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[jvm-packages] Create demo and test for xgboost4j early stopping. (#7252)

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Jiaming Yuan 2021-09-25 03:29:27 +08:00 committed by GitHub
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5 changed files with 103 additions and 9 deletions
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10
doc/jvm/xgboost4j_spark_tutorial.rst
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@ -162,17 +162,17 @@ Example of setting a missing value (e.g. -999) to the "missing" parameter in XGB
doing this with missing values encoded as NaN, you will want to set ``setHandleInvalid = "keep"`` on VectorAssembler
in order to keep the NaN values in the dataset. You would then set the "missing" parameter to whatever you want to be
treated as missing. However this may cause a large amount of memory use if your dataset is very sparse. For example:
.. code-block:: scala
val assembler = new VectorAssembler().setInputCols(feature_names.toArray).setOutputCol("features").setHandleInvalid("keep")
// conversion to dense vector using Array()
val featurePipeline = new Pipeline().setStages(Array(assembler))
val featureModel = featurePipeline.fit(df_training)
val featureDf = featureModel.transform(df_training)
val xgbParam = Map("eta" -> 0.1f,
"max_depth" -> 2,
"objective" -> "multi:softprob",
@ -181,10 +181,10 @@ Example of setting a missing value (e.g. -999) to the "missing" parameter in XGB
"num_workers" -> 2,
"allow_non_zero_for_missing" -> "true",
"missing" -> -999)
val xgb = new XGBoostClassifier(xgbParam)
val xgbclassifier = xgb.fit(featureDf)
2. Before calling VectorAssembler you can transform the values you want to represent missing into an irregular value
that is not 0, NaN, or Null and set the "missing" parameter to 0. The irregular value should ideally be chosen to be

1
jvm-packages/xgboost4j-example/README.md
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@ -10,6 +10,7 @@ XGBoost4J Code Examples
* [Cross validation](src/main/java/ml/dmlc/xgboost4j/java/example/CrossValidation.java)
* [Predicting leaf indices](src/main/java/ml/dmlc/xgboost4j/java/example/PredictLeafIndices.java)
* [External Memory](src/main/java/ml/dmlc/xgboost4j/java/example/ExternalMemory.java)
* [Early Stopping](src/main/java/ml/dmlc/xgboost4j/java/example/EarlyStopping.java)
## Scala API

4
jvm-packages/xgboost4j-example/src/main/java/ml/dmlc/xgboost4j/java/example/BasicWalkThrough.java
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@ -1,5 +1,5 @@
/*
Copyright (c) 2014 by Contributors
Copyright (c) 2014-2021 by Contributors
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
@ -115,7 +115,7 @@ public class BasicWalkThrough {
DataLoader.CSRSparseData spData = DataLoader.loadSVMFile("../../demo/data/agaricus.txt.train");
DMatrix trainMat2 = new DMatrix(spData.rowHeaders, spData.colIndex, spData.data,
DMatrix.SparseType.CSR);
DMatrix.SparseType.CSR, 127);
trainMat2.setLabel(spData.labels);
//specify watchList

67
jvm-packages/xgboost4j-example/src/main/java/ml/dmlc/xgboost4j/java/example/EarlyStopping.java Normal file
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@ -0,0 +1,67 @@
/*
Copyright (c) 2021 by Contributors
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://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.
*/
package ml.dmlc.xgboost4j.java.example;
import java.io.IOException;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.Map;
import ml.dmlc.xgboost4j.java.Booster;
import ml.dmlc.xgboost4j.java.DMatrix;
import ml.dmlc.xgboost4j.java.XGBoost;
import ml.dmlc.xgboost4j.java.XGBoostError;
import ml.dmlc.xgboost4j.java.example.util.DataLoader;
public class EarlyStopping {
public static void main(String[] args) throws IOException, XGBoostError {
DataLoader.CSRSparseData trainCSR =
DataLoader.loadSVMFile("../../demo/data/agaricus.txt.train");
DataLoader.CSRSparseData testCSR =
DataLoader.loadSVMFile("../../demo/data/agaricus.txt.test");
Map<String, Object> paramMap = new HashMap<String, Object>() {
{
put("max_depth", 3);
put("objective", "binary:logistic");
put("maximize_evaluation_metrics", "false");
}
};
DMatrix trainXy = new DMatrix(trainCSR.rowHeaders, trainCSR.colIndex, trainCSR.data,
DMatrix.SparseType.CSR, 127);
trainXy.setLabel(trainCSR.labels);
DMatrix testXy = new DMatrix(testCSR.rowHeaders, testCSR.colIndex, testCSR.data,
DMatrix.SparseType.CSR, 127);
testXy.setLabel(testCSR.labels);
int nRounds = 128;
int nEarlyStoppingRounds = 4;
Map<String, DMatrix> watches = new LinkedHashMap<>();
watches.put("training", trainXy);
watches.put("test", testXy);
float[][] metrics = new float[watches.size()][nRounds];
Booster booster = XGBoost.train(trainXy, paramMap, nRounds,
watches, metrics, null, null, nEarlyStoppingRounds);
int bestIter = Integer.valueOf(booster.getAttr("best_iteration"));
float bestScore = Float.valueOf(booster.getAttr("best_score"));
System.out.printf("Best iter: %d, Best score: %f\n", bestIter, bestScore);
}
}

30
jvm-packages/xgboost4j/src/test/java/ml/dmlc/xgboost4j/java/BoosterImplTest.java
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@ -16,8 +16,6 @@
package ml.dmlc.xgboost4j.java;
import java.io.*;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.Arrays;
import java.util.HashMap;
import java.util.LinkedHashMap;
@ -347,6 +345,34 @@ public class BoosterImplTest {
}
}
@Test
public void testEarlyStoppingAttributes() throws XGBoostError, IOException {
DMatrix trainMat = new DMatrix(this.train_uri);
DMatrix testMat = new DMatrix(this.test_uri);
Map<String, Object> paramMap = new HashMap<String, Object>() {
{
put("max_depth", 3);
put("objective", "binary:logistic");
put("maximize_evaluation_metrics", "false");
}
};
Map<String, DMatrix> watches = new LinkedHashMap<>();
watches.put("training", trainMat);
watches.put("test", testMat);
int round = 30;
int earlyStoppingRound = 4;
float[][] metrics = new float[watches.size()][round];
Booster booster = XGBoost.train(trainMat, paramMap, round,
watches, metrics, null, null, earlyStoppingRound);
int bestIter = Integer.valueOf(booster.getAttr("best_iteration"));
float bestScore = Float.valueOf(booster.getAttr("best_score"));
TestCase.assertEquals(bestIter, round - 1);
TestCase.assertEquals(bestScore, metrics[watches.size() - 1][round - 1]);
}
private void testWithQuantileHisto(DMatrix trainingSet, Map<String, DMatrix> watches, int round,
Map<String, Object> paramMap, float threshold) throws XGBoostError {
float[][] metrics = new float[watches.size()][round];