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Posted to reviews@spark.apache.org by tgaloppo <gi...@git.apache.org> on 2014/12/31 06:46:52 UTC
[GitHub] spark pull request: SPARK-5020 [MLlib] GaussianMixtureModel.predic...
GitHub user tgaloppo opened a pull request:
https://github.com/apache/spark/pull/3854
SPARK-5020 [MLlib] GaussianMixtureModel.predictMembership() should take an RDD only
Removed unnecessary parameters to predictMembership()
CC: @jkbradley
You can merge this pull request into a Git repository by running:
$ git pull https://github.com/tgaloppo/spark spark-5020
Alternatively you can review and apply these changes as the patch at:
https://github.com/apache/spark/pull/3854.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 #3854
----
commit c15405c78345e9a46549a398c6b59bed80274f9e
Author: Travis Galoppo <tr...@localhost.localdomain>
Date: 2014-10-30T18:50:47Z
SPARK-4156
commit 5c96c576c5011f37fa7b84e88b7f1f8f48b82310
Author: Travis Galoppo <tr...@localhost.localdomain>
Date: 2014-11-11T23:30:42Z
Merge remote-tracking branch 'upstream/master'
commit c1a8e16ac9dc301d9eafca44100c5a857de903d5
Author: Travis Galoppo <tr...@localhost.localdomain>
Date: 2014-11-11T23:31:44Z
Made GaussianMixtureModel class serializable
Modified sum function for better performance
commit 719d8cc119e4ce117d33732c72c6c42da7456ae4
Author: Travis Galoppo <tj...@columbia.edu>
Date: 2014-11-13T01:23:53Z
Added scala test suite with basic test
commit 86fb3829388484e51de46ffe96d237b63b752aeb
Author: Travis Galoppo <tj...@columbia.edu>
Date: 2014-11-17T22:46:08Z
Merge remote-tracking branch 'upstream/master'
commit e6ea8051a5e883121d650a5a8d7e79600cc642ed
Author: Travis Galoppo <tj...@columbia.edu>
Date: 2014-11-18T00:52:12Z
Merged with master branch; update test suite with latest context changes.
Improved cluster initialization strategy.
commit 676e523a830020adf317d3c5bf445f94ed5c8a35
Author: Travis Galoppo <tj...@columbia.edu>
Date: 2014-12-03T15:14:19Z
Fixed to no longer ignore delta value provided on command line
commit 8aaa17d14a39d32a9164d044318d54f30df86202
Author: Travis Galoppo <tj...@columbia.edu>
Date: 2014-12-03T15:15:01Z
Added additional train() method to companion object for cluster count and tolerance parameters.
Modified cluster initialization strategy to use an initial covariance matrix derived from the sample points used to initialize the mean.
commit 9770261fc67a56a3ef9178f77e42d4e0deecd433
Author: Travis Galoppo <tj...@columbia.edu>
Date: 2014-12-12T17:04:15Z
Corrected a variety of style and naming issues.
commit e7d413b8e7e8614097b0c3823652677f38062775
Author: Travis Galoppo <tj...@columbia.edu>
Date: 2014-12-12T19:10:47Z
Moved multivariate Gaussian utility class to mllib/stat/impl
Improved comments
commit dc9c74264631a80dbb718a7be4c184ccae6277c0
Author: Travis Galoppo <tj...@columbia.edu>
Date: 2014-12-12T19:12:36Z
Moved MultivariateGaussian utility class
commit 97044cff25d7e7450296706669b1c1ba6cf692f0
Author: Travis Galoppo <tj...@columbia.edu>
Date: 2014-12-16T01:09:46Z
Fixed style issues
commit f407b4c22257a03409f4ab4dd15ed92738f58140
Author: FlytxtRnD <me...@flytxt.com>
Date: 2014-12-16T11:47:40Z
Added predict() to return the cluster labels and membership values
commit b99ecc4d35bc548486d728741fc17658f07d83a5
Author: tgaloppo <tj...@columbia.edu>
Date: 2014-12-16T12:32:51Z
Merge pull request #1 from FlytxtRnD/predictBranch
Added predict() to return the cluster labels and membership values
commit 2df336b6609ed4edc201ea6c26aa7b3faba4f284
Author: Travis Galoppo <tj...@columbia.edu>
Date: 2014-12-16T12:37:48Z
Fixed style issue
commit c3b8ce0fa808dbc95b6f19aee574c3f66863635e
Author: Travis Galoppo <tj...@columbia.edu>
Date: 2014-12-16T12:38:02Z
Merge branch 'master' of https://github.com/tgaloppo/spark
Adds predict() method
commit d695034fab97c617b4c590896898235a8218dc6b
Author: Travis Galoppo <tj...@columbia.edu>
Date: 2014-12-16T13:18:58Z
Fixed style issues
commit 9be2534d67b0ac0f43ca083c0940afa81474e458
Author: Travis Galoppo <tj...@columbia.edu>
Date: 2014-12-16T13:32:45Z
Style issue
commit 8b633f33a1a9b0ebc0f0af84bc2164cbd199bcbc
Author: Travis Galoppo <tj...@columbia.edu>
Date: 2014-12-16T13:34:30Z
Style issue
commit 42b2142ed2a7440869d75b3fc926a74d9d19e30b
Author: Travis Galoppo <tj...@columbia.edu>
Date: 2014-12-17T16:15:17Z
Added functionality to allow setting of GMM starting point.
Added two cluster test to testing suite.
commit 20ebca18ee09b31d201f21658c7b464fd0f5fad7
Author: Travis Galoppo <tj...@columbia.edu>
Date: 2014-12-17T16:20:10Z
Removed unusued code
commit cff73e0de3c7dd68fe7a23db385459678a646099
Author: Travis Galoppo <tj...@columbia.edu>
Date: 2014-12-17T20:22:49Z
Replaced accumulators with RDD.aggregate
commit 308c8ad9d88d275f11be0d3733f016d3119f98ee
Author: Travis Galoppo <tj...@columbia.edu>
Date: 2014-12-18T06:11:47Z
Numerous changes to improve code
commit 227ad66302f0d1166b452dc70b7cd3784a6f81e3
Author: Travis Galoppo <tj...@columbia.edu>
Date: 2014-12-18T13:18:18Z
Moved prediction methods into model class.
commit 578c2d101f6e87d19850e75c066a685124a8b3ed
Author: Travis Galoppo <tj...@columbia.edu>
Date: 2014-12-18T13:32:22Z
Removed unused import
commit 1de73f399a28060890c8617f1abddad46b30c132
Author: Travis Galoppo <tj...@columbia.edu>
Date: 2014-12-18T21:45:28Z
Removed redundant array from array creation
commit b97fe00d17c9d6665bb63f1f0bcbd968a875dfe8
Author: Travis Galoppo <tj...@columbia.edu>
Date: 2014-12-19T01:28:02Z
Minor fixes and tweaks.
commit 9b2fc2a96f6c5f44dbb6601c5c2f89b78352bed2
Author: Travis Galoppo <tj...@columbia.edu>
Date: 2014-12-20T00:34:15Z
Style improvements
Changed ExpectationSum to a private class
commit acf1fba6b0084511272cf4e19e0cab4587a11d16
Author: Travis Galoppo <tj...@columbia.edu>
Date: 2014-12-22T14:26:28Z
Fixed parameter comment in GaussianMixtureModel
Made maximum iterations an optional parameter to DenseGmmEM
commit 709e4bf854984b2eb3e5ed36c8a15590edf7e891
Author: Travis Galoppo <tj...@columbia.edu>
Date: 2014-12-22T18:32:35Z
fixed usage line to include optional maxIterations parameter
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[GitHub] spark pull request: SPARK-5020 [MLlib] GaussianMixtureModel.predic...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the pull request:
https://github.com/apache/spark/pull/3854#issuecomment-68466535
[Test build #558 has finished](https://amplab.cs.berkeley.edu/jenkins/job/NewSparkPullRequestBuilder/558/consoleFull) for PR 3854 at commit [`0f1d96e`](https://github.com/apache/spark/commit/0f1d96e2b4292edbf0a4c9db82fc2969016b0587).
* 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-5020 [MLlib] GaussianMixtureModel.predic...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the pull request:
https://github.com/apache/spark/pull/3854#issuecomment-68473301
Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/SparkPullRequestBuilder/24971/
Test PASSed.
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[GitHub] spark pull request: SPARK-5020 [MLlib] GaussianMixtureModel.predic...
Posted by tgaloppo <gi...@git.apache.org>.
Github user tgaloppo commented on the pull request:
https://github.com/apache/spark/pull/3854#issuecomment-68425054
My repo seems to have some lingering commit tags.
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[GitHub] spark pull request: SPARK-5020 [MLlib] GaussianMixtureModel.predic...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the pull request:
https://github.com/apache/spark/pull/3854#issuecomment-68469714
[Test build #24971 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/24971/consoleFull) for PR 3854 at commit [`1bf4669`](https://github.com/apache/spark/commit/1bf4669cde6b5729b60d75e40fbf19db4b8b0998).
* This patch merges cleanly.
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[GitHub] spark pull request: SPARK-5020 [MLlib] GaussianMixtureModel.predic...
Posted by mengxr <gi...@git.apache.org>.
Github user mengxr commented on the pull request:
https://github.com/apache/spark/pull/3854#issuecomment-68465590
It may be hard for users to tell the difference between `predict` and `predictMembership`, because `predict` is also predicting the membership. `predictFuzzy` or `predictSoft` sounds better to me.
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[GitHub] spark pull request: SPARK-5020 [MLlib] GaussianMixtureModel.predic...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the pull request:
https://github.com/apache/spark/pull/3854#issuecomment-68473299
[Test build #24971 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/24971/consoleFull) for PR 3854 at commit [`1bf4669`](https://github.com/apache/spark/commit/1bf4669cde6b5729b60d75e40fbf19db4b8b0998).
* This patch **passes all tests**.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark pull request: SPARK-5020 [MLlib] GaussianMixtureModel.predic...
Posted by mengxr <gi...@git.apache.org>.
Github user mengxr commented on the pull request:
https://github.com/apache/spark/pull/3854#issuecomment-68469638
test this please
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[GitHub] spark pull request: SPARK-5020 [MLlib] GaussianMixtureModel.predic...
Posted by jkbradley <gi...@git.apache.org>.
Github user jkbradley commented on the pull request:
https://github.com/apache/spark/pull/3854#issuecomment-68425644
About the commit tags, I'm not quite sure how to remove them. Does rebasing fix it? If not, then you could checkout master again and copy the few changes in (and then do a force push to your PR branch).
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[GitHub] spark pull request: SPARK-5020 [MLlib] GaussianMixtureModel.predic...
Posted by tgaloppo <gi...@git.apache.org>.
Github user tgaloppo commented on the pull request:
https://github.com/apache/spark/pull/3854#issuecomment-68467812
Ok, I will rename the method to predictSoft()
Not sure what to make of the streaming failure ??
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[GitHub] spark pull request: SPARK-5020 [MLlib] GaussianMixtureModel.predic...
Posted by jkbradley <gi...@git.apache.org>.
Github user jkbradley commented on the pull request:
https://github.com/apache/spark/pull/3854#issuecomment-68466757
streaming failure
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[GitHub] spark pull request: SPARK-5020 [MLlib] GaussianMixtureModel.predic...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the pull request:
https://github.com/apache/spark/pull/3854#issuecomment-68425021
Can one of the admins verify this patch?
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[GitHub] spark pull request: SPARK-5020 [MLlib] GaussianMixtureModel.predic...
Posted by asfgit <gi...@git.apache.org>.
Github user asfgit closed the pull request at:
https://github.com/apache/spark/pull/3854
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[GitHub] spark pull request: SPARK-5020 [MLlib] GaussianMixtureModel.predic...
Posted by jkbradley <gi...@git.apache.org>.
Github user jkbradley commented on the pull request:
https://github.com/apache/spark/pull/3854#issuecomment-68466378
+1 for predictSoft
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[GitHub] spark pull request: SPARK-5020 [MLlib] GaussianMixtureModel.predic...
Posted by jkbradley <gi...@git.apache.org>.
Github user jkbradley commented on the pull request:
https://github.com/apache/spark/pull/3854#issuecomment-68425605
I should have been clearer; I meant for predictMembership to be public. I thought perhaps the implementation would become of a private method, but I realize now it is fine leaving the code within predictMembership alone. Once the private modifier is removed, I think this will be good to go.
Thanks!
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[GitHub] spark pull request: SPARK-5020 [MLlib] GaussianMixtureModel.predic...
Posted by tgaloppo <gi...@git.apache.org>.
Github user tgaloppo commented on the pull request:
https://github.com/apache/spark/pull/3854#issuecomment-68427096
@jkbradley No, private modifier was a gaffe on my part. This is corrected.
I think I have corrected the lingering commits... rebase did not work for me, but a hard reset seems to have done the trick.
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[GitHub] spark pull request: SPARK-5020 [MLlib] GaussianMixtureModel.predic...
Posted by jkbradley <gi...@git.apache.org>.
Github user jkbradley commented on the pull request:
https://github.com/apache/spark/pull/3854#issuecomment-68462718
@tgaloppo Ok, thanks for the fix! LGTM once the tests are done.
@tgaloppo @mengxr As long as this method is being edited, do you like the name ```predictMembership``` for soft clustering? I assume we may eventually use the same term for other clustering methods, includes LDA.
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[GitHub] spark pull request: SPARK-5020 [MLlib] GaussianMixtureModel.predic...
Posted by jkbradley <gi...@git.apache.org>.
Github user jkbradley commented on the pull request:
https://github.com/apache/spark/pull/3854#issuecomment-68469941
@tgaloppo The streaming failure is unrelated; it's an unreliable test (which is being fixed). Nothing for you to do.
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[GitHub] spark pull request: SPARK-5020 [MLlib] GaussianMixtureModel.predic...
Posted by mengxr <gi...@git.apache.org>.
Github user mengxr commented on the pull request:
https://github.com/apache/spark/pull/3854#issuecomment-68475232
LGTM. Merged into master. Thanks!
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[GitHub] spark pull request: SPARK-5020 [MLlib] GaussianMixtureModel.predic...
Posted by tgaloppo <gi...@git.apache.org>.
Github user tgaloppo commented on the pull request:
https://github.com/apache/spark/pull/3854#issuecomment-68465266
@jkbradley I am not crazy about the name predictMembership() ... to me it implies the hard assignment; a simple change like predictMemberships() might be more clear, or predictSoft(), or (thinking from a slightly different direction) allocate(). Any of those should be robust enough to reuse for soft k-means or LDA (or other such partial assignment algorithms).
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[GitHub] spark pull request: SPARK-5020 [MLlib] GaussianMixtureModel.predic...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the pull request:
https://github.com/apache/spark/pull/3854#issuecomment-68462618
[Test build #558 has started](https://amplab.cs.berkeley.edu/jenkins/job/NewSparkPullRequestBuilder/558/consoleFull) for PR 3854 at commit [`0f1d96e`](https://github.com/apache/spark/commit/0f1d96e2b4292edbf0a4c9db82fc2969016b0587).
* This patch merges cleanly.
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[GitHub] spark pull request: SPARK-5020 [MLlib] GaussianMixtureModel.predic...
Posted by mengxr <gi...@git.apache.org>.
Github user mengxr commented on the pull request:
https://github.com/apache/spark/pull/3854#issuecomment-68469634
add to whitelist
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