Components: ML, MLlib
> Affects Versions: 2.1.0
> Reporter: Aseem Bansal
>
> I worked on some code to convert ml package RandomForestClassificationModel
> to mllib package RandomForestModel. It was needed because we need to make
> predictions on the order of ms. I found that the results are inconsistent
> although the underlying DecisionTreeModel are exactly the same.
> The below code can be used to reproduce the issue. Can run this as a simple
> Java app as long as you have spark dependencies set up properly.
> {noformat}
> import org.apache.spark.ml.Transformer;
> import org.apache.spark.ml.classification.*;
> import org.apache.spark.ml.linalg.*;
> import org.apache.spark.ml.regression.RandomForestRegressionModel;
> import org.apache.spark.mllib.linalg.DenseVector;
> import org.apache.spark.mllib.linalg.Vector;
> import org.apache.spark.mllib.tree.configuration.Algo;
> import org.apache.spark.mllib.tree.model.DecisionTreeModel;
> import org.apache.spark.mllib.tree.model.RandomForestModel;
> import org.apache.spark.sql.Dataset;
> import org.apache.spark.sql.Row;
> import org.apache.spark.sql.RowFactory;
> import org.apache.spark.sql.SparkSession;
> import org.apache.spark.sql.types.DataTypes;
> import org.apache.spark.sql.types.Metadata;
> import org.apache.spark.sql.types.StructField;
> import org.apache.spark.sql.types.StructType;
> import scala.Enumeration;
> import java.util.ArrayList;
> import java.util.List;
> import java.util.Random;
> abstract class Predictor {
> abstract double predict(Vector vector);
> }
> public class MainConvertModels {
> public static final int seed = 42;
> public static void main(String[] args) {
> int numRows = 1000;
> int numFeatures = 3;
> int numClasses = 2;
> double trainFraction = 0.8;
> double testFraction = 0.2;
> SparkSession spark = SparkSession.builder()
> .appName("conversion app")
> .master("local")
> .getOrCreate();
> // Dataset<Row> data = getData(spark, "libsvm",
> "/opt/spark2/data/mllib/sample_libsvm_data.txt");
> Dataset<Row> data = getDummyData(spark, numRows, numFeatures,
> numClasses);
> Dataset<Row>[] splits = data.randomSplit(new double[]{trainFraction,
> testFraction}, seed);
> Dataset<Row> trainingData = splits[0];
> Dataset<Row> testData = splits[1];
> testData.cache();
> List<Double> labels = getLabels(testData);
> List<DenseVector> features = getFeatures(testData);
> DecisionTreeClassifier classifier1 = new DecisionTreeClassifier();
> DecisionTreeClassificationModel model1 =
> classifier1.fit(trainingData);
> final DecisionTreeModel convertedModel1 =
> convertDecisionTreeModel(model1, Algo.Classification());
> RandomForestClassifier classifier = new RandomForestClassifier();
> RandomForestClassificationModel model2 = classifier.fit(trainingData);
> final RandomForestModel convertedModel2 =
> convertRandomForestModel(model2);
> LogisticRegression lr = new LogisticRegression();
> LogisticRegressionModel model3 = lr.fit(trainingData);
> final org.apache.spark.mllib.classification.LogisticRegressionModel
> convertedModel3 = convertLogisticRegressionModel(model3);
> System.out.println(
> "****** DecisionTreeClassifier\n" +
> "** Original **" + getInfo(model1, testData) + "\n" +
> "** New **" + getInfo(new Predictor() {
> double predict(Vector vector) {return
> convertedModel1.predict(vector);}
> }, labels, features) + "\n" +
> "\n" +
> "****** RandomForestClassifier\n" +
> "** Original **" + getInfo(model2, testData) + "\n" +
> "** New **" + getInfo(new Predictor() {double
> predict(Vector vector) {return convertedModel2.predict(vector);}}, labels,
> features) + "\n" +
> "\n" +
> "****** LogisticRegression\n" +
> "** Original **" + getInfo(model3, testData) + "\n" +
> "** New **" + getInfo(new Predictor() {double
> predict(Vector vector) { return convertedModel3.predict(vector);}}, labels,
> features) + "\n" +
> "");
> }
> static Dataset<Row> getData(SparkSession spark, String format, String
> location) {
> return spark.read()
> .format(format)
> .load(location);
> }
> static Dataset<Row> getDummyData(SparkSession spark, int numberRows, int
> numberFeatures, int labelUpperBound) {
> StructType schema = new StructType(new StructField[]{
> new StructField("label", DataTypes.DoubleType, false,
> Metadata.empty()),
> new StructField("features", new VectorUDT(), false,
> Metadata.empty())
> });
> double[][] vectors = prepareData(numberRows, numberFeatures);
> Random random = new Random(seed);
> List<Row> dataTest = new ArrayList<>();
> for (double[] vector : vectors) {
> double label = (double) random.nextInt(2);
> dataTest.add(RowFactory.create(label, Vectors.dense(vector)));
> }
> return spark.createDataFrame(dataTest, schema);
> }
> static double[][] prepareData(int numRows, int numFeatures) {
> Random random = new Random(seed);
> double[][] result = new double[numRows][numFeatures];
> for (int row = 0; row < numRows; row++) {
> for (int feature = 0; feature < numFeatures; feature++) {
> result[row][feature] = random.nextDouble();
> }
> }
> return result;
> }
> static String getInfo(Predictor predictor,
> List<Double> labels,
> List<DenseVector> features) {
> Long startTime = System.currentTimeMillis();
> List<Double> predictions = new ArrayList<>();
> for (DenseVector feature : features) {
> predictions.add(predictor.predict(feature));
> }
> return getInfo(startTime, labels, predictions);
> }
> static List<Double> getLabels(Dataset<Row> testData) {
> List<Double> labels = new ArrayList<>();
> List<DenseVector> vectors = new ArrayList<>();
> for (Row row : testData.collectAsList()) {
> vectors.add(new DenseVector(((org.apache.spark.ml.linalg.Vector)
> row.get(1)).toArray()));
> labels.add(row.getDouble(0));
> }
> return labels;
> }
> static List<DenseVector> getFeatures(Dataset<Row> testData) {
> List<DenseVector> features = new ArrayList<>();
> for (Row row : testData.collectAsList()) {
> features.add(new DenseVector(((org.apache.spark.ml.linalg.Vector)
> row.get(1)).toArray()));
> }
> return features;
> }
> static String getInfo(Transformer model, Dataset<Row> testData) {
> Dataset<Row> predictions = model.transform(testData);
> predictions.cache();
> Dataset<Row> correctPredictions = predictions.filter("label ==
> prediction");
> correctPredictions.cache();
> Dataset<Row> incorrectPredictions = predictions.filter("label !=
> prediction");
> incorrectPredictions.cache();
> Long truePositives = correctPredictions.filter("prediction ==
> 1.0").count();
> Long trueNegatives = correctPredictions.filter("prediction ==
> 0.0").count();
> Long falsePositives = incorrectPredictions.filter("prediction ==
> 1.0").count();
> Long falseNegatives = incorrectPredictions.filter("prediction ==
> 0.0").count();
> return getInfo(null, truePositives, trueNegatives, falsePositives,
> falseNegatives);
> }
> static String getInfo(Long startTime, List<Double> labels, List<Double>
> predictions) {
> Long endTime = System.currentTimeMillis();
> if (labels.size() != predictions.size()) {
> throw new RuntimeException("labels size is " + labels.size() +
> " but predictions size is " + predictions.size());
> }
> Long truePositives = 0L;
> Long trueNegatives = 0L;
> Long falsePositives = 0L;
> Long falseNegatives = 0L;
> for (int i = 0; i < labels.size(); i++) {
> double label = labels.get(i);
> double prediction = predictions.get(i);
> if (label == prediction) {
> if (prediction == 1.0) {
> truePositives += 1;
> } else {
> trueNegatives += 1;
> }
> } else {
> if (prediction == 1.0) {
> falsePositives += 1;
> } else {
> falseNegatives += 1;
> }
> }
> }
> return getInfo(endTime - startTime, truePositives, trueNegatives,
> falsePositives, falseNegatives);
> }
> static double ratio(Long numerator, Long denominator) {
> if (numerator == 0 || denominator == 0) {
> return 0;
> }
> return ((double) numerator) / denominator;
> }
> static String getInfo(Long timeTakenMilliseconds, Long truePositives,
> Long trueNegatives, Long falsePositives,
> Long falseNegatives) {
> Long testDataCount = truePositives + trueNegatives + falsePositives +
> falseNegatives;
> double accuracy = ratio(truePositives + trueNegatives, testDataCount);
> double precision = ratio(truePositives, truePositives +
> falsePositives);
> double recall = ratio(truePositives, truePositives + falseNegatives);
> String last = "";
> if (timeTakenMilliseconds != null) {
> last = ", Average time taken (ms) " +
> ratio(timeTakenMilliseconds, testDataCount);
> }
> return (
> "true positives " + truePositives
> + ", true negatives " + trueNegatives
> + ", false positives " + falsePositives
> + ", false negatives " + falseNegatives
> + ", total " + testDataCount
> + "\n\t accuracy " + accuracy
> + ", precision " + precision
> + ", recall " + recall
> + last
> );
> }
> static DecisionTreeModel
> convertDecisionTreeModel(org.apache.spark.ml.tree.DecisionTreeModel model,
> Enumeration.Value algo)
> {
> return new DecisionTreeModel(model.rootNode().toOld(1), algo);
> }
> static RandomForestModel
> convertRandomForestModel(org.apache.spark.ml.tree.TreeEnsembleModel model) {
> Enumeration.Value algo;
> if (model instanceof RandomForestRegressionModel) {
> algo = Algo.Regression();
> } else {
> algo = Algo.Classification();
> }
> Object[] decisionTreeModels = model.trees();
> DecisionTreeModel[] convertedDecisionTreeModels = new
> DecisionTreeModel[decisionTreeModels.length];
> for (int i = 0; i < decisionTreeModels.length; i++) {
> org.apache.spark.ml.tree.DecisionTreeModel originalModel =
> (org.apache.spark.ml.tree.DecisionTreeModel) decisionTreeModels[i];
> DecisionTreeModel convertedModel =
> convertDecisionTreeModel(originalModel, algo);
> convertedDecisionTreeModels[i] = convertedModel;
> }
> RandomForestModel result = new RandomForestModel(algo,
> convertedDecisionTreeModels);
> return result;
> }
> static org.apache.spark.mllib.classification.LogisticRegressionModel
> convertLogisticRegressionModel(LogisticRegressionModel model) {
> org.apache.spark.mllib.classification.LogisticRegressionModel
> convertedModel;
> try {
> convertedModel = new
> org.apache.spark.mllib.classification.LogisticRegressionModel(
> new DenseVector(model.coefficients().toArray()),
> model.intercept(),
> model.numFeatures(),
> model.numClasses()
> );
> } catch (Exception e) {
> //Should be SparkException but that does not compile.
> // Raised when we have Multinomial Linear Regression
> // Cannot check as the relevant variable is private
> Vector coefficients = matrixToVector(model.coefficientMatrix());
> for (double v : coefficients.toArray()) {
> System.out.println(v);
> }
> System.out.println("**********");
> for (double v : model.interceptVector().toDense().values()) {
> System.out.println(v);
> }
> convertedModel = new
> org.apache.spark.mllib.classification.LogisticRegressionModel(
> coefficients,
> model.interceptVector().toDense().values()[0], //TODO fix
> this.
> model.numFeatures(),
> model.numClasses()
> );
> }
> convertedModel.setThreshold(model.getThreshold());
> return convertedModel;
> }
> static Vector matrixToVector(Matrix matrix) {
> Vector result;
> if (matrix instanceof DenseMatrix) {
> result = new DenseVector(((DenseMatrix) matrix).values());
> } else {
> SparseMatrix _matrix = (SparseMatrix) matrix;
> result = new org.apache.spark.mllib.linalg.SparseVector(
> _matrix.numActives(),
> _matrix.rowIndices(),
> _matrix.values()
> );
> }
> return result;
> }
> }
> {noformat}
> The output looks like the below. In the below the Original refers to ml
> package version and New refers to mllib package version.
> - I converted the mllib version Decision tree to ml version Decision tree.
> Gave both versions same input and I received the exact same output.
> - Then converted the mllib version Random Forest to ml version Random Forest
> giving both the same underlying Decision trees (using the previoeus
> conversion method). Gave both versions same input but I received different
> output.
> {noformat}
> ****** DecisionTreeClassifier
> ** Original **true positives 8128, true negatives 1923, false positives 7942,
> false negatives 1897, total 19890
> accuracy 0.5053293112116641, precision 0.5057871810827629, recall
> 0.8107730673316709
> ** New **true positives 8128, true negatives 1923, false positives 7942,
> false negatives 1897, total 19890
> accuracy 0.5053293112116641, precision 0.5057871810827629, recall
> 0.8107730673316709, Average time taken (ms) 0.001558572146807441
> ****** RandomForestClassifier
> ** Original **true positives 3940, true negatives 5915, false positives 3950,
> false negatives 6085, total 19890
> accuracy 0.49547511312217196, precision 0.49936628643852976, recall
> 0.39301745635910224
> ** New **true positives 2461, true negatives 7350, false positives 2515,
> false negatives 7564, total 19890
> accuracy 0.4932629462041227, precision 0.4945739549839228, recall
> 0.2454862842892768, Average time taken (ms) 0.01085972850678733
> ****** LogisticRegression
> ** Original **true positives 6728, true negatives 3321, false positives 6544,
> false negatives 3297, total 19890
> accuracy 0.5052287581699346, precision 0.5069318866787221, recall
> 0.6711221945137157
> ** New **true positives 6728, true negatives 3321, false positives 6544,
> false negatives 3297, total 19890
> accuracy 0.5052287581699346, precision 0.5069318866787221, recall
> 0.6711221945137157, Average time taken (ms) 0.001558572146807441
> {noformat}
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