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Posted to reviews@spark.apache.org by zhengruifeng <gi...@git.apache.org> on 2017/02/23 06:49:05 UTC
[GitHub] spark pull request #17034: [SPARK-19704][ML] AFTSurvivalRegression should su...
GitHub user zhengruifeng opened a pull request:
https://github.com/apache/spark/pull/17034
[SPARK-19704][ML] AFTSurvivalRegression should support numeric censorCol
## What changes were proposed in this pull request?
make `AFTSurvivalRegression` support numeric censorCol
## How was this patch tested?
existing tests and added tests
You can merge this pull request into a Git repository by running:
$ git pull https://github.com/zhengruifeng/spark aft_numeric_censor
Alternatively you can review and apply these changes as the patch at:
https://github.com/apache/spark/pull/17034.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 #17034
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[GitHub] spark pull request #17034: [SPARK-19704][ML] AFTSurvivalRegression should su...
Posted by zhengruifeng <gi...@git.apache.org>.
Github user zhengruifeng commented on a diff in the pull request:
https://github.com/apache/spark/pull/17034#discussion_r103858261
--- Diff: mllib/src/test/scala/org/apache/spark/ml/regression/AFTSurvivalRegressionSuite.scala ---
@@ -27,6 +27,8 @@ import org.apache.spark.ml.util.TestingUtils._
import org.apache.spark.mllib.random.{ExponentialGenerator, WeibullGenerator}
import org.apache.spark.mllib.util.MLlibTestSparkContext
import org.apache.spark.sql.{DataFrame, Row}
+import org.apache.spark.sql.functions._
+import org.apache.spark.sql.types._
--- End diff --
Yes, I will update this. Thanks for your reviewing!
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[GitHub] spark issue #17034: [SPARK-19704][ML] AFTSurvivalRegression should support n...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/17034
**[Test build #73330 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/73330/testReport)** for PR 17034 at commit [`fd59ca9`](https://github.com/apache/spark/commit/fd59ca90422300f0d2e54bc809555c54edb43af8).
* This patch passes all tests.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark pull request #17034: [SPARK-19704][ML] AFTSurvivalRegression should su...
Posted by MLnick <gi...@git.apache.org>.
Github user MLnick commented on a diff in the pull request:
https://github.com/apache/spark/pull/17034#discussion_r102727229
--- Diff: mllib/src/test/scala/org/apache/spark/ml/regression/AFTSurvivalRegressionSuite.scala ---
@@ -361,6 +363,36 @@ class AFTSurvivalRegressionSuite
}
}
+ test("should support all NumericType censors, and not support other types") {
+ val df = spark.createDataFrame(Seq(
+ (0, Vectors.dense(0)),
+ (1, Vectors.dense(1)),
+ (2, Vectors.dense(2)),
+ (3, Vectors.dense(3)),
+ (4, Vectors.dense(4))
+ )).toDF("label", "features")
+ .withColumn("censor", lit(0.0))
+ val aft = new AFTSurvivalRegression().setMaxIter(1)
+ val expected = aft.fit(df)
+
+ val types = Seq(ShortType, LongType, IntegerType, FloatType, ByteType, DecimalType(10, 0))
+ types.foreach { t =>
+ val actual = aft.fit(df.select(col("label"), col("features"),
+ col("censor").cast(t)))
+ assert(expected.intercept === actual.intercept)
+ assert(expected.coefficients === actual.coefficients)
+ }
+
+ val dfWithStringCensors = spark.createDataFrame(Seq(
--- End diff --
Technically I guess this could be part of `checkNumericTypes` similar to checking weight and label cols, but since it is specific to AFT this is ok.
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[GitHub] spark issue #17034: [SPARK-19704][ML] AFTSurvivalRegression should support n...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/17034
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[GitHub] spark issue #17034: [SPARK-19704][ML] AFTSurvivalRegression should support n...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/17034
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[GitHub] spark issue #17034: [SPARK-19704][ML] AFTSurvivalRegression should support n...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/17034
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Posted by AmplabJenkins <gi...@git.apache.org>.
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https://github.com/apache/spark/pull/17034
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[GitHub] spark issue #17034: [SPARK-19704][ML] AFTSurvivalRegression should support n...
Posted by AmplabJenkins <gi...@git.apache.org>.
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[GitHub] spark pull request #17034: [SPARK-19704][ML] AFTSurvivalRegression should su...
Posted by MLnick <gi...@git.apache.org>.
Github user MLnick commented on a diff in the pull request:
https://github.com/apache/spark/pull/17034#discussion_r103864147
--- Diff: mllib/src/test/scala/org/apache/spark/ml/regression/AFTSurvivalRegressionSuite.scala ---
@@ -27,6 +27,9 @@ import org.apache.spark.ml.util.TestingUtils._
import org.apache.spark.mllib.random.{ExponentialGenerator, WeibullGenerator}
import org.apache.spark.mllib.util.MLlibTestSparkContext
import org.apache.spark.sql.{DataFrame, Row}
+import org.apache.spark.sql.functions.{col, lit}
+import org.apache.spark.sql.types.{ByteType, DecimalType, FloatType, IntegerType, LongType,
+ ShortType}
--- End diff --
The style rule is generally to use `_` when you're importing >= 5 things. You can revert it back, thanks!
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[GitHub] spark pull request #17034: [SPARK-19704][ML] AFTSurvivalRegression should su...
Posted by zhengruifeng <gi...@git.apache.org>.
Github user zhengruifeng commented on a diff in the pull request:
https://github.com/apache/spark/pull/17034#discussion_r103858210
--- Diff: mllib/src/test/scala/org/apache/spark/ml/regression/AFTSurvivalRegressionSuite.scala ---
@@ -361,6 +363,36 @@ class AFTSurvivalRegressionSuite
}
}
+ test("should support all NumericType censors, and not support other types") {
+ val df = spark.createDataFrame(Seq(
+ (0, Vectors.dense(0)),
+ (1, Vectors.dense(1)),
+ (2, Vectors.dense(2)),
+ (3, Vectors.dense(3)),
+ (4, Vectors.dense(4))
+ )).toDF("label", "features")
+ .withColumn("censor", lit(0.0))
+ val aft = new AFTSurvivalRegression().setMaxIter(1)
+ val expected = aft.fit(df)
+
+ val types = Seq(ShortType, LongType, IntegerType, FloatType, ByteType, DecimalType(10, 0))
+ types.foreach { t =>
+ val actual = aft.fit(df.select(col("label"), col("features"),
+ col("censor").cast(t)))
+ assert(expected.intercept === actual.intercept)
+ assert(expected.coefficients === actual.coefficients)
+ }
+
+ val dfWithStringCensors = spark.createDataFrame(Seq(
+ (0, Vectors.dense(0, 2, 3), "0")
+ )).toDF("label", "features", "censor")
+ val thrown = intercept[IllegalArgumentException] {
--- End diff --
This place follows the implementation in `MLTestingUtils.checkNumericTypes`, so I prefer not to change this.
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[GitHub] spark pull request #17034: [SPARK-19704][ML] AFTSurvivalRegression should su...
Posted by asfgit <gi...@git.apache.org>.
Github user asfgit closed the pull request at:
https://github.com/apache/spark/pull/17034
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[GitHub] spark issue #17034: [SPARK-19704][ML] AFTSurvivalRegression should support n...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/17034
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[GitHub] spark issue #17034: [SPARK-19704][ML] AFTSurvivalRegression should support n...
Posted by imatiach-msft <gi...@git.apache.org>.
Github user imatiach-msft commented on the issue:
https://github.com/apache/spark/pull/17034
great fix, LGTM! I added minor comments.
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[GitHub] spark issue #17034: [SPARK-19704][ML] AFTSurvivalRegression should support n...
Posted by MLnick <gi...@git.apache.org>.
Github user MLnick commented on the issue:
https://github.com/apache/spark/pull/17034
As commented we could I guess try to fit in the additional tests into `checkNumericTypes` - but it's specific to AFT so doesn't seem worth it for now.
So, this LGTM.
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[GitHub] spark issue #17034: [SPARK-19704][ML] AFTSurvivalRegression should support n...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/17034
**[Test build #73330 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/73330/testReport)** for PR 17034 at commit [`fd59ca9`](https://github.com/apache/spark/commit/fd59ca90422300f0d2e54bc809555c54edb43af8).
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[GitHub] spark issue #17034: [SPARK-19704][ML] AFTSurvivalRegression should support n...
Posted by zhengruifeng <gi...@git.apache.org>.
Github user zhengruifeng commented on the issue:
https://github.com/apache/spark/pull/17034
Jenkins, retest this please
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[GitHub] spark pull request #17034: [SPARK-19704][ML] AFTSurvivalRegression should su...
Posted by imatiach-msft <gi...@git.apache.org>.
Github user imatiach-msft commented on a diff in the pull request:
https://github.com/apache/spark/pull/17034#discussion_r103853075
--- Diff: mllib/src/test/scala/org/apache/spark/ml/regression/AFTSurvivalRegressionSuite.scala ---
@@ -361,6 +363,36 @@ class AFTSurvivalRegressionSuite
}
}
+ test("should support all NumericType censors, and not support other types") {
+ val df = spark.createDataFrame(Seq(
+ (0, Vectors.dense(0)),
+ (1, Vectors.dense(1)),
+ (2, Vectors.dense(2)),
+ (3, Vectors.dense(3)),
+ (4, Vectors.dense(4))
+ )).toDF("label", "features")
+ .withColumn("censor", lit(0.0))
+ val aft = new AFTSurvivalRegression().setMaxIter(1)
+ val expected = aft.fit(df)
+
+ val types = Seq(ShortType, LongType, IntegerType, FloatType, ByteType, DecimalType(10, 0))
+ types.foreach { t =>
+ val actual = aft.fit(df.select(col("label"), col("features"),
+ col("censor").cast(t)))
+ assert(expected.intercept === actual.intercept)
+ assert(expected.coefficients === actual.coefficients)
+ }
+
+ val dfWithStringCensors = spark.createDataFrame(Seq(
+ (0, Vectors.dense(0, 2, 3), "0")
+ )).toDF("label", "features", "censor")
+ val thrown = intercept[IllegalArgumentException] {
--- End diff --
can you wrap this in a withClue("Column censor must be of type NumericType but was actually of type StringType") {
...
}
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[GitHub] spark issue #17034: [SPARK-19704][ML] AFTSurvivalRegression should support n...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/17034
**[Test build #73743 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/73743/testReport)** for PR 17034 at commit [`31293b2`](https://github.com/apache/spark/commit/31293b2dc9483b8bcf7639420a23fc4f2b219598).
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[GitHub] spark issue #17034: [SPARK-19704][ML] AFTSurvivalRegression should support n...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/17034
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[GitHub] spark issue #17034: [SPARK-19704][ML] AFTSurvivalRegression should support n...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/17034
**[Test build #73731 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/73731/testReport)** for PR 17034 at commit [`0185b45`](https://github.com/apache/spark/commit/0185b454aaa043406c39d1e8f19c98d3d345a836).
* This patch passes all tests.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark issue #17034: [SPARK-19704][ML] AFTSurvivalRegression should support n...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/17034
**[Test build #73738 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/73738/testReport)** for PR 17034 at commit [`31293b2`](https://github.com/apache/spark/commit/31293b2dc9483b8bcf7639420a23fc4f2b219598).
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[GitHub] spark issue #17034: [SPARK-19704][ML] AFTSurvivalRegression should support n...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/17034
**[Test build #73731 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/73731/testReport)** for PR 17034 at commit [`0185b45`](https://github.com/apache/spark/commit/0185b454aaa043406c39d1e8f19c98d3d345a836).
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[GitHub] spark issue #17034: [SPARK-19704][ML] AFTSurvivalRegression should support n...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/17034
**[Test build #73743 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/73743/testReport)** for PR 17034 at commit [`31293b2`](https://github.com/apache/spark/commit/31293b2dc9483b8bcf7639420a23fc4f2b219598).
* This patch passes all tests.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark issue #17034: [SPARK-19704][ML] AFTSurvivalRegression should support n...
Posted by MLnick <gi...@git.apache.org>.
Github user MLnick commented on the issue:
https://github.com/apache/spark/pull/17034
Thanks! Merged to master.
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[GitHub] spark issue #17034: [SPARK-19704][ML] AFTSurvivalRegression should support n...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/17034
Test PASSed.
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[GitHub] spark pull request #17034: [SPARK-19704][ML] AFTSurvivalRegression should su...
Posted by imatiach-msft <gi...@git.apache.org>.
Github user imatiach-msft commented on a diff in the pull request:
https://github.com/apache/spark/pull/17034#discussion_r103853263
--- Diff: mllib/src/test/scala/org/apache/spark/ml/regression/AFTSurvivalRegressionSuite.scala ---
@@ -27,6 +27,8 @@ import org.apache.spark.ml.util.TestingUtils._
import org.apache.spark.mllib.random.{ExponentialGenerator, WeibullGenerator}
import org.apache.spark.mllib.util.MLlibTestSparkContext
import org.apache.spark.sql.{DataFrame, Row}
+import org.apache.spark.sql.functions._
+import org.apache.spark.sql.types._
--- End diff --
I think it is discouraged for readability reasons to use _, consider specifying the list of types here
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