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* [SPARK-7558] Demarcate tests in unit-tests.logAndrew Or2015-05-29100-307/+224
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Right now `unit-tests.log` are not of much value because we can't tell where the test boundaries are easily. This patch adds log statements before and after each test to outline the test boundaries, e.g.: ``` ===== TEST OUTPUT FOR o.a.s.serializer.KryoSerializerSuite: 'kryo with parallelize for primitive arrays' ===== 15/05/27 12:36:39.596 pool-1-thread-1-ScalaTest-running-KryoSerializerSuite INFO SparkContext: Starting job: count at KryoSerializerSuite.scala:230 15/05/27 12:36:39.596 dag-scheduler-event-loop INFO DAGScheduler: Got job 3 (count at KryoSerializerSuite.scala:230) with 4 output partitions (allowLocal=false) 15/05/27 12:36:39.596 dag-scheduler-event-loop INFO DAGScheduler: Final stage: ResultStage 3(count at KryoSerializerSuite.scala:230) 15/05/27 12:36:39.596 dag-scheduler-event-loop INFO DAGScheduler: Parents of final stage: List() 15/05/27 12:36:39.597 dag-scheduler-event-loop INFO DAGScheduler: Missing parents: List() 15/05/27 12:36:39.597 dag-scheduler-event-loop INFO DAGScheduler: Submitting ResultStage 3 (ParallelCollectionRDD[5] at parallelize at KryoSerializerSuite.scala:230), which has no missing parents ... 15/05/27 12:36:39.624 pool-1-thread-1-ScalaTest-running-KryoSerializerSuite INFO DAGScheduler: Job 3 finished: count at KryoSerializerSuite.scala:230, took 0.028563 s 15/05/27 12:36:39.625 pool-1-thread-1-ScalaTest-running-KryoSerializerSuite INFO KryoSerializerSuite: ***** FINISHED o.a.s.serializer.KryoSerializerSuite: 'kryo with parallelize for primitive arrays' ***** ... ``` Author: Andrew Or <andrew@databricks.com> Closes #6441 from andrewor14/demarcate-tests and squashes the following commits: 879b060 [Andrew Or] Fix compile after rebase d622af7 [Andrew Or] Merge branch 'master' of github.com:apache/spark into demarcate-tests 017c8ba [Andrew Or] Merge branch 'master' of github.com:apache/spark into demarcate-tests 7790b6c [Andrew Or] Fix tests after logical merge conflict c7460c0 [Andrew Or] Merge branch 'master' of github.com:apache/spark into demarcate-tests c43ffc4 [Andrew Or] Fix tests? 8882581 [Andrew Or] Fix tests ee22cda [Andrew Or] Fix log message fa9450e [Andrew Or] Merge branch 'master' of github.com:apache/spark into demarcate-tests 12d1e1b [Andrew Or] Various whitespace changes (minor) 69cbb24 [Andrew Or] Make all test suites extend SparkFunSuite instead of FunSuite bbce12e [Andrew Or] Fix manual things that cannot be covered through automation da0b12f [Andrew Or] Add core tests as dependencies in all modules f7d29ce [Andrew Or] Introduce base abstract class for all test suites
* [SPARK-7940] Enforce whitespace checking for DO, TRY, CATCH, FINALLY, MATCH, ↵Reynold Xin2015-05-292-3/+3
| | | | | | | | | | | | LARROW, RARROW in style checker. … Author: Reynold Xin <rxin@databricks.com> Closes #6491 from rxin/more-whitespace and squashes the following commits: f6e63dc [Reynold Xin] [SPARK-7940] Enforce whitespace checking for DO, TRY, CATCH, FINALLY, MATCH, LARROW, RARROW in style checker.
* [SPARK-7946] [MLLIB] DecayFactor wrongly set in StreamingKMeansMechCoder2015-05-292-1/+8
| | | | | | | | | Author: MechCoder <manojkumarsivaraj334@gmail.com> Closes #6497 from MechCoder/spark-7946 and squashes the following commits: 2fdd0a3 [MechCoder] Add non-regression test 8c988c6 [MechCoder] [SPARK-7946] DecayFactor wrongly set in StreamingKMeans
* [SPARK-7912] [SPARK-7921] [MLLIB] Update OneHotEncoder to handle ML ↵Xiangrui Meng2015-05-292-59/+143
| | | | | | | | | | | | | | | | | | | | | | | | | | | attributes and change includeFirst to dropLast This PR contains two major changes to `OneHotEncoder`: 1. more robust handling of ML attributes. If the input attribute is unknown, we look at the values to get the max category index 2. change `includeFirst` to `dropLast` and leave the default to `true`. There are couple benefits: a. consistent with other tutorials of one-hot encoding (or dummy coding) (e.g., http://www.ats.ucla.edu/stat/mult_pkg/faq/general/dummy.htm) b. keep the indices unmodified in the output vector. If we drop the first, all indices will be shifted by 1. c. If users use `StringIndex`, the last element is the least frequent one. Sorry for including two changes in one PR! I'll update the user guide in another PR. jkbradley sryza Author: Xiangrui Meng <meng@databricks.com> Closes #6466 from mengxr/SPARK-7912 and squashes the following commits: a280dca [Xiangrui Meng] fix tests d8f234d [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-7912 171b276 [Xiangrui Meng] mention the difference between our impl vs sklearn's 00dfd96 [Xiangrui Meng] update OneHotEncoder in Python 208ddad [Xiangrui Meng] update OneHotEncoder to handle ML attributes and change includeFirst to dropLast
* [SPARK-7922] [MLLIB] use DataFrames for user/item factors in ALSModelXiangrui Meng2015-05-281-44/+57
| | | | | | | | | | | | | Expose user/item factors in DataFrames. This is to be more consistent with the pipeline API. It also helps maintain consistent APIs across languages. This PR also removed fitting params from `ALSModel`. coderxiang Author: Xiangrui Meng <meng@databricks.com> Closes #6468 from mengxr/SPARK-7922 and squashes the following commits: 7bfb1d5 [Xiangrui Meng] update ALSModel in PySpark 1ba5607 [Xiangrui Meng] use DataFrames for user/item factors in ALS
* [SPARK-7927] [MLLIB] Enforce whitespace for more tokens in style checkerXiangrui Meng2015-05-2833-71/+88
| | | | | | | | | | | | rxin Author: Xiangrui Meng <meng@databricks.com> Closes #6481 from mengxr/mllib-scalastyle and squashes the following commits: 3ca4d61 [Xiangrui Meng] revert scalastyle config 30961ba [Xiangrui Meng] adjust spaces in mllib/test 571b5c5 [Xiangrui Meng] fix spaces in mllib
* [SPARK-7577] [ML] [DOC] add bucketizer docXusen Yin2015-05-281-0/+80
| | | | | | | | | | | | | CC jkbradley Author: Xusen Yin <yinxusen@gmail.com> Closes #6451 from yinxusen/SPARK-7577 and squashes the following commits: e2dc32e [Xusen Yin] rename colums e350e49 [Xusen Yin] add all demos 006ddf1 [Xusen Yin] add java test 3238481 [Xusen Yin] add bucketizer
* [SPARK-7198] [MLLIB] VectorAssembler should output ML attributesXiangrui Meng2015-05-282-5/+83
| | | | | | | | | | | | | | | | | | | | `VectorAssembler` should carry over ML attributes. For unknown attributes, we assume numeric values. This PR handles the following cases: 1. DoubleType with ML attribute: carry over 2. DoubleType without ML attribute: numeric value 3. Scalar type: numeric value 4. VectorType with all ML attributes: carry over and update names 5. VectorType with number of ML attributes: assume all numeric 6. VectorType without ML attributes: check the first row and get the number of attributes jkbradley Author: Xiangrui Meng <meng@databricks.com> Closes #6452 from mengxr/SPARK-7198 and squashes the following commits: a9d2469 [Xiangrui Meng] add space facdb1f [Xiangrui Meng] VectorAssembler should output ML attributes
* [SPARK-7911] [MLLIB] A workaround for VectorUDT serialize (or deserialize) ↵Xiangrui Meng2015-05-281-5/+14
| | | | | | | | | | | | | | being called multiple times ~~A PythonUDT shouldn't be serialized into external Scala types in PythonRDD. I'm not sure whether this should fix one of the bugs related to SQL UDT/UDF in PySpark.~~ The fix above didn't work. So I added a workaround for this. If a Python UDF is applied to a Python UDT. This will put the Python SQL types as inputs. Still incorrect, but at least it doesn't throw exceptions on the Scala side. davies harsha2010 Author: Xiangrui Meng <meng@databricks.com> Closes #6442 from mengxr/SPARK-7903 and squashes the following commits: c257d2a [Xiangrui Meng] add a workaround for VectorUDT
* [SPARK-7535] [.1] [MLLIB] minor changes to the pipeline APIXiangrui Meng2015-05-266-32/+71
| | | | | | | | | | | | | | | | | | | | | 1. removed `Params.validateParams(extra)` 2. added `Evaluate.evaluate(dataset, paramPairs*)` 3. updated `RegressionEvaluator` doc jkbradley Author: Xiangrui Meng <meng@databricks.com> Closes #6392 from mengxr/SPARK-7535.1 and squashes the following commits: 5ff5af8 [Xiangrui Meng] add unit test for CV.validateParams f1f8369 [Xiangrui Meng] update CV.validateParams() to test estimatorParamMaps 607445d [Xiangrui Meng] merge master 8716f5f [Xiangrui Meng] specify default metric name in RegressionEvaluator e4e5631 [Xiangrui Meng] update RegressionEvaluator doc 801e864 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-7535.1 fcbd3e2 [Xiangrui Meng] Merge branch 'master' into SPARK-7535.1 2192316 [Xiangrui Meng] remove validateParams(extra); add evaluate(dataset, extra*)
* [SPARK-7748] [MLLIB] Graduate spark.ml from alphaXiangrui Meng2015-05-2643-201/+267
| | | | | | | | | | | | | | | | | | With descent coverage of feature transformers, algorithms, and model tuning support, it is time to graduate `spark.ml` from alpha. This PR changes all `AlphaComponent` annotations to either `DeveloperApi` or `Experimental`, depending on whether we expect a class/method to be used by end users (who use the pipeline API to assemble/tune their ML pipelines but not to create new pipeline components.) `UnaryTransformer` becomes a `DeveloperApi` in this PR. jkbradley harsha2010 Author: Xiangrui Meng <meng@databricks.com> Closes #6417 from mengxr/SPARK-7748 and squashes the following commits: effbccd [Xiangrui Meng] organize imports c15028e [Xiangrui Meng] added missing docs 1b2e5f8 [Xiangrui Meng] update package doc 73ca791 [Xiangrui Meng] alpha -> ex/dev for the rest 93819db [Xiangrui Meng] alpha -> ex/dev in ml.param 55ca073 [Xiangrui Meng] alpha -> ex/dev in ml.feature 83572f1 [Xiangrui Meng] add Experimental and DeveloperApi tags (wip)
* [SPARK-7844] [MLLIB] Fix broken tests in KernelDensityMechCoder2015-05-262-5/+7
| | | | | | | | | | | | | The densities in KernelDensity are scaled down by (number of parallel processes X number of points). It should be just no.of samples. This results in broken tests in KernelDensitySuite which haven't been tested properly. Author: MechCoder <manojkumarsivaraj334@gmail.com> Closes #6383 from MechCoder/spark-7844 and squashes the following commits: ab81302 [MechCoder] Math->math 9b8ed50 [MechCoder] Make one pass to update count a92fe50 [MechCoder] [SPARK-7844] Fix broken tests in KernelDensity
* [SPARK-7833] [ML] Add python wrapper for RegressionEvaluatorRam Sriharsha2015-05-242-2/+3
| | | | | | | | | | Author: Ram Sriharsha <rsriharsha@hw11853.local> Closes #6365 from harsha2010/SPARK-7833 and squashes the following commits: 923f288 [Ram Sriharsha] cleanup 7623b7d [Ram Sriharsha] python style fix 9743f83 [Ram Sriharsha] [SPARK-7833][ml] Add python wrapper for RegressionEvaluator
* [SPARK-7404] [ML] Add RegressionEvaluator to spark.mlRam Sriharsha2015-05-222-0/+155
| | | | | | | | | | | | | | | | Author: Ram Sriharsha <rsriharsha@hw11853.local> Closes #6344 from harsha2010/SPARK-7404 and squashes the following commits: 16b9d77 [Ram Sriharsha] consistent naming 7f100b6 [Ram Sriharsha] cleanup c46044d [Ram Sriharsha] Merge with Master + Code Review Fixes 188fa0a [Ram Sriharsha] Merge branch 'master' into SPARK-7404 f5b6a4c [Ram Sriharsha] cleanup doc 97beca5 [Ram Sriharsha] update test to use R packages 32dd310 [Ram Sriharsha] fix indentation f93b812 [Ram Sriharsha] fix test 1b6ebb3 [Ram Sriharsha] [SPARK-7404][ml] Add RegressionEvaluator to spark.ml
* [SPARK-7578] [ML] [DOC] User guide for spark.ml Normalizer, IDF, StandardScalerJoseph K. Bradley2015-05-213-6/+153
| | | | | | | | | | | | | | | | Added user guide sections with code examples. Also added small Java unit tests to test Java example in guide. CC: mengxr Author: Joseph K. Bradley <joseph@databricks.com> Closes #6127 from jkbradley/feature-guide-2 and squashes the following commits: cd47f4b [Joseph K. Bradley] Updated based on code review f16bcec [Joseph K. Bradley] Fixed merge issues and update Python examples print calls for Python 3 0a862f9 [Joseph K. Bradley] Added Normalizer, StandardScaler to ml-features doc, plus small Java unit tests a21c2d6 [Joseph K. Bradley] Updated ml-features.md with IDF
* [SPARK-7535] [.0] [MLLIB] Audit the pipeline APIs for 1.4Xiangrui Meng2015-05-2112-19/+20
| | | | | | | | | | | | | | | | | | | | | | | | Some changes to the pipeilne APIs: 1. Estimator/Transformer/ doesn’t need to extend Params since PipelineStage already does. 1. Move Evaluator to ml.evaluation. 1. Mention larger metric values are better. 1. PipelineModel doc. “compiled” -> “fitted” 1. Hide object PolynomialExpansion. 1. Hide object VectorAssembler. 1. Word2Vec.minCount (and other) -> group param 1. ParamValidators -> DeveloperApi 1. Hide MetadataUtils/SchemaUtils. jkbradley Author: Xiangrui Meng <meng@databricks.com> Closes #6322 from mengxr/SPARK-7535.0 and squashes the following commits: 9e9c7da [Xiangrui Meng] move JavaEvaluator to ml.evaluation as well e179480 [Xiangrui Meng] move Evaluation to ml.evaluation in PySpark 08ef61f [Xiangrui Meng] update pipieline APIs
* [SPARK-7219] [MLLIB] Output feature attributes in HashingTFXiangrui Meng2015-05-213-8/+101
| | | | | | | | | | | | | | | This PR updates `HashingTF` to output ML attributes that tell the number of features in the output column. We need to expand `UnaryTransformer` to support output metadata. A `df outputMetadata: Metadata` is not sufficient because the metadata may also depends on the input data. Though this is not true for `HashingTF`, I think it is reasonable to update `UnaryTransformer` in a separate PR. `checkParams` is added to verify common requirements for params. I will send a separate PR to use it in other test suites. jkbradley Author: Xiangrui Meng <meng@databricks.com> Closes #6308 from mengxr/SPARK-7219 and squashes the following commits: 9bd2922 [Xiangrui Meng] address comments e82a68a [Xiangrui Meng] remove sqlContext from test suite 995535b [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-7219 2194703 [Xiangrui Meng] add test for attributes 178ae23 [Xiangrui Meng] update HashingTF with tests 91a6106 [Xiangrui Meng] WIP
* [SPARK-7794] [MLLIB] update RegexTokenizer default settingsXiangrui Meng2015-05-212-25/+25
| | | | | | | | | | The previous default is `{gaps: false, pattern: "\\p{L}+|[^\\p{L}\\s]+"}`. The default pattern is hard to understand. This PR changes the default to `{gaps: true, pattern: "\\s+"}`. jkbradley Author: Xiangrui Meng <meng@databricks.com> Closes #6330 from mengxr/SPARK-7794 and squashes the following commits: 5ee7cde [Xiangrui Meng] update RegexTokenizer default settings
* [SPARK-7498] [MLLIB] add varargs back to setDefaultXiangrui Meng2015-05-212-4/+4
| | | | | | | | | | We removed `varargs` due to Java compilation issues. That was a false alarm because I didn't run `build/sbt clean`. So this PR reverts the changes. jkbradley Author: Xiangrui Meng <meng@databricks.com> Closes #6320 from mengxr/SPARK-7498 and squashes the following commits: 74a7259 [Xiangrui Meng] add varargs back to setDefault
* [SPARK-7585] [ML] [DOC] VectorIndexer user guide sectionJoseph K. Bradley2015-05-212-1/+13
| | | | | | | | | | | | | Added VectorIndexer section to ML user guide. Also added javaCategoryMaps() method and Java unit test for it. CC: mengxr Author: Joseph K. Bradley <joseph@databricks.com> Closes #6255 from jkbradley/vector-indexer-guide and squashes the following commits: dbb8c4c [Joseph K. Bradley] simplified VectorIndexerModel.javaCategoryMaps f692084 [Joseph K. Bradley] Added VectorIndexer section to ML user guide. Also added javaCategoryMaps() method and Java unit test for it.
* [SPARK-7793] [MLLIB] Use getOrElse for getting the threshold of SVM modelShuo Xiang2015-05-211-1/+1
| | | | | | | | | | | | | | same issue and fix as in Spark-7694. Author: Shuo Xiang <shuoxiangpub@gmail.com> Closes #6321 from coderxiang/nb and squashes the following commits: a5e6de4 [Shuo Xiang] use getOrElse for svmmodel.tostring 2cb0177 [Shuo Xiang] Merge remote-tracking branch 'upstream/master' into nb 5f109b4 [Shuo Xiang] Merge remote-tracking branch 'upstream/master' c5c5bfe [Shuo Xiang] Merge remote-tracking branch 'upstream/master' 98804c9 [Shuo Xiang] fix bug in topBykey and update test
* [SPARK-7752] [MLLIB] Use lowercase letters for NaiveBayes.modelTypeXiangrui Meng2015-05-213-55/+70
| | | | | | | | | | | | | | | | to be consistent with other string names in MLlib. This PR also updates the implementation to use vals instead of hardcoded strings. jkbradley leahmcguire Author: Xiangrui Meng <meng@databricks.com> Closes #6277 from mengxr/SPARK-7752 and squashes the following commits: f38b662 [Xiangrui Meng] add another case _ back in test ae5c66a [Xiangrui Meng] model type -> modelType 711d1c6 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-7752 40ae53e [Xiangrui Meng] fix Java test suite 264a814 [Xiangrui Meng] add case _ back 3c456a8 [Xiangrui Meng] update NB user guide 17bba53 [Xiangrui Meng] update naive Bayes to use lowercase model type strings
* [SPARK-7753] [MLLIB] Update KernelDensity APIXiangrui Meng2015-05-203-48/+82
| | | | | | | | | | | Update `KernelDensity` API to make it extensible to different kernels in the future. `bandwidth` is used instead of `standardDeviation`. The static `kernelDensity` method is removed from `Statistics`. The implementation is updated using BLAS, while the algorithm remains the same. sryza srowen Author: Xiangrui Meng <meng@databricks.com> Closes #6279 from mengxr/SPARK-7753 and squashes the following commits: 4cdfadc [Xiangrui Meng] add example code in the doc 767fd5a [Xiangrui Meng] update KernelDensity API
* [SPARK-7774] [MLLIB] add sqlContext to MLlibTestSparkContextXiangrui Meng2015-05-2014-79/+20
| | | | | | | | | | | to simplify test suites that require a SQLContext. Author: Xiangrui Meng <meng@databricks.com> Closes #6303 from mengxr/SPARK-7774 and squashes the following commits: 0622b5a [Xiangrui Meng] update some other test suites e1f9b8d [Xiangrui Meng] add sqlContext to MLlibTestSparkContext
* [SPARK-7762] [MLLIB] set default value for outputColXiangrui Meng2015-05-203-2/+39
| | | | | | | | | | | | | Set a default value for `outputCol` instead of forcing users to name it. This is useful for intermediate transformers in the pipeline. jkbradley Author: Xiangrui Meng <meng@databricks.com> Closes #6289 from mengxr/SPARK-7762 and squashes the following commits: 54edebc [Xiangrui Meng] merge master bff8667 [Xiangrui Meng] update unit test 171246b [Xiangrui Meng] add unit test for outputCol a4321bd [Xiangrui Meng] set default value for outputCol
* [SPARK-7537] [MLLIB] spark.mllib API updatesXiangrui Meng2015-05-202-0/+13
| | | | | | | | | | | | | | | | Minor updates to the spark.mllib APIs: 1. Add `DeveloperApi` to `PMMLExportable` and add `Experimental` to `toPMML` methods. 2. Mention `RankingMetrics.of` in the `RankingMetrics` constructor. Author: Xiangrui Meng <meng@databricks.com> Closes #6280 from mengxr/SPARK-7537 and squashes the following commits: 1bd2583 [Xiangrui Meng] organize imports 94afa7a [Xiangrui Meng] mark all toPMML methods experimental 4c40da1 [Xiangrui Meng] mention the factory method for RankingMetrics for Java users 88c62d0 [Xiangrui Meng] add DeveloperApi to PMMLExportable
* [SPARK-6094] [MLLIB] Add MultilabelMetrics in PySpark/MLlibYanbo Liang2015-05-201-0/+8
| | | | | | | | | | Add MultilabelMetrics in PySpark/MLlib Author: Yanbo Liang <ybliang8@gmail.com> Closes #6276 from yanboliang/spark-6094 and squashes the following commits: b8e3343 [Yanbo Liang] Add MultilabelMetrics in PySpark/MLlib
* [SPARK-7654] [MLLIB] Migrate MLlib to the DataFrame reader/writer APIXiangrui Meng2015-05-2010-12/+12
| | | | | | | | | | parquetFile -> read.parquet rxin Author: Xiangrui Meng <meng@databricks.com> Closes #6281 from mengxr/SPARK-7654 and squashes the following commits: a79b612 [Xiangrui Meng] parquetFile -> read.parquet
* [SPARK-7663] [MLLIB] Add requirement for word2vec modelXusen Yin2015-05-201-0/+3
| | | | | | | | | | | | | | | JIRA issue [link](https://issues.apache.org/jira/browse/SPARK-7663). We should check the model size of word2vec, to prevent the unexpected empty. CC srowen. Author: Xusen Yin <yinxusen@gmail.com> Closes #6228 from yinxusen/SPARK-7663 and squashes the following commits: 21770c5 [Xusen Yin] check the vocab size 54ae63e [Xusen Yin] add requirement for word2vec model
* [SPARK-7652] [MLLIB] Update the implementation of naive Bayes prediction ↵Liang-Chi Hsieh2015-05-191-17/+24
| | | | | | | | | | | | | | | | with BLAS JIRA: https://issues.apache.org/jira/browse/SPARK-7652 Author: Liang-Chi Hsieh <viirya@gmail.com> Closes #6189 from viirya/naive_bayes_blas_prediction and squashes the following commits: ab611fd [Liang-Chi Hsieh] Remove unnecessary space. ddc48b9 [Liang-Chi Hsieh] Merge remote-tracking branch 'upstream/master' into naive_bayes_blas_prediction b5772b4 [Liang-Chi Hsieh] Fix binary compatibility. 2f65186 [Liang-Chi Hsieh] Remove toDense. 1b6cdfe [Liang-Chi Hsieh] Update the implementation of naive Bayes prediction with BLAS.
* [SPARK-7586] [ML] [DOC] Add docs of Word2Vec in ml packageXusen Yin2015-05-191-0/+76
| | | | | | | | | | | | | | | | | CC jkbradley. JIRA [issue](https://issues.apache.org/jira/browse/SPARK-7586). Author: Xusen Yin <yinxusen@gmail.com> Closes #6181 from yinxusen/SPARK-7586 and squashes the following commits: 77014c5 [Xusen Yin] comment fix 57a4c07 [Xusen Yin] small fix for docs 1178c8f [Xusen Yin] remove the correctness check in java suite 1c3f389 [Xusen Yin] delete sbt commit 1af152b [Xusen Yin] check python example code 1b5369e [Xusen Yin] add docs of word2vec
* [SPARK-7678] [ML] Fix default random seed in HasSeedJoseph K. Bradley2015-05-196-12/+14
| | | | | | | | | | | | | | Changed shared param HasSeed to have default based on hashCode of class name, instead of random number. Also, removed fixed random seeds from Word2Vec and ALS. CC: mengxr Author: Joseph K. Bradley <joseph@databricks.com> Closes #6251 from jkbradley/scala-fixed-seed and squashes the following commits: 0e37184 [Joseph K. Bradley] Fixed Word2VecSuite, ALSSuite in spark.ml to use original fixed random seeds 678ec3a [Joseph K. Bradley] Removed fixed random seeds from Word2Vec and ALS. Changed shared param HasSeed to have default based on hashCode of class name, instead of random number.
* [SPARK-7047] [ML] ml.Model optional parent supportJoseph K. Bradley2015-05-193-1/+7
| | | | | | | | | | | | Made Model.parent transient. Added Model.hasParent to test for null parent CC: mengxr Author: Joseph K. Bradley <joseph@databricks.com> Closes #5914 from jkbradley/parent-optional and squashes the following commits: d501774 [Joseph K. Bradley] Made Model.parent transient. Added Model.hasParent to test for null parent
* [SPARK-7581] [ML] [DOC] User guide for spark.ml PolynomialExpansionXusen Yin2015-05-191-0/+91
| | | | | | | | | | | | | | | | | | JIRA [here](https://issues.apache.org/jira/browse/SPARK-7581). CC jkbradley Author: Xusen Yin <yinxusen@gmail.com> Closes #6113 from yinxusen/SPARK-7581 and squashes the following commits: 1a7d80d [Xusen Yin] merge with master 892a8e9 [Xusen Yin] fix python 3 compatibility ec935bf [Xusen Yin] small fix 3e9fa1d [Xusen Yin] delete note 69fcf85 [Xusen Yin] simplify and add python example 81d21dc [Xusen Yin] add programming guide for Polynomial Expansion 40babfb [Xusen Yin] add java test suite for PolynomialExpansion
* [SPARK-7681] [MLLIB] Add SparseVector support for gemvLiang-Chi Hsieh2015-05-183-31/+224
| | | | | | | | | | | | | | | | | | JIRA: https://issues.apache.org/jira/browse/SPARK-7681 Author: Liang-Chi Hsieh <viirya@gmail.com> Closes #6209 from viirya/sparsevector_gemv and squashes the following commits: ce0bb8b [Liang-Chi Hsieh] Still need to scal y when beta is 0.0 because it clears out y. b890e63 [Liang-Chi Hsieh] Do not delete multiply for DenseVector. 57a8c1e [Liang-Chi Hsieh] Add MimaExcludes for v1.4. 458d1ae [Liang-Chi Hsieh] List DenseMatrix.multiply and SparseMatrix.multiply to MimaExcludes too. 054f05d [Liang-Chi Hsieh] Fix scala style. 410381a [Liang-Chi Hsieh] Address comments. Make Matrix.multiply more generalized. 4616696 [Liang-Chi Hsieh] Add support for SparseVector with SparseMatrix. 5d6d07a [Liang-Chi Hsieh] Merge remote-tracking branch 'upstream/master' into sparsevector_gemv c069507 [Liang-Chi Hsieh] Add SparseVector support for gemv with DenseMatrix.
* [SPARK-7380] [MLLIB] pipeline stages should be copyable in PythonXiangrui Meng2015-05-183-7/+8
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This PR makes pipeline stages in Python copyable and hence simplifies some implementations. It also includes the following changes: 1. Rename `paramMap` and `defaultParamMap` to `_paramMap` and `_defaultParamMap`, respectively. 2. Accept a list of param maps in `fit`. 3. Use parent uid and name to identify param. jkbradley Author: Xiangrui Meng <meng@databricks.com> Author: Joseph K. Bradley <joseph@databricks.com> Closes #6088 from mengxr/SPARK-7380 and squashes the following commits: 413c463 [Xiangrui Meng] remove unnecessary doc 4159f35 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-7380 611c719 [Xiangrui Meng] fix python style 68862b8 [Xiangrui Meng] update _java_obj initialization 927ad19 [Xiangrui Meng] fix ml/tests.py 0138fc3 [Xiangrui Meng] update feature transformers and fix a bug in RegexTokenizer 9ca44fb [Xiangrui Meng] simplify Java wrappers and add tests c7d84ef [Xiangrui Meng] update ml/tests.py to test copy params 7e0d27f [Xiangrui Meng] merge master 46840fb [Xiangrui Meng] update wrappers b6db1ed [Xiangrui Meng] update all self.paramMap to self._paramMap 46cb6ed [Xiangrui Meng] merge master a163413 [Xiangrui Meng] fix style 1042e80 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-7380 9630eae [Xiangrui Meng] fix Identifiable._randomUID 13bd70a [Xiangrui Meng] update ml/tests.py 64a536c [Xiangrui Meng] use _fit/_transform/_evaluate to simplify the impl 02abf13 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into copyable-python 66ce18c [Joseph K. Bradley] some cleanups before sending to Xiangrui 7431272 [Joseph K. Bradley] Rebased with master
* [SPARK-7694] [MLLIB] Use getOrElse for getting the threshold of LR modelShuo Xiang2015-05-171-1/+1
| | | | | | | | | | | | | The `toString` method of `LogisticRegressionModel` calls `get` method on an Option (threshold) without a safeguard. In spark-shell, the following code `val model = algorithm.run(data).clearThreshold()` in lbfgs code will fail as `toString `method will be called right after `clearThreshold()` to show the results in the REPL. Author: Shuo Xiang <shuoxiangpub@gmail.com> Closes #6224 from coderxiang/getorelse and squashes the following commits: d5f53c9 [Shuo Xiang] use getOrElse for getting the threshold of LR model 5f109b4 [Shuo Xiang] Merge remote-tracking branch 'upstream/master' c5c5bfe [Shuo Xiang] Merge remote-tracking branch 'upstream/master' 98804c9 [Shuo Xiang] fix bug in topBykey and update test
* [SPARK-7654][MLlib] Migrate MLlib to the DataFrame reader/writer API.Reynold Xin2015-05-1611-14/+14
| | | | | | | | Author: Reynold Xin <rxin@databricks.com> Closes #6211 from rxin/mllib-reader and squashes the following commits: 79a2cb9 [Reynold Xin] [SPARK-7654][MLlib] Migrate MLlib to the DataFrame reader/writer API.
* [SPARK-7473] [MLLIB] Add reservoir sample in RandomForestAiHe2015-05-152-4/+3
| | | | | | | | | | | | | reservoir feature sample by using existing api Author: AiHe <ai.he@ussuning.com> Closes #5988 from AiHe/reservoir and squashes the following commits: e7a41ac [AiHe] remove non-robust testing case 28ffb9a [AiHe] set seed as rng.nextLong 37459e1 [AiHe] set fixed seed 1e98a4c [AiHe] [MLLIB][tree] Add reservoir sample in RandomForest
* [SPARK-7668] [MLLIB] Preserve isTransposed property for Matrix after calling ↵Liang-Chi Hsieh2015-05-151-2/+3
| | | | | | | | | | | | map function JIRA: https://issues.apache.org/jira/browse/SPARK-7668 Author: Liang-Chi Hsieh <viirya@gmail.com> Closes #6188 from viirya/fix_matrix_map and squashes the following commits: 2a7cc97 [Liang-Chi Hsieh] Preserve isTransposed property for Matrix after calling map function.
* [SPARK-6258] [MLLIB] GaussianMixture Python API parity checkYanbo Liang2015-05-152-11/+22
| | | | | | | | | | | | | | | | | | | Implement Python API for major disparities of GaussianMixture cluster algorithm between Scala & Python ```scala GaussianMixture setInitialModel GaussianMixtureModel k ``` Author: Yanbo Liang <ybliang8@gmail.com> Closes #6087 from yanboliang/spark-6258 and squashes the following commits: b3af21c [Yanbo Liang] fix typo 2b645c1 [Yanbo Liang] fix doc 638b4b7 [Yanbo Liang] address comments b5bcade [Yanbo Liang] GaussianMixture Python API parity check
* [SPARK-7407] [MLLIB] use uid + name to identify parametersXiangrui Meng2015-05-1445-198/+413
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | A param instance is strongly attached to an parent in the current implementation. So if we make a copy of an estimator or a transformer in pipelines and other meta-algorithms, it becomes error-prone to copy the params to the copied instances. In this PR, a param is identified by its parent's UID and the param name. So it becomes loosely attached to its parent and all its derivatives. The UID is preserved during copying or fitting. All components now have a default constructor and a constructor that takes a UID as input. I keep the constructors for Param in this PR to reduce the amount of diff and moved `parent` as a mutable field. This PR still needs some clean-ups, and there are several spark.ml PRs pending. I'll try to get them merged first and then update this PR. jkbradley Author: Xiangrui Meng <meng@databricks.com> Closes #6019 from mengxr/SPARK-7407 and squashes the following commits: c4c8120 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-7407 520f0a2 [Xiangrui Meng] address comments 2569168 [Xiangrui Meng] fix tests 873caca [Xiangrui Meng] fix tests in OneVsRest; fix a racing condition in shouldOwn 409ea08 [Xiangrui Meng] minor updates 83a163c [Xiangrui Meng] update JavaDeveloperApiExample 5db5325 [Xiangrui Meng] update OneVsRest 7bde7ae [Xiangrui Meng] merge master 697fdf9 [Xiangrui Meng] update Bucketizer 7b4f6c2 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-7407 629d402 [Xiangrui Meng] fix LRSuite 154516f [Xiangrui Meng] merge master aa4a611 [Xiangrui Meng] fix examples/compile a4794dd [Xiangrui Meng] change Param to use to reduce the size of diff fdbc415 [Xiangrui Meng] all tests passed c255f17 [Xiangrui Meng] fix tests in ParamsSuite 818e1db [Xiangrui Meng] merge master e1160cf [Xiangrui Meng] fix tests fbc39f0 [Xiangrui Meng] pass test:compile 108937e [Xiangrui Meng] pass compile 8726d39 [Xiangrui Meng] use parent uid in Param eaeed35 [Xiangrui Meng] update Identifiable
* [SPARK-7620] [ML] [MLLIB] Removed calling size, length in while condition to ↵DB Tsai2015-05-1313-44/+73
| | | | | | | | | | | avoid extra JVM call Author: DB Tsai <dbt@netflix.com> Closes #6137 from dbtsai/clean and squashes the following commits: 185816d [DB Tsai] fix compilication issue f418d08 [DB Tsai] first commit
* [SPARK-7612] [MLLIB] update NB training to use mllib's BLASXiangrui Meng2015-05-131-23/+20
| | | | | | | | | | | This is similar to the changes to k-means, which gives us better control on the performance. dbtsai Author: Xiangrui Meng <meng@databricks.com> Closes #6128 from mengxr/SPARK-7612 and squashes the following commits: b5c24c5 [Xiangrui Meng] merge master a90e3ec [Xiangrui Meng] update NB training to use mllib's BLAS
* [SPARK-7545] [MLLIB] Added check in Bernoulli Naive Bayes to make sure that ↵leahmcguire2015-05-132-3/+58
| | | | | | | | | | | | | | | | | | | | both training and predict features have values of 0 or 1 Author: leahmcguire <lmcguire@salesforce.com> Closes #6073 from leahmcguire/binaryCheckNB and squashes the following commits: b8442c2 [leahmcguire] changed to if else for value checks 911bf83 [leahmcguire] undid reformat 4eedf1e [leahmcguire] moved bernoulli check 9ee9e84 [leahmcguire] fixed style error 3f3b32c [leahmcguire] fixed zero one check so only called in combiner 831fd27 [leahmcguire] got test working f44bb3c [leahmcguire] removed changes from CV branch 67253f0 [leahmcguire] added check to bernoulli to ensure feature values are zero or one f191c71 [leahmcguire] fixed name 58d060b [leahmcguire] changed param name and test according to comments 04f0d3c [leahmcguire] Added stats from cross validation as a val in the cross validation model to save them for user access
* [SPARK-7593] [ML] Python Api for ml.feature.BucketizerBurak Yavuz2015-05-132-2/+15
| | | | | | | | | | | | | Added `ml.feature.Bucketizer` to PySpark. cc mengxr Author: Burak Yavuz <brkyvz@gmail.com> Closes #6124 from brkyvz/ml-bucket and squashes the following commits: 05285be [Burak Yavuz] added sphinx doc 6abb6ed [Burak Yavuz] added support for Bucketizer
* [SPARK-7528] [MLLIB] make RankingMetrics Java-friendlyXiangrui Meng2015-05-122-4/+87
| | | | | | | | | | `RankingMetrics` contains a ClassTag, which is hard to create in Java. This PR adds a factory method `of` for Java users. coderxiang Author: Xiangrui Meng <meng@databricks.com> Closes #6098 from mengxr/SPARK-7528 and squashes the following commits: e5d57ae [Xiangrui Meng] make RankingMetrics Java-friendly
* [SPARK-7573] [ML] OneVsRest cleanupsJoseph K. Bradley2015-05-123-31/+23
| | | | | | | | | | | | | | | | | | Minor cleanups discussed with [~mengxr]: * move OneVsRest from reduction to classification sub-package * make model constructor private Some doc cleanups too CC: harsha2010 Could you please verify this looks OK? Thanks! Author: Joseph K. Bradley <joseph@databricks.com> Closes #6097 from jkbradley/onevsrest-cleanup and squashes the following commits: 4ecd48d [Joseph K. Bradley] org imports 430b065 [Joseph K. Bradley] moved OneVsRest from reduction subpackage to classification. small java doc style fixes 9f8b9b9 [Joseph K. Bradley] Small cleanups to OneVsRest. Made model constructor private to ml package.
* [SPARK-7557] [ML] [DOC] User guide for spark.ml HashingTF, TokenizerJoseph K. Bradley2015-05-121-0/+81
| | | | | | | | | | | | | | | | | | Added feature transformer subsection to spark.ml guide, with HashingTF and Tokenizer. Added JavaHashingTFSuite to test Java examples in new guide. I've run Scala, Python examples in the Spark/PySpark shells. I ran the Java examples via the test suite (with small modifications for printing). CC: mengxr Author: Joseph K. Bradley <joseph@databricks.com> Closes #6093 from jkbradley/hashingtf-guide and squashes the following commits: d5d213f [Joseph K. Bradley] small fix dd6e91a [Joseph K. Bradley] fixes from code review of user guide 33c3ff9 [Joseph K. Bradley] small fix bc6058c [Joseph K. Bradley] fix link 361a174 [Joseph K. Bradley] Added subsection for feature transformers to spark.ml guide, with HashingTF and Tokenizer. Added JavaHashingTFSuite to test Java examples in new guide
* [SPARK-7571] [MLLIB] rename Math to mathXiangrui Meng2015-05-129-15/+15
| | | | | | | | | | `scala.Math` is deprecated since 2.8. This PR only touchs `Math` usages in MLlib. dbtsai Author: Xiangrui Meng <meng@databricks.com> Closes #6092 from mengxr/SPARK-7571 and squashes the following commits: fe8f8d3 [Xiangrui Meng] Math -> math
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