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Posted to reviews@spark.apache.org by jkbradley <gi...@git.apache.org> on 2014/08/02 22:48:08 UTC
[GitHub] spark pull request: [SPARK-2197] [mllib] Java DecisionTree bug fix...
GitHub user jkbradley opened a pull request:
https://github.com/apache/spark/pull/1740
[SPARK-2197] [mllib] Java DecisionTree bug fix and easy-of-use
Bug fix: Before, when an RDD was created in Java and passed to DecisionTree.train(), the fake class tag caused problems.
* Fix: DecisionTree: Used new RDD.retag() method to allow passing RDDs from Java.
Other improvements to Decision Trees for easy-of-use with Java:
* impurity classes: Added instance() methods to help with Java interface.
* Strategy: Added Java-friendly constructor
** Note: I removed quantileCalculationStrategy from the Java-friendly constructor since (a) it is a special class and (b) there is only 1 option currently. I suspect we will redo the API before the other options are included.
CC: @mengxr
You can merge this pull request into a Git repository by running:
$ git pull https://github.com/jkbradley/spark dt-java-new
Alternatively you can review and apply these changes as the patch at:
https://github.com/apache/spark/pull/1740.patch
To close this pull request, make a commit to your master/trunk branch
with (at least) the following in the commit message:
This closes #1740
----
commit 225822fe38762596b8c917a867e5cdbb2d9b4b55
Author: Joseph K. Bradley <jo...@gmail.com>
Date: 2014-08-01T21:50:42Z
Bug: In DecisionTree, the method sequentialBinSearchForOrderedCategoricalFeatureInClassification() indexed bins from 0 to (math.pow(2, featureCategories.toInt - 1) - 1). This upper bound is the bound for unordered categorical features, not ordered ones. The upper bound should be the arity (i.e., max value) of the feature.
Added new test to DecisionTreeSuite to catch this: "regression stump with categorical variables of arity 2"
Bug fix: Modified upper bound discussed above.
Also: Small improvements to coding style in DecisionTree.
commit f1a8283c5cb6a497a9ac60c8ce1859dbe9a051b0
Author: Joseph K. Bradley <jo...@gmail.com>
Date: 2014-08-01T22:56:09Z
Added old JavaDecisionTreeSuite, to be updated later
commit 13a585e5b818735dfc6aa481547fc201ddfc1798
Author: Joseph K. Bradley <jo...@gmail.com>
Date: 2014-08-02T00:18:12Z
Merge remote-tracking branch 'upstream/master' into dt-java
commit 320853f464ca8658d7e28a9f39f288da33c88b23
Author: Joseph K. Bradley <jo...@gmail.com>
Date: 2014-08-02T00:40:53Z
Added JavaDecisionTreeSuite, partly written
commit d78ada636f490db6fb1e4a9f75af7f492c07f222
Author: Joseph K. Bradley <jo...@gmail.com>
Date: 2014-08-02T06:32:49Z
Merge remote-tracking branch 'upstream/master' into dt-java
commit f7b5ca1ed464de5d7d20f4c006621afa8d8b9e56
Author: Joseph K. Bradley <jo...@gmail.com>
Date: 2014-08-02T19:56:47Z
Improvements to make it easier to run DecisionTree from Java.
* DecisionTree: Used new RDD.retag() method to allow passing RDDs from Java.
* impurity classes: Added instance() methods to help with Java interface.
* Strategy: Added Java-friendly constructor
** Note: I removed quantileCalculationStrategy from the Java-friendly constructor since (a) it is a special class and (b) there is only 1 option currently. I suspect we will redo the API before the other options are included.
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[GitHub] spark pull request: [SPARK-2197] [mllib] Java DecisionTree bug fix...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the pull request:
https://github.com/apache/spark/pull/1740#issuecomment-50985488
QA results for PR 1740:<br>- This patch PASSES unit tests.<br>- This patch merges cleanly<br>- This patch adds no public classes<br><br>For more information see test ouptut:<br>https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/17811/consoleFull
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[GitHub] spark pull request: [SPARK-2197] [mllib] Java DecisionTree bug fix...
Posted by mengxr <gi...@git.apache.org>.
Github user mengxr commented on a diff in the pull request:
https://github.com/apache/spark/pull/1740#discussion_r15733162
--- Diff: mllib/src/main/scala/org/apache/spark/mllib/tree/configuration/Strategy.scala ---
@@ -60,4 +62,31 @@ class Strategy (
val isMulticlassWithCategoricalFeatures
= isMulticlassClassification && (categoricalFeaturesInfo.size > 0)
+ /**
+ * Java-friendly constructor.
+ *
+ * @param algo classification or regression
+ * @param impurity criterion used for information gain calculation
+ * @param maxDepth Maximum depth of the tree.
+ * E.g., depth 0 means 1 leaf node; depth 1 means 1 internal node + 2 leaf nodes.
+ * @param numClassesForClassification number of classes for classification. Default value is 2
+ * leads to binary classification
+ * @param maxBins maximum number of bins used for splitting features
+ * @param categoricalFeaturesInfo A map storing information about the categorical variables and
+ * the number of discrete values they take. For example, an entry
+ * (n -> k) implies the feature n is categorical with k categories
+ * 0, 1, 2, ... , k-1. It's important to note that features are
+ * zero-indexed.
+ */
+ def this(
+ algo: Algo,
+ impurity: Impurity,
+ maxDepth: Int,
+ numClassesForClassification: Int,
+ maxBins: Int,
+ categoricalFeaturesInfo: java.util.Map[java.lang.Integer, java.lang.Integer]) {
+ this(algo, impurity, maxDepth, numClassesForClassification, maxBins, Sort,
+ categoricalFeaturesInfo.map{ case (a, b) => (a.toInt, b.toInt) }.toMap)
--- End diff --
This seems to work:
~~~
import scala.collection.JavaConverters._
categoricalFeaturesInfo.asInstanceOf[java.util.Map[Int, Int]].asScala.toMap
~~~
`JavaConverters` is preferred because the conversion is explicit via `asScala`
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[GitHub] spark pull request: [SPARK-2197] [mllib] Java DecisionTree bug fix...
Posted by mengxr <gi...@git.apache.org>.
Github user mengxr commented on a diff in the pull request:
https://github.com/apache/spark/pull/1740#discussion_r15732025
--- Diff: mllib/src/main/scala/org/apache/spark/mllib/tree/configuration/Strategy.scala ---
@@ -60,4 +62,31 @@ class Strategy (
val isMulticlassWithCategoricalFeatures
= isMulticlassClassification && (categoricalFeaturesInfo.size > 0)
+ /**
+ * Java-friendly constructor.
+ *
+ * @param algo classification or regression
+ * @param impurity criterion used for information gain calculation
+ * @param maxDepth Maximum depth of the tree.
+ * E.g., depth 0 means 1 leaf node; depth 1 means 1 internal node + 2 leaf nodes.
+ * @param numClassesForClassification number of classes for classification. Default value is 2
+ * leads to binary classification
+ * @param maxBins maximum number of bins used for splitting features
+ * @param categoricalFeaturesInfo A map storing information about the categorical variables and
+ * the number of discrete values they take. For example, an entry
+ * (n -> k) implies the feature n is categorical with k categories
+ * 0, 1, 2, ... , k-1. It's important to note that features are
+ * zero-indexed.
+ */
+ def this(
+ algo: Algo,
+ impurity: Impurity,
+ maxDepth: Int,
+ numClassesForClassification: Int,
+ maxBins: Int,
+ categoricalFeaturesInfo: java.util.Map[java.lang.Integer, java.lang.Integer]) {
+ this(algo, impurity, maxDepth, numClassesForClassification, maxBins, Sort,
+ categoricalFeaturesInfo.map{ case (a, b) => (a.toInt, b.toInt) }.toMap)
--- End diff --
Could you try `categoricalFeatureInfo.asScala`?
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[GitHub] spark pull request: [SPARK-2197] [mllib] Java DecisionTree bug fix...
Posted by jkbradley <gi...@git.apache.org>.
Github user jkbradley commented on a diff in the pull request:
https://github.com/apache/spark/pull/1740#discussion_r15732689
--- Diff: mllib/src/main/scala/org/apache/spark/mllib/tree/configuration/Strategy.scala ---
@@ -60,4 +62,31 @@ class Strategy (
val isMulticlassWithCategoricalFeatures
= isMulticlassClassification && (categoricalFeaturesInfo.size > 0)
+ /**
+ * Java-friendly constructor.
+ *
+ * @param algo classification or regression
+ * @param impurity criterion used for information gain calculation
+ * @param maxDepth Maximum depth of the tree.
+ * E.g., depth 0 means 1 leaf node; depth 1 means 1 internal node + 2 leaf nodes.
+ * @param numClassesForClassification number of classes for classification. Default value is 2
+ * leads to binary classification
+ * @param maxBins maximum number of bins used for splitting features
+ * @param categoricalFeaturesInfo A map storing information about the categorical variables and
+ * the number of discrete values they take. For example, an entry
+ * (n -> k) implies the feature n is categorical with k categories
+ * 0, 1, 2, ... , k-1. It's important to note that features are
+ * zero-indexed.
+ */
+ def this(
+ algo: Algo,
+ impurity: Impurity,
+ maxDepth: Int,
+ numClassesForClassification: Int,
+ maxBins: Int,
+ categoricalFeaturesInfo: java.util.Map[java.lang.Integer, java.lang.Integer]) {
+ this(algo, impurity, maxDepth, numClassesForClassification, maxBins, Sort,
+ categoricalFeaturesInfo.map{ case (a, b) => (a.toInt, b.toInt) }.toMap)
--- End diff --
I tried using that, but could not figure out how to make it work. The issue is that the integer type used by the map is not converted properly. Is there a good way to do that?
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[GitHub] spark pull request: [SPARK-2197] [mllib] Java DecisionTree bug fix...
Posted by mengxr <gi...@git.apache.org>.
Github user mengxr commented on a diff in the pull request:
https://github.com/apache/spark/pull/1740#discussion_r15732026
--- Diff: mllib/src/main/scala/org/apache/spark/mllib/tree/configuration/Strategy.scala ---
@@ -17,6 +17,8 @@
package org.apache.spark.mllib.tree.configuration
+import scala.collection.JavaConversions._
--- End diff --
`JavaConversions` -> `JavaConverters`
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[GitHub] spark pull request: [SPARK-2197] [mllib] Java DecisionTree bug fix...
Posted by mengxr <gi...@git.apache.org>.
Github user mengxr commented on a diff in the pull request:
https://github.com/apache/spark/pull/1740#discussion_r15732032
--- Diff: mllib/src/test/java/org/apache/spark/mllib/tree/JavaDecisionTreeSuite.java ---
@@ -0,0 +1,110 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements. See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You 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 org.apache.spark.mllib.tree;
+
+import scala.Int;
+import scala.collection.immutable.Map;
+import scala.collection.JavaConverters.*;
+import scala.Predef;
+import scala.Tuple2;
+
+import org.apache.spark.api.java.JavaRDD;
+import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.mllib.regression.LabeledPoint;
+import org.apache.spark.mllib.tree.DecisionTree;
+import org.apache.spark.mllib.tree.configuration.Algo;
+import org.apache.spark.mllib.tree.configuration.QuantileStrategy;
+import org.apache.spark.mllib.tree.configuration.Strategy;
+import org.apache.spark.mllib.tree.impurity.Gini;
+import org.apache.spark.mllib.tree.impurity.Gini$;
+import org.apache.spark.mllib.tree.impurity.Impurity;
+import org.apache.spark.mllib.tree.model.DecisionTreeModel;
+import org.junit.After;
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.Test;
+
+import java.io.Serializable;
+import java.util.HashMap;
+import java.util.List;
--- End diff --
Please organize imports into groups in the following order:
1. java imports
2. scala imports
3. 3rd-party imports (junit here)
4. spark imports
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[GitHub] spark pull request: [SPARK-2197] [mllib] Java DecisionTree bug fix...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the pull request:
https://github.com/apache/spark/pull/1740#issuecomment-50984577
QA tests have started for PR 1740. This patch merges cleanly. <br>View progress: https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/17811/consoleFull
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[GitHub] spark pull request: [SPARK-2197] [mllib] Java DecisionTree bug fix...
Posted by mengxr <gi...@git.apache.org>.
Github user mengxr commented on the pull request:
https://github.com/apache/spark/pull/1740#issuecomment-50997066
LGTM. Merged into both master and branch-1.1. Thanks!!
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[GitHub] spark pull request: [SPARK-2197] [mllib] Java DecisionTree bug fix...
Posted by asfgit <gi...@git.apache.org>.
Github user asfgit closed the pull request at:
https://github.com/apache/spark/pull/1740
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[GitHub] spark pull request: [SPARK-2197] [mllib] Java DecisionTree bug fix...
Posted by jkbradley <gi...@git.apache.org>.
Github user jkbradley commented on a diff in the pull request:
https://github.com/apache/spark/pull/1740#discussion_r15733387
--- Diff: mllib/src/main/scala/org/apache/spark/mllib/tree/configuration/Strategy.scala ---
@@ -60,4 +62,31 @@ class Strategy (
val isMulticlassWithCategoricalFeatures
= isMulticlassClassification && (categoricalFeaturesInfo.size > 0)
+ /**
+ * Java-friendly constructor.
+ *
+ * @param algo classification or regression
+ * @param impurity criterion used for information gain calculation
+ * @param maxDepth Maximum depth of the tree.
+ * E.g., depth 0 means 1 leaf node; depth 1 means 1 internal node + 2 leaf nodes.
+ * @param numClassesForClassification number of classes for classification. Default value is 2
+ * leads to binary classification
+ * @param maxBins maximum number of bins used for splitting features
+ * @param categoricalFeaturesInfo A map storing information about the categorical variables and
+ * the number of discrete values they take. For example, an entry
+ * (n -> k) implies the feature n is categorical with k categories
+ * 0, 1, 2, ... , k-1. It's important to note that features are
+ * zero-indexed.
+ */
+ def this(
+ algo: Algo,
+ impurity: Impurity,
+ maxDepth: Int,
+ numClassesForClassification: Int,
+ maxBins: Int,
+ categoricalFeaturesInfo: java.util.Map[java.lang.Integer, java.lang.Integer]) {
+ this(algo, impurity, maxDepth, numClassesForClassification, maxBins, Sort,
+ categoricalFeaturesInfo.map{ case (a, b) => (a.toInt, b.toInt) }.toMap)
--- End diff --
It does; thanks!
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[GitHub] spark pull request: [SPARK-2197] [mllib] Java DecisionTree bug fix...
Posted by mengxr <gi...@git.apache.org>.
Github user mengxr commented on the pull request:
https://github.com/apache/spark/pull/1740#issuecomment-50977449
Thanks! This looks good to me except minor style issues.
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[GitHub] spark pull request: [SPARK-2197] [mllib] Java DecisionTree bug fix...
Posted by jkbradley <gi...@git.apache.org>.
Github user jkbradley commented on the pull request:
https://github.com/apache/spark/pull/1740#issuecomment-50980396
Thanks for the comments! I pushed the changes. The only remaining item is JavaConverters for Strategy; I'm not sure how to get it to work there.
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[GitHub] spark pull request: [SPARK-2197] [mllib] Java DecisionTree bug fix...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the pull request:
https://github.com/apache/spark/pull/1740#issuecomment-50974053
QA tests have started for PR 1740. This patch merges cleanly. <br>View progress: https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/17778/consoleFull
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[GitHub] spark pull request: [SPARK-2197] [mllib] Java DecisionTree bug fix...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the pull request:
https://github.com/apache/spark/pull/1740#issuecomment-50980415
QA tests have started for PR 1740. This patch merges cleanly. <br>View progress: https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/17797/consoleFull
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[GitHub] spark pull request: [SPARK-2197] [mllib] Java DecisionTree bug fix...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the pull request:
https://github.com/apache/spark/pull/1740#issuecomment-50981238
QA results for PR 1740:<br>- This patch PASSES unit tests.<br>- This patch merges cleanly<br>- This patch adds no public classes<br><br>For more information see test ouptut:<br>https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/17797/consoleFull
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[GitHub] spark pull request: [SPARK-2197] [mllib] Java DecisionTree bug fix...
Posted by mengxr <gi...@git.apache.org>.
Github user mengxr commented on a diff in the pull request:
https://github.com/apache/spark/pull/1740#discussion_r15732035
--- Diff: mllib/src/test/scala/org/apache/spark/mllib/tree/DecisionTreeSuite.scala ---
@@ -17,6 +17,8 @@
package org.apache.spark.mllib.tree
+import scala.collection.JavaConversions._
--- End diff --
ditto: use `JavaConverters`
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[GitHub] spark pull request: [SPARK-2197] [mllib] Java DecisionTree bug fix...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the pull request:
https://github.com/apache/spark/pull/1740#issuecomment-50975734
QA results for PR 1740:<br>- This patch PASSES unit tests.<br>- This patch merges cleanly<br>- This patch adds no public classes<br><br>For more information see test ouptut:<br>https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/17778/consoleFull
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