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Posted to reviews@spark.apache.org by zhengruifeng <gi...@git.apache.org> on 2016/03/30 16:12:57 UTC
[GitHub] spark pull request: [SPARK-14272][MLLIB] Evaluate GaussianMixtureM...
GitHub user zhengruifeng opened a pull request:
https://github.com/apache/spark/pull/12064
[SPARK-14272][MLLIB] Evaluate GaussianMixtureModel with LogLooklihood
## What changes were proposed in this pull request?
add public api to evaluate GaussianMixtureModel: computeLogLikelihood
## How was this patch tested?
manual tests
You can merge this pull request into a Git repository by running:
$ git pull https://github.com/zhengruifeng/spark gmm_metric
Alternatively you can review and apply these changes as the patch at:
https://github.com/apache/spark/pull/12064.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 #12064
----
commit 3284e06bafcb8d22732911402fa2d04e0aa3d085
Author: Zheng RuiFeng <ru...@foxmail.com>
Date: 2016-03-30T13:33:03Z
create gmm_metric
commit 5e2aff78df74ed50a57ac8130dd67761bcddb682
Author: Zheng RuiFeng <ru...@foxmail.com>
Date: 2016-03-30T14:09:11Z
update
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[GitHub] spark issue #12064: [SPARK-14272][ML] Evaluate GaussianMixtureModel with Log...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/12064
**[Test build #71500 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/71500/testReport)** for PR 12064 at commit [`d6fa8fa`](https://github.com/apache/spark/commit/d6fa8fa83ebfb3a77185da1c63991a778841e84b).
* This patch **fails PySpark unit tests**.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark issue #12064: [SPARK-14272][ML] Evaluate GaussianMixtureModel with Log...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/12064
**[Test build #71245 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/71245/testReport)** for PR 12064 at commit [`9af6c92`](https://github.com/apache/spark/commit/9af6c9235601ba50865fb7be10a3486bc0f32c50).
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[GitHub] spark issue #12064: [SPARK-14272][ML] Evaluate GaussianMixtureModel with Log...
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[GitHub] spark issue #12064: [SPARK-14272][ML] Add Loglikelihood in GaussianMixtureSu...
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[GitHub] spark issue #12064: [SPARK-14272][ML] Evaluate GaussianMixtureModel with Log...
Posted by zhengruifeng <gi...@git.apache.org>.
Github user zhengruifeng commented on the issue:
https://github.com/apache/spark/pull/12064
jenkins, retest this please
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[GitHub] spark issue #12064: [SPARK-14272][ML] Evaluate GaussianMixtureModel with Log...
Posted by zhengruifeng <gi...@git.apache.org>.
Github user zhengruifeng commented on the issue:
https://github.com/apache/spark/pull/12064
ping @yanboliang
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[GitHub] spark issue #12064: [SPARK-14272][ML] Evaluate GaussianMixtureModel with Log...
Posted by zhengruifeng <gi...@git.apache.org>.
Github user zhengruifeng commented on the issue:
https://github.com/apache/spark/pull/12064
@yanboliang Updated! Thanks for reviewing!
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https://github.com/apache/spark/pull/12064
**[Test build #71641 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/71641/testReport)** for PR 12064 at commit [`cbec946`](https://github.com/apache/spark/commit/cbec946583536283bf31dd5fb4f61b724e502e68).
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[GitHub] spark issue #12064: [SPARK-14272][ML] Evaluate GaussianMixtureModel with Log...
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https://github.com/apache/spark/pull/12064
**[Test build #71121 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/71121/testReport)** for PR 12064 at commit [`1856e59`](https://github.com/apache/spark/commit/1856e59d471e0989ae90557eaab35558619f1035).
* This patch passes all tests.
* This patch merges cleanly.
* This patch adds no public classes.
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**[Test build #66743 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/66743/consoleFull)** for PR 12064 at commit [`cbe92b6`](https://github.com/apache/spark/commit/cbe92b66c4108aca65ee7770066413a95072ee31).
* This patch passes all tests.
* This patch merges cleanly.
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**[Test build #71121 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/71121/testReport)** for PR 12064 at commit [`1856e59`](https://github.com/apache/spark/commit/1856e59d471e0989ae90557eaab35558619f1035).
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**[Test build #71550 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/71550/testReport)** for PR 12064 at commit [`fd85c5d`](https://github.com/apache/spark/commit/fd85c5d221a0cc52c8b5f4662182d487e34db63b).
* This patch **fails Spark unit tests**.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark pull request: [SPARK-14272][MLLIB] Evaluate GaussianMixtureM...
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**[Test build #54522 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/54522/consoleFull)** for PR 12064 at commit [`5e2aff7`](https://github.com/apache/spark/commit/5e2aff78df74ed50a57ac8130dd67761bcddb682).
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**[Test build #71432 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/71432/testReport)** for PR 12064 at commit [`68f72fa`](https://github.com/apache/spark/commit/68f72fa84afbe9381bebbb620c0ceda7e48dd36e).
* This patch **fails Scala style tests**.
* This patch merges cleanly.
* This patch adds no public classes.
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**[Test build #71245 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/71245/testReport)** for PR 12064 at commit [`9af6c92`](https://github.com/apache/spark/commit/9af6c9235601ba50865fb7be10a3486bc0f32c50).
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**[Test build #71550 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/71550/testReport)** for PR 12064 at commit [`fd85c5d`](https://github.com/apache/spark/commit/fd85c5d221a0cc52c8b5f4662182d487e34db63b).
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**[Test build #66739 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/66739/consoleFull)** for PR 12064 at commit [`29841d0`](https://github.com/apache/spark/commit/29841d0efe8d0541f4faa10b986257c564670462).
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[GitHub] spark pull request #12064: [SPARK-14272][ML] Evaluate GaussianMixtureModel w...
Posted by yanboliang <gi...@git.apache.org>.
Github user yanboliang commented on a diff in the pull request:
https://github.com/apache/spark/pull/12064#discussion_r96365726
--- Diff: python/pyspark/ml/clustering.py ---
@@ -281,6 +281,14 @@ def probability(self):
"""
return self._call_java("probability")
+ @property
+ @since("2.2.0")
+ def logLikelihood(self):
--- End diff --
Add this to doc test.
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ping @yanboliang
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Posted by yanboliang <gi...@git.apache.org>.
Github user yanboliang commented on a diff in the pull request:
https://github.com/apache/spark/pull/12064#discussion_r95537252
--- Diff: mllib/src/main/scala/org/apache/spark/ml/clustering/GaussianMixture.scala ---
@@ -130,6 +130,25 @@ class GaussianMixtureModel private[ml] (
}
/**
+ * Return the total log-likelihood for this model on the given data.
+ */
+ @Since("2.2.0")
+ def computeLogLikelihood(dataset: Dataset[_]): Double = {
--- End diff --
I have a question here, should we provide the final ```logLikelihood``` of the model in its summary as well? Since lots of users will use it to evaluate the current model, that they don't need to take another pass on data.
This will expose a public API, cc @jkbradley @sethah @srowen @MLnick to discuss the API.
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[GitHub] spark pull request #12064: [SPARK-14272][ML] Evaluate GaussianMixtureModel w...
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https://github.com/apache/spark/pull/12064#discussion_r95858775
--- Diff: mllib/src/main/scala/org/apache/spark/ml/clustering/GaussianMixture.scala ---
@@ -130,6 +130,25 @@ class GaussianMixtureModel private[ml] (
}
/**
+ * Return the total log-likelihood for this model on the given data.
+ */
+ @Since("2.2.0")
+ def computeLogLikelihood(dataset: Dataset[_]): Double = {
--- End diff --
+1 for putting it in the summary. If you want to evaluate a new dataset, then let's add an evaluate() method which returns a summary.
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[GitHub] spark issue #12064: [SPARK-14272][ML] Add Loglikelihood in GaussianMixtureSu...
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Jenkins, retest this please.
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[GitHub] spark issue #12064: [SPARK-14272][ML] Evaluate GaussianMixtureModel with Log...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/12064
**[Test build #71436 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/71436/testReport)** for PR 12064 at commit [`d333642`](https://github.com/apache/spark/commit/d3336429dfb6564f93ddaa615771882fc72eed58).
* This patch passes all tests.
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* This patch adds no public classes.
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[GitHub] spark issue #12064: [SPARK-14272][ML] Evaluate GaussianMixtureModel with Log...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/12064
**[Test build #71419 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/71419/testReport)** for PR 12064 at commit [`fe2c424`](https://github.com/apache/spark/commit/fe2c424a4aa08f5f50387069db26f179e50395d4).
* This patch **fails MiMa tests**.
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[GitHub] spark pull request #12064: [SPARK-14272][ML] Add Loglikelihood in GaussianMi...
Posted by asfgit <gi...@git.apache.org>.
Github user asfgit closed the pull request at:
https://github.com/apache/spark/pull/12064
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[GitHub] spark issue #12064: [SPARK-14272][ML] Evaluate GaussianMixtureModel with Log...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/12064
**[Test build #71598 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/71598/testReport)** for PR 12064 at commit [`eb27bcc`](https://github.com/apache/spark/commit/eb27bcc9c571cda08303a65b65c2d3d947e900ac).
* This patch passes all tests.
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[GitHub] spark issue #12064: [SPARK-14272][ML] Add Loglikelihood in GaussianMixtureSu...
Posted by AmplabJenkins <gi...@git.apache.org>.
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[GitHub] spark issue #12064: [SPARK-14272][ML] Add Loglikelihood in GaussianMixtureSu...
Posted by yanboliang <gi...@git.apache.org>.
Github user yanboliang commented on the issue:
https://github.com/apache/spark/pull/12064
LGTM, merged into master. Thanks!
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[GitHub] spark pull request #12064: [SPARK-14272][ML] Evaluate GaussianMixtureModel w...
Posted by yanboliang <gi...@git.apache.org>.
Github user yanboliang commented on a diff in the pull request:
https://github.com/apache/spark/pull/12064#discussion_r95544814
--- Diff: mllib/src/test/scala/org/apache/spark/ml/clustering/GaussianMixtureSuite.scala ---
@@ -142,6 +142,32 @@ class GaussianMixtureSuite extends SparkFunSuite with MLlibTestSparkContext
assert(!model.hasSummary)
}
+ test("check LogLikelihood") {
--- End diff --
I think we don't need to bother a separate test, you can add check for ```logLikelihood``` on the existing test(multivariate data and check againt R mvnormalmixEM) which is equivalent to what you wrote but with more reasonable dataset.
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[GitHub] spark issue #12064: [SPARK-14272][ML] Evaluate GaussianMixtureModel with Log...
Posted by zhengruifeng <gi...@git.apache.org>.
Github user zhengruifeng commented on the issue:
https://github.com/apache/spark/pull/12064
Jenkins, retest this please
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[GitHub] spark issue #12064: [SPARK-14272][ML] Evaluate GaussianMixtureModel with Log...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/12064
**[Test build #71566 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/71566/testReport)** for PR 12064 at commit [`fd85c5d`](https://github.com/apache/spark/commit/fd85c5d221a0cc52c8b5f4662182d487e34db63b).
* This patch **fails PySpark unit tests**.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark issue #12064: [SPARK-14272][ML] Evaluate GaussianMixtureModel with Log...
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[GitHub] spark issue #12064: [SPARK-14272][ML] Evaluate GaussianMixtureModel with Log...
Posted by SparkQA <gi...@git.apache.org>.
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https://github.com/apache/spark/pull/12064
**[Test build #71114 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/71114/testReport)** for PR 12064 at commit [`083e4f9`](https://github.com/apache/spark/commit/083e4f932ee9bd65d211bcb8506d53bb35c160f6).
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[GitHub] spark issue #12064: [SPARK-14272][ML] Evaluate GaussianMixtureModel with Log...
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[GitHub] spark issue #12064: [SPARK-14272][ML] Evaluate GaussianMixtureModel with Log...
Posted by zhengruifeng <gi...@git.apache.org>.
Github user zhengruifeng commented on the issue:
https://github.com/apache/spark/pull/12064
jenkins, retest this please
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[GitHub] spark issue #12064: [SPARK-14272][ML] Evaluate GaussianMixtureModel with Log...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/12064
**[Test build #71113 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/71113/testReport)** for PR 12064 at commit [`8c2d529`](https://github.com/apache/spark/commit/8c2d5291affd75081da8152cfb6a1afc7e44a656).
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