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Posted to reviews@spark.apache.org by sryza <gi...@git.apache.org> on 2015/04/14 01:50:48 UTC
[GitHub] spark pull request: SPARK-5888. [MLLIB]. Add OneHotEncoder as a Tr...
GitHub user sryza opened a pull request:
https://github.com/apache/spark/pull/5500
SPARK-5888. [MLLIB]. Add OneHotEncoder as a Transformer
This patch adds a one hot encoder for categorical features. Planning to add documentation and another test after getting feedback on the approach.
A couple choices made here:
* There's an `includeFirst` option which, if false, creates numCategories - 1 columns and, if true, creates numCategories columns. The default is true, which is the behavior in scikit-learn.
* The user is expected to pass a `Seq` of category names when instantiating a `OneHotEncoder`. These can be easily gotten from a `StringIndexer`. The names are used for the output column names, which take the form colName_categoryName.
You can merge this pull request into a Git repository by running:
$ git pull https://github.com/sryza/spark sandy-spark-5888
Alternatively you can review and apply these changes as the patch at:
https://github.com/apache/spark/pull/5500.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 #5500
----
commit 04590bc362d011cc92b7ca1e703c15e090805b71
Author: Sandy Ryza <sa...@cloudera.com>
Date: 2015-04-13T23:40:04Z
SPARK-5888. [MLLIB]. Add OneHotEncoder as a Transformer
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[GitHub] spark pull request: SPARK-5888. [MLLIB]. Add OneHotEncoder as a Tr...
Posted by sryza <gi...@git.apache.org>.
Github user sryza commented on the pull request:
https://github.com/apache/spark/pull/5500#issuecomment-97589096
Hey @mengxr this should be ready for review again.
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[GitHub] spark pull request: SPARK-5888. [MLLIB]. Add OneHotEncoder as a Tr...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the pull request:
https://github.com/apache/spark/pull/5500#issuecomment-95038494
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[GitHub] spark pull request: SPARK-5888. [MLLIB]. Add OneHotEncoder as a Tr...
Posted by mengxr <gi...@git.apache.org>.
Github user mengxr commented on a diff in the pull request:
https://github.com/apache/spark/pull/5500#discussion_r28827831
--- Diff: mllib/src/main/scala/org/apache/spark/ml/feature/OneHotEncoder.scala ---
@@ -0,0 +1,109 @@
+/*
+ * 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.ml.feature
+
+import org.apache.spark.annotation.AlphaComponent
+import org.apache.spark.ml.UnaryTransformer
+import org.apache.spark.ml.attribute.NominalAttribute
+import org.apache.spark.mllib.linalg.{Vector, Vectors, VectorUDT}
+import org.apache.spark.ml.param._
+import org.apache.spark.ml.param.shared.{HasInputCol, HasOutputCol}
+import org.apache.spark.ml.util.SchemaUtils
+import org.apache.spark.sql.types.{DataType, DoubleType, StructType}
+
+/**
+ * A one-hot encoder that maps a column of label indices to a column of binary vectors, with
+ * at most a single one-value. By default, the binary vector has an element for each category, so
+ * with 5 categories, an input value of 2.0 would map to an output vector of
+ * (0.0, 0.0, 1.0, 0.0, 0.0). If includeFirst is set to false, the first category is omitted, so the
+ * output vector for the previous example would be (0.0, 1.0, 0.0, 0.0) and an input value
+ * of 0.0 would map to a vector of all zeros. Omitting the first category enables the vector
+ * columns to be independent.
+ */
+@AlphaComponent
+class OneHotEncoder extends UnaryTransformer[Double, Vector, OneHotEncoder]
+ with HasInputCol with HasOutputCol {
+
+ /**
+ * Whether to include a component in the encoded vectors for the first category, defaults to true.
+ * @group param
+ */
+ final val includeFirst: Param[Boolean] =
+ new Param[Boolean](this, "includeFirst", "include first category")
+ setDefault(includeFirst -> true)
+
+ /**
+ * The names of the categories. Used to identify them in the attributes of the output column.
+ * This is a required parameter.
+ * @group param
+ */
+ final val labelNames: Param[Array[String]] =
--- End diff --
Label names should be extracted from the metadata, e.g., generated by `StringIndexer`.
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[GitHub] spark pull request: SPARK-5888. [MLLIB]. Add OneHotEncoder as a Tr...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the pull request:
https://github.com/apache/spark/pull/5500#issuecomment-92553426
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[GitHub] spark pull request: SPARK-5888. [MLLIB]. Add OneHotEncoder as a Tr...
Posted by mengxr <gi...@git.apache.org>.
Github user mengxr commented on a diff in the pull request:
https://github.com/apache/spark/pull/5500#discussion_r28827821
--- Diff: mllib/src/main/scala/org/apache/spark/ml/feature/OneHotEncoder.scala ---
@@ -0,0 +1,109 @@
+/*
+ * 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.ml.feature
+
+import org.apache.spark.annotation.AlphaComponent
+import org.apache.spark.ml.UnaryTransformer
+import org.apache.spark.ml.attribute.NominalAttribute
+import org.apache.spark.mllib.linalg.{Vector, Vectors, VectorUDT}
+import org.apache.spark.ml.param._
+import org.apache.spark.ml.param.shared.{HasInputCol, HasOutputCol}
+import org.apache.spark.ml.util.SchemaUtils
+import org.apache.spark.sql.types.{DataType, DoubleType, StructType}
+
+/**
+ * A one-hot encoder that maps a column of label indices to a column of binary vectors, with
+ * at most a single one-value. By default, the binary vector has an element for each category, so
+ * with 5 categories, an input value of 2.0 would map to an output vector of
+ * (0.0, 0.0, 1.0, 0.0, 0.0). If includeFirst is set to false, the first category is omitted, so the
+ * output vector for the previous example would be (0.0, 1.0, 0.0, 0.0) and an input value
+ * of 0.0 would map to a vector of all zeros. Omitting the first category enables the vector
+ * columns to be independent.
--- End diff --
Without the first category the rest could be still dependent. We should say "Including the first category would make the vector columns linearly dependent because they sum up to one."
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[GitHub] spark pull request: SPARK-5888. [MLLIB]. Add OneHotEncoder as a Tr...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the pull request:
https://github.com/apache/spark/pull/5500#issuecomment-92539907
[Test build #30206 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/30206/consoleFull) for PR 5500 at commit [`04590bc`](https://github.com/apache/spark/commit/04590bc362d011cc92b7ca1e703c15e090805b71).
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[GitHub] spark pull request: SPARK-5888. [MLLIB]. Add OneHotEncoder as a Tr...
Posted by mengxr <gi...@git.apache.org>.
Github user mengxr commented on a diff in the pull request:
https://github.com/apache/spark/pull/5500#discussion_r28827864
--- Diff: mllib/src/test/scala/org/apache/spark/ml/feature/OneHotEncoderSuite.scala ---
@@ -0,0 +1,86 @@
+/*
+ * 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.ml.feature
+
+import org.apache.spark.ml.attribute.{NominalAttribute, Attribute}
+import org.apache.spark.mllib.linalg.Vector
+import org.apache.spark.mllib.util.MLlibTestSparkContext
+
+import org.apache.spark.sql.{DataFrame, SQLContext}
+
+import org.scalatest.FunSuite
--- End diff --
organize imports
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[GitHub] spark pull request: SPARK-5888. [MLLIB]. Add OneHotEncoder as a Tr...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the pull request:
https://github.com/apache/spark/pull/5500#issuecomment-96767787
[Test build #31010 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/31010/consoleFull) for PR 5500 at commit [`7e53579`](https://github.com/apache/spark/commit/7e535798306719352e65903da44d96aa31cb10e7).
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[GitHub] spark pull request: SPARK-5888. [MLLIB]. Add OneHotEncoder as a Tr...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the pull request:
https://github.com/apache/spark/pull/5500#issuecomment-95017876
[Test build #30725 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/30725/consoleFull) for PR 5500 at commit [`7e53579`](https://github.com/apache/spark/commit/7e535798306719352e65903da44d96aa31cb10e7).
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[GitHub] spark pull request: SPARK-5888. [MLLIB]. Add OneHotEncoder as a Tr...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the pull request:
https://github.com/apache/spark/pull/5500#issuecomment-93842807
[Test build #30436 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/30436/consoleFull) for PR 5500 at commit [`64da101`](https://github.com/apache/spark/commit/64da101d8fa1676a34ff4ebfb80e1597a3e688fe).
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[GitHub] spark pull request: SPARK-5888. [MLLIB]. Add OneHotEncoder as a Tr...
Posted by mengxr <gi...@git.apache.org>.
Github user mengxr commented on the pull request:
https://github.com/apache/spark/pull/5500#issuecomment-97593571
@sryza I think we can add label names later. For this PR, if the input column carries a nominal attribute with values, we can use it for names. Otherwise, we put no names in the output column.
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[GitHub] spark pull request: SPARK-5888. [MLLIB]. Add OneHotEncoder as a Tr...
Posted by sryza <gi...@git.apache.org>.
Github user sryza commented on the pull request:
https://github.com/apache/spark/pull/5500#issuecomment-93841917
Updated the patch conform to the approach described above.
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[GitHub] spark pull request: SPARK-5888. [MLLIB]. Add OneHotEncoder as a Tr...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the pull request:
https://github.com/apache/spark/pull/5500#issuecomment-95038490
[Test build #30725 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/30725/consoleFull) for PR 5500 at commit [`7e53579`](https://github.com/apache/spark/commit/7e535798306719352e65903da44d96aa31cb10e7).
* This patch **passes all tests**.
* This patch merges cleanly.
* This patch adds no public classes.
* This patch does not change any dependencies.
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[GitHub] spark pull request: SPARK-5888. [MLLIB]. Add OneHotEncoder as a Tr...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the pull request:
https://github.com/apache/spark/pull/5500#issuecomment-92553404
[Test build #30206 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/30206/consoleFull) for PR 5500 at commit [`04590bc`](https://github.com/apache/spark/commit/04590bc362d011cc92b7ca1e703c15e090805b71).
* This patch **passes all tests**.
* This patch merges cleanly.
* This patch adds the following public classes _(experimental)_:
* `class OneHotEncoder(labelNames: Seq[String], includeFirst: Boolean = true) extends Transformer`
* This patch does not change any dependencies.
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[GitHub] spark pull request: SPARK-5888. [MLLIB]. Add OneHotEncoder as a Tr...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the pull request:
https://github.com/apache/spark/pull/5500#issuecomment-93857048
[Test build #30436 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/30436/consoleFull) for PR 5500 at commit [`64da101`](https://github.com/apache/spark/commit/64da101d8fa1676a34ff4ebfb80e1597a3e688fe).
* This patch **passes all tests**.
* This patch merges cleanly.
* This patch adds no public classes.
* This patch does not change any dependencies.
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[GitHub] spark pull request: SPARK-5888. [MLLIB]. Add OneHotEncoder as a Tr...
Posted by mengxr <gi...@git.apache.org>.
Github user mengxr commented on the pull request:
https://github.com/apache/spark/pull/5500#issuecomment-93565804
@sryza Thanks for adding `OneHotEncoder` to `spark.ml`. One thing I want to discuss is the expected input of `OneHotEncoder`. There are two use cases:
1. input a string column and output a vector column with binary values
2. input a column with category indices and output a vector column with binary values
The input to 2) would be the output from `StringIndexer` we recently merged. I would call 1) `OneHotEncoder`, which is a `UnaryTransformer`, and 2) `StringVectorizer`, which is a combination of `StringIndexer` and `OneHotEncoder`. If both of us agree on the semantics, we can implement 1) as OneHotEncoder in this PR and add `StringVectorizer` in another PR. Does it sound good to you?
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[GitHub] spark pull request: SPARK-5888. [MLLIB]. Add OneHotEncoder as a Tr...
Posted by mengxr <gi...@git.apache.org>.
Github user mengxr commented on a diff in the pull request:
https://github.com/apache/spark/pull/5500#discussion_r28460811
--- Diff: mllib/src/main/scala/org/apache/spark/ml/feature/OneHotEncoder.scala ---
@@ -0,0 +1,66 @@
+/*
+ * 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.ml.feature
+
+import org.apache.spark.annotation.AlphaComponent
+import org.apache.spark.ml.Transformer
+import org.apache.spark.ml.attribute.NominalAttribute
+import org.apache.spark.ml.param._
+import org.apache.spark.sql.DataFrame
+import org.apache.spark.sql.functions._
+import org.apache.spark.sql.types.{StringType, StructType}
+
+@AlphaComponent
+class OneHotEncoder(labelNames: Seq[String], includeFirst: Boolean = true) extends Transformer
--- End diff --
Need JavaDoc. For pipeline components, we use default constructor and set parameter values in setters. Since OneHotEncoder is a unary transformer, you can extend `UnaryTransformer` directly and then overwrite `createTransformFunc`. Please check the implementation of `StringIndexer` and see how to define parameters and their default values.
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[GitHub] spark pull request: SPARK-5888. [MLLIB]. Add OneHotEncoder as a Tr...
Posted by mengxr <gi...@git.apache.org>.
Github user mengxr commented on a diff in the pull request:
https://github.com/apache/spark/pull/5500#discussion_r28827825
--- Diff: mllib/src/main/scala/org/apache/spark/ml/feature/OneHotEncoder.scala ---
@@ -0,0 +1,109 @@
+/*
+ * 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.ml.feature
+
+import org.apache.spark.annotation.AlphaComponent
+import org.apache.spark.ml.UnaryTransformer
+import org.apache.spark.ml.attribute.NominalAttribute
+import org.apache.spark.mllib.linalg.{Vector, Vectors, VectorUDT}
+import org.apache.spark.ml.param._
+import org.apache.spark.ml.param.shared.{HasInputCol, HasOutputCol}
+import org.apache.spark.ml.util.SchemaUtils
+import org.apache.spark.sql.types.{DataType, DoubleType, StructType}
+
+/**
+ * A one-hot encoder that maps a column of label indices to a column of binary vectors, with
+ * at most a single one-value. By default, the binary vector has an element for each category, so
+ * with 5 categories, an input value of 2.0 would map to an output vector of
+ * (0.0, 0.0, 1.0, 0.0, 0.0). If includeFirst is set to false, the first category is omitted, so the
+ * output vector for the previous example would be (0.0, 1.0, 0.0, 0.0) and an input value
+ * of 0.0 would map to a vector of all zeros. Omitting the first category enables the vector
+ * columns to be independent.
+ */
+@AlphaComponent
+class OneHotEncoder extends UnaryTransformer[Double, Vector, OneHotEncoder]
+ with HasInputCol with HasOutputCol {
+
+ /**
+ * Whether to include a component in the encoded vectors for the first category, defaults to true.
+ * @group param
+ */
+ final val includeFirst: Param[Boolean] =
--- End diff --
Use `BooleanParam` instead of `Param[Boolean]` for Java API compatibility.
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[GitHub] spark pull request: SPARK-5888. [MLLIB]. Add OneHotEncoder as a Tr...
Posted by sryza <gi...@git.apache.org>.
Github user sryza commented on the pull request:
https://github.com/apache/spark/pull/5500#issuecomment-93802687
@mengxr that makes sense to me, but did you mean to switch 1 and 2? I.e. in this PR we should implement `OneHotEncoder`, which takes an input column with category indices and outputs a vector column, and in a later PR we can implement `StringVectorizer` which chains `StringIndexer` with `OneHotEncoder`.
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[GitHub] spark pull request: SPARK-5888. [MLLIB]. Add OneHotEncoder as a Tr...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the pull request:
https://github.com/apache/spark/pull/5500#issuecomment-93857058
Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/SparkPullRequestBuilder/30436/
Test PASSed.
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