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* [SPARK-11888][ML] Decision tree persistence in spark.mlJoseph K. Bradley2016-03-166-6/+6
| | | | | | | | | | | | | | | | | | | | ### What changes were proposed in this pull request? Made these MLReadable and MLWritable: DecisionTreeClassifier, DecisionTreeClassificationModel, DecisionTreeRegressor, DecisionTreeRegressionModel * The shared implementation is in treeModels.scala * I use case classes to create a DataFrame to save, and I use the Dataset API to parse loaded files. Other changes: * Made CategoricalSplit.numCategories public (to use in persistence) * Fixed a bug in DefaultReadWriteTest.testEstimatorAndModelReadWrite, where it did not call the checkModelData function passed as an argument. This caused an error in LDASuite, which I fixed. ### How was this patch tested? Persistence is tested via unit tests. For each algorithm, there are 2 non-trivial trees (depth 2). One is built with continuous features, and one with categorical; this ensures that both types of splits are tested. Author: Joseph K. Bradley <joseph@databricks.com> Closes #11581 from jkbradley/dt-io.
* [SPARK-13823][CORE][STREAMING][SQL] Always specify Charset in String <-> ↵Sean Owen2016-03-131-2/+2
| | | | | | | | | | | | | | | | | | | | byte[] conversions (and remaining Coverity items) ## What changes were proposed in this pull request? - Fixes calls to `new String(byte[])` or `String.getBytes()` that rely on platform default encoding, to use UTF-8 - Same for `InputStreamReader` and `OutputStreamWriter` constructors - Standardizes on UTF-8 everywhere - Standardizes specifying the encoding with `StandardCharsets.UTF-8`, not the Guava constant or "UTF-8" (which means handling `UnuspportedEncodingException`) - (also addresses the other remaining Coverity scan issues, which are pretty trivial; these are separated into commit https://github.com/srowen/spark/commit/1deecd8d9ca986d8adb1a42d315890ce5349d29c ) ## How was this patch tested? Jenkins tests Author: Sean Owen <sowen@cloudera.com> Closes #11657 from srowen/SPARK-13823.
* [SPARK-13841][SQL] Removes Dataset.collectRows()/takeRows()Cheng Lian2016-03-131-1/+1
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? This PR removes two methods, `collectRows()` and `takeRows()`, from `Dataset[T]`. These methods were added in PR #11443, and were later considered not useful. ## How was this patch tested? Existing tests should do the work. Author: Cheng Lian <lian@databricks.com> Closes #11678 from liancheng/remove-collect-rows-and-take-rows.
* [SPARK-13244][SQL] Migrates DataFrame to DatasetCheng Lian2016-03-1029-99/+118
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? This PR unifies DataFrame and Dataset by migrating existing DataFrame operations to Dataset and make `DataFrame` a type alias of `Dataset[Row]`. Most Scala code changes are source compatible, but Java API is broken as Java knows nothing about Scala type alias (mostly replacing `DataFrame` with `Dataset<Row>`). There are several noticeable API changes related to those returning arrays: 1. `collect`/`take` - Old APIs in class `DataFrame`: ```scala def collect(): Array[Row] def take(n: Int): Array[Row] ``` - New APIs in class `Dataset[T]`: ```scala def collect(): Array[T] def take(n: Int): Array[T] def collectRows(): Array[Row] def takeRows(n: Int): Array[Row] ``` Two specialized methods `collectRows` and `takeRows` are added because Java doesn't support returning generic arrays. Thus, for example, `DataFrame.collect(): Array[T]` actually returns `Object` instead of `Array<T>` from Java side. Normally, Java users may fall back to `collectAsList` and `takeAsList`. The two new specialized versions are added to avoid performance regression in ML related code (but maybe I'm wrong and they are not necessary here). 1. `randomSplit` - Old APIs in class `DataFrame`: ```scala def randomSplit(weights: Array[Double], seed: Long): Array[DataFrame] def randomSplit(weights: Array[Double]): Array[DataFrame] ``` - New APIs in class `Dataset[T]`: ```scala def randomSplit(weights: Array[Double], seed: Long): Array[Dataset[T]] def randomSplit(weights: Array[Double]): Array[Dataset[T]] ``` Similar problem as above, but hasn't been addressed for Java API yet. We can probably add `randomSplitAsList` to fix this one. 1. `groupBy` Some original `DataFrame.groupBy` methods have conflicting signature with original `Dataset.groupBy` methods. To distinguish these two, typed `Dataset.groupBy` methods are renamed to `groupByKey`. Other noticeable changes: 1. Dataset always do eager analysis now We used to support disabling DataFrame eager analysis to help reporting partially analyzed malformed logical plan on analysis failure. However, Dataset encoders requires eager analysi during Dataset construction. To preserve the error reporting feature, `AnalysisException` now takes an extra `Option[LogicalPlan]` argument to hold the partially analyzed plan, so that we can check the plan tree when reporting test failures. This plan is passed by `QueryExecution.assertAnalyzed`. ## How was this patch tested? Existing tests do the work. ## TODO - [ ] Fix all tests - [ ] Re-enable MiMA check - [ ] Update ScalaDoc (`since`, `group`, and example code) Author: Cheng Lian <lian@databricks.com> Author: Yin Huai <yhuai@databricks.com> Author: Wenchen Fan <wenchen@databricks.com> Author: Cheng Lian <liancheng@users.noreply.github.com> Closes #11443 from liancheng/ds-to-df.
* [SPARK-13702][CORE][SQL][MLLIB] Use diamond operator for generic instance ↵Dongjoon Hyun2016-03-098-12/+12
| | | | | | | | | | | | | | | | | | | | | | | | | creation in Java code. ## What changes were proposed in this pull request? In order to make `docs/examples` (and other related code) more simple/readable/user-friendly, this PR replaces existing codes like the followings by using `diamond` operator. ``` - final ArrayList<Product2<Object, Object>> dataToWrite = - new ArrayList<Product2<Object, Object>>(); + final ArrayList<Product2<Object, Object>> dataToWrite = new ArrayList<>(); ``` Java 7 or higher supports **diamond** operator which replaces the type arguments required to invoke the constructor of a generic class with an empty set of type parameters (<>). Currently, Spark Java code use mixed usage of this. ## How was this patch tested? Manual. Pass the existing tests. Author: Dongjoon Hyun <dongjoon@apache.org> Closes #11541 from dongjoon-hyun/SPARK-13702.
* [SPARK-13715][MLLIB] Remove last usages of jblas in testsSean Owen2016-03-082-27/+29
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? Remove last usage of jblas, in tests ## How was this patch tested? Jenkins tests -- the same ones that are being modified. Author: Sean Owen <sowen@cloudera.com> Closes #11560 from srowen/SPARK-13715.
* [SPARK-13583][CORE][STREAMING] Remove unused imports and add checkstyle ruleDongjoon Hyun2016-03-0311-11/+0
| | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? After SPARK-6990, `dev/lint-java` keeps Java code healthy and helps PR review by saving much time. This issue aims remove unused imports from Java/Scala code and add `UnusedImports` checkstyle rule to help developers. ## How was this patch tested? ``` ./dev/lint-java ./build/sbt compile ``` Author: Dongjoon Hyun <dongjoon@apache.org> Closes #11438 from dongjoon-hyun/SPARK-13583.
* [SPARK-13423][WIP][CORE][SQL][STREAMING] Static analysis fixes for 2.xSean Owen2016-03-031-1/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Make some cross-cutting code improvements according to static analysis. These are individually up for discussion since they exist in separate commits that can be reverted. The changes are broadly: - Inner class should be static - Mismatched hashCode/equals - Overflow in compareTo - Unchecked warnings - Misuse of assert, vs junit.assert - get(a) + getOrElse(b) -> getOrElse(a,b) - Array/String .size -> .length (occasionally, -> .isEmpty / .nonEmpty) to avoid implicit conversions - Dead code - tailrec - exists(_ == ) -> contains find + nonEmpty -> exists filter + size -> count - reduce(_+_) -> sum map + flatten -> map The most controversial may be .size -> .length simply because of its size. It is intended to avoid implicits that might be expensive in some places. ## How was the this patch tested? Existing Jenkins unit tests. Author: Sean Owen <sowen@cloudera.com> Closes #11292 from srowen/SPARK-13423.
* [SPARK-12830] Java style: disallow trailing whitespaces.Reynold Xin2016-01-141-1/+1
| | | | | | Author: Reynold Xin <rxin@databricks.com> Closes #10764 from rxin/SPARK-12830.
* [SPARK-12618][CORE][STREAMING][SQL] Clean up build warnings: 2.0.0 editionSean Owen2016-01-082-11/+11
| | | | | | | | Fix most build warnings: mostly deprecated API usages. I'll annotate some of the changes below. CC rxin who is leading the charge to remove the deprecated APIs. Author: Sean Owen <sowen@cloudera.com> Closes #10570 from srowen/SPARK-12618.
* [SPARK-6724][MLLIB] Support model save/load for FPGrowthModelYanbo Liang2016-01-051-0/+40
| | | | | | | | Support model save/load for FPGrowthModel Author: Yanbo Liang <ybliang8@gmail.com> Closes #9267 from yanboliang/spark-6724.
* [SPARK-11605][MLLIB] ML 1.6 QA: API: Java compatibility, docsYuhao Yang2015-12-081-3/+35
| | | | | | | | | | | | | | | | | | | | | | | | | jira: https://issues.apache.org/jira/browse/SPARK-11605 Check Java compatibility for MLlib for this release. fix: 1. `StreamingTest.registerStream` needs java friendly interface. 2. `GradientBoostedTreesModel.computeInitialPredictionAndError` and `GradientBoostedTreesModel.updatePredictionError` has java compatibility issue. Mark them as `developerAPI`. TBD: [updated] no fix for now per discussion. `org.apache.spark.mllib.classification.LogisticRegressionModel` `public scala.Option<java.lang.Object> getThreshold();` has wrong return type for Java invocation. `SVMModel` has the similar issue. Yet adding a `scala.Option<java.util.Double> getThreshold()` would result in an overloading error due to the same function signature. And adding a new function with different name seems to be not necessary. cc jkbradley feynmanliang Author: Yuhao Yang <hhbyyh@gmail.com> Closes #10102 from hhbyyh/javaAPI.
* [SPARK-6990][BUILD] Add Java linting script; fix minor warningsDmitry Erastov2015-12-042-4/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This replaces https://github.com/apache/spark/pull/9696 Invoke Checkstyle and print any errors to the console, failing the step. Use Google's style rules modified according to https://cwiki.apache.org/confluence/display/SPARK/Spark+Code+Style+Guide Some important checks are disabled (see TODOs in `checkstyle.xml`) due to multiple violations being present in the codebase. Suggest fixing those TODOs in a separate PR(s). More on Checkstyle can be found on the [official website](http://checkstyle.sourceforge.net/). Sample output (from [build 46345](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/46345/consoleFull)) (duplicated because I run the build twice with different profiles): > Checkstyle checks failed at following occurrences: [ERROR] src/main/java/org/apache/spark/sql/execution/datasources/parquet/UnsafeRowParquetRecordReader.java:[217,7] (coding) MissingSwitchDefault: switch without "default" clause. > [ERROR] src/main/java/org/apache/spark/sql/execution/datasources/parquet/SpecificParquetRecordReaderBase.java:[198,10] (modifier) ModifierOrder: 'protected' modifier out of order with the JLS suggestions. > [ERROR] src/main/java/org/apache/spark/sql/execution/datasources/parquet/UnsafeRowParquetRecordReader.java:[217,7] (coding) MissingSwitchDefault: switch without "default" clause. > [ERROR] src/main/java/org/apache/spark/sql/execution/datasources/parquet/SpecificParquetRecordReaderBase.java:[198,10] (modifier) ModifierOrder: 'protected' modifier out of order with the JLS suggestions. > [error] running /home/jenkins/workspace/SparkPullRequestBuilder2/dev/lint-java ; received return code 1 Also fix some of the minor violations that didn't require sweeping changes. Apologies for the previous botched PRs - I finally figured out the issue. cr: JoshRosen, pwendell > I state that the contribution is my original work, and I license the work to the project under the project's open source license. Author: Dmitry Erastov <derastov@gmail.com> Closes #9867 from dskrvk/master.
* [SPARK-11672][ML] set active SQLContext in JavaDefaultReadWriteSuiteXiangrui Meng2015-11-151-1/+6
| | | | | | | | The same as #9694, but for Java test suite. yhuai Author: Xiangrui Meng <meng@databricks.com> Closes #9719 from mengxr/SPARK-11672.4.
* [SPARK-11672][ML] flaky spark.ml read/write testsXiangrui Meng2015-11-121-2/+2
| | | | | | | | | | We set `sqlContext = null` in `afterAll`. However, this doesn't change `SQLContext.activeContext` and then `SQLContext.getOrCreate` might use the `SparkContext` from previous test suite and hence causes the error. This PR calls `clearActive` in `beforeAll` and `afterAll` to avoid using an old context from other test suites. cc: yhuai Author: Xiangrui Meng <meng@databricks.com> Closes #9677 from mengxr/SPARK-11672.2.
* [SPARK-11672][ML] disable spark.ml read/write testsXiangrui Meng2015-11-111-2/+2
| | | | | | | | | | | | Saw several failures on Jenkins, e.g., https://amplab.cs.berkeley.edu/jenkins/job/NewSparkPullRequestBuilder/2040/testReport/org.apache.spark.ml.util/JavaDefaultReadWriteSuite/testDefaultReadWrite/. This is the first failure in master build: https://amplab.cs.berkeley.edu/jenkins/job/Spark-Master-SBT/3982/ I cannot reproduce it on local. So temporarily disable the tests and I will look into the issue under the same JIRA. I'm going to merge the PR after Jenkins passes compile. Author: Xiangrui Meng <meng@databricks.com> Closes #9641 from mengxr/SPARK-11672.
* [SPARK-11069][ML] Add RegexTokenizer option to convert to lowercaseYuhao Yang2015-11-091-0/+1
| | | | | | | | | | | | | | jira: https://issues.apache.org/jira/browse/SPARK-11069 quotes from jira: Tokenizer converts strings to lowercase automatically, but RegexTokenizer does not. It would be nice to add an option to RegexTokenizer to convert to lowercase. Proposal: call the Boolean Param "toLowercase" set default to false (so behavior does not change) Actually sklearn converts to lowercase before tokenizing too Author: Yuhao Yang <hhbyyh@gmail.com> Closes #9092 from hhbyyh/tokenLower.
* [SPARK-6517][MLLIB] Implement the Algorithm of Hierarchical ClusteringYu ISHIKAWA2015-11-091-0/+73
| | | | | | | | | | | | | | | | | | I implemented a hierarchical clustering algorithm again. This PR doesn't include examples, documentation and spark.ml APIs. I am going to send another PRs later. https://issues.apache.org/jira/browse/SPARK-6517 - This implementation based on a bi-sectiong K-means clustering. - It derives from the freeman-lab 's implementation - The basic idea is not changed from the previous version. (#2906) - However, It is 1000x faster than the previous version through parallel processing. Thank you for your great cooperation, RJ Nowling(rnowling), Jeremy Freeman(freeman-lab), Xiangrui Meng(mengxr) and Sean Owen(srowen). Author: Yu ISHIKAWA <yuu.ishikawa@gmail.com> Author: Xiangrui Meng <meng@databricks.com> Author: Yu ISHIKAWA <yu-iskw@users.noreply.github.com> Closes #5267 from yu-iskw/new-hierarchical-clustering.
* [SPARK-11217][ML] save/load for non-meta estimators and transformersXiangrui Meng2015-11-061-0/+74
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This PR implements the default save/load for non-meta estimators and transformers using the JSON serialization of param values. The saved metadata includes: * class name * uid * timestamp * paramMap The save/load interface is similar to DataFrames. We use the current active context by default, which should be sufficient for most use cases. ~~~scala instance.save("path") instance.write.context(sqlContext).overwrite().save("path") Instance.load("path") ~~~ The param handling is different from the design doc. We didn't save default and user-set params separately, and when we load it back, all parameters are user-set. This does cause issues. But it also cause other issues if we modify the default params. TODOs: * [x] Java test * [ ] a follow-up PR to implement default save/load for all non-meta estimators and transformers cc jkbradley Author: Xiangrui Meng <meng@databricks.com> Closes #9454 from mengxr/SPARK-11217.
* [SPARK-10592] [ML] [PySpark] Deprecate weights and use coefficients instead ↵vectorijk2015-11-021-3/+3
| | | | | | | | | | in ML models Deprecated in `LogisticRegression` and `LinearRegression` Author: vectorijk <jiangkai@gmail.com> Closes #9311 from vectorijk/spark-10592.
* [SPARK-10668] [ML] Use WeightedLeastSquares in LinearRegression with L…lewuathe2015-10-191-1/+2
| | | | | | | | | | | …2 regularization if the number of features is small Author: lewuathe <lewuathe@me.com> Author: Lewuathe <sasaki@treasure-data.com> Author: Kai Sasaki <sasaki@treasure-data.com> Author: Lewuathe <lewuathe@me.com> Closes #8884 from Lewuathe/SPARK-10668.
* [SPARK-10763] [ML] [JAVA] [TEST] Update Java MLLIB/ML tests to use ↵Holden Karau2015-09-2310-39/+42
| | | | | | | | | | simplified dataframe construction As introduced in https://issues.apache.org/jira/browse/SPARK-10630 we now have an easier way to create dataframes from local Java lists. Lets update the tests to use those. Author: Holden Karau <holden@pigscanfly.ca> Closes #8886 from holdenk/SPARK-10763-update-java-mllib-ml-tests-to-use-simplified-dataframe-construction.
* [SPARK-10706] [MLLIB] Add java wrapper for random vector rddMeihua Wu2015-09-221-0/+17
| | | | | | | | | | Add java wrapper for random vector rdd holdenk srowen Author: Meihua Wu <meihuawu@umich.edu> Closes #8841 from rotationsymmetry/SPARK-10706.
* [SPARK-10626] [MLLIB] create java friendly method for random rddHolden Karau2015-09-211-0/+30
| | | | | | | | SPARK-3136 added a large number of functions for creating Java RandomRDDs, but for people that want to use custom RandomDataGenerators we should make a Java friendly method. Author: Holden Karau <holden@pigscanfly.ca> Closes #8782 from holdenk/SPARK-10626-create-java-friendly-method-for-randomRDD.
* [SPARK-10537] [ML] document LIBSVM source options in public API doc and some ↵Xiangrui Meng2015-09-111-12/+12
| | | | | | | | | | | | | | | | | minor improvements We should document options in public API doc. Otherwise, it is hard to find out the options without looking at the code. I tried to make `DefaultSource` private and put the documentation to package doc. However, since then there exists no public class under `source.libsvm`, the Java package doc doesn't show up in the generated html file (http://bugs.java.com/bugdatabase/view_bug.do?bug_id=4492654). So I put the doc to `DefaultSource` instead. There are several minor updates in this PR: 1. Do `vectorType == "sparse"` only once. 2. Update `hashCode` and `equals`. 3. Remove inherited doc. 4. Delete temp dir in `afterAll`. Lewuathe Author: Xiangrui Meng <meng@databricks.com> Closes #8699 from mengxr/SPARK-10537.
* [SPARK-10117] [MLLIB] Implement SQL data source API for reading LIBSVM datalewuathe2015-09-091-0/+80
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | It is convenient to implement data source API for LIBSVM format to have a better integration with DataFrames and ML pipeline API. Two option is implemented. * `numFeatures`: Specify the dimension of features vector * `featuresType`: Specify the type of output vector. `sparse` is default. Author: lewuathe <lewuathe@me.com> Closes #8537 from Lewuathe/SPARK-10117 and squashes the following commits: 986999d [lewuathe] Change unit test phrase 11d513f [lewuathe] Fix some reviews 21600a4 [lewuathe] Merge branch 'master' into SPARK-10117 9ce63c7 [lewuathe] Rewrite service loader file 1fdd2df [lewuathe] Merge branch 'SPARK-10117' of github.com:Lewuathe/spark into SPARK-10117 ba3657c [lewuathe] Merge branch 'master' into SPARK-10117 0ea1c1c [lewuathe] LibSVMRelation is registered into META-INF 4f40891 [lewuathe] Improve test suites 5ab62ab [lewuathe] Merge branch 'master' into SPARK-10117 8660d0e [lewuathe] Fix Java unit test b56a948 [lewuathe] Merge branch 'master' into SPARK-10117 2c12894 [lewuathe] Remove unnecessary tag 7d693c2 [lewuathe] Resolv conflict 62010af [lewuathe] Merge branch 'master' into SPARK-10117 a97ee97 [lewuathe] Fix some points aef9564 [lewuathe] Fix 70ee4dd [lewuathe] Add Java test 3fd8dce [lewuathe] [SPARK-10117] Implement SQL data source API for reading LIBSVM data 40d3027 [lewuathe] Add Java test 7056d4a [lewuathe] Merge branch 'master' into SPARK-10117 99accaa [lewuathe] [SPARK-10117] Implement SQL data source API for reading LIBSVM data
* [SPARK-10013] [ML] [JAVA] [TEST] remove java assert from java unit testsHolden Karau2015-09-054-52/+54
| | | | | | | | From Jira: We should use assertTrue, etc. instead to make sure the asserts are not ignored in tests. Author: Holden Karau <holden@pigscanfly.ca> Closes #8607 from holdenk/SPARK-10013-remove-java-assert-from-java-unit-tests.
* [SPARK-9680] [MLLIB] [DOC] StopWordsRemovers user guide and Java ↵Feynman Liang2015-08-271-0/+72
| | | | | | | | | | | | | compatibility test * Adds user guide for ml.feature.StopWordsRemovers, ran code examples on my machine * Cleans up scaladocs for public methods * Adds test for Java compatibility * Follow up Python user guide code example is tracked by SPARK-10249 Author: Feynman Liang <fliang@databricks.com> Closes #8436 from feynmanliang/SPARK-10230.
* [SPARK-10257] [MLLIB] Removes Guava from all spark.mllib Java testsFeynman Liang2015-08-2714-74/+71
| | | | | | | | | | | | * Replaces instances of `Lists.newArrayList` with `Arrays.asList` * Replaces `commons.lang.StringUtils` over `com.google.collections.Strings` * Replaces `List` interface over `ArrayList` implementations This PR along with #8445 #8446 #8447 completely removes all `com.google.collections.Lists` dependencies within mllib's Java tests. Author: Feynman Liang <fliang@databricks.com> Closes #8451 from feynmanliang/SPARK-10257.
* [SPARK-9613] [HOTFIX] Fix usage of JavaConverters removed in Scala 2.11Jacek Laskowski2015-08-271-1/+1
| | | | | | | | | | | | | | | | | Fix for [JavaConverters.asJavaListConverter](http://www.scala-lang.org/api/2.10.5/index.html#scala.collection.JavaConverters$) being removed in 2.11.7 and hence the build fails with the 2.11 profile enabled. Tested with the default 2.10 and 2.11 profiles. BUILD SUCCESS in both cases. Build for 2.10: ./build/mvn -Pyarn -Phadoop-2.6 -Dhadoop.version=2.7.1 -DskipTests clean install and 2.11: ./dev/change-scala-version.sh 2.11 ./build/mvn -Pyarn -Phadoop-2.6 -Dhadoop.version=2.7.1 -Dscala-2.11 -DskipTests clean install Author: Jacek Laskowski <jacek@japila.pl> Closes #8479 from jaceklaskowski/SPARK-9613-hotfix.
* [SPARK-10256] [ML] Removes guava dependency from spark.ml.classification ↵Feynman Liang2015-08-271-2/+2
| | | | | | | | JavaTests Author: Feynman Liang <fliang@databricks.com> Closes #8447 from feynmanliang/SPARK-10256.
* [SPARK-10255] [ML] Removes Guava dependencies from spark.ml.param JavaTestsFeynman Liang2015-08-272-6/+6
| | | | | | Author: Feynman Liang <fliang@databricks.com> Closes #8446 from feynmanliang/SPARK-10255.
* [SPARK-10254] [ML] Removes Guava dependencies in spark.ml.feature JavaTestsFeynman Liang2015-08-2711-30/+35
| | | | | | | | | * Replaces `com.google.common` dependencies with `java.util.Arrays` * Small clean up in `JavaNormalizerSuite` Author: Feynman Liang <fliang@databricks.com> Closes #8445 from feynmanliang/SPARK-10254.
* [SPARK-9613] [CORE] Ban use of JavaConversions and migrate all existing uses ↵Sean Owen2015-08-251-3/+4
| | | | | | | | | | | | to JavaConverters Replace `JavaConversions` implicits with `JavaConverters` Most occurrences I've seen so far are necessary conversions; a few have been avoidable. None are in critical code as far as I see, yet. Author: Sean Owen <sowen@cloudera.com> Closes #8033 from srowen/SPARK-9613.
* [SPARK-9893] User guide with Java test suite for VectorSlicerXusen Yin2015-08-211-0/+85
| | | | | | | | | | Add user guide for `VectorSlicer`, with Java test suite and Python version VectorSlicer. Note that Python version does not support selecting by names now. Author: Xusen Yin <yinxusen@gmail.com> Closes #8267 from yinxusen/SPARK-9893.
* [SPARK-9245] [MLLIB] LDA topic assignmentsJoseph K. Bradley2015-08-201-0/+7
| | | | | | | | | | For each (document, term) pair, return top topic. Note that instances of (doc, term) pairs within a document (a.k.a. "tokens") are exchangeable, so we should provide an estimate per document-term, rather than per token. CC: rotationsymmetry mengxr Author: Joseph K. Bradley <joseph@databricks.com> Closes #8329 from jkbradley/lda-topic-assignments.
* [SPARK-10138] [ML] move setters to MultilayerPerceptronClassifier and add ↵Xiangrui Meng2015-08-201-0/+74
| | | | | | | | | | Java test suite Otherwise, setters do not return self type. jkbradley avulanov Author: Xiangrui Meng <meng@databricks.com> Closes #8342 from mengxr/SPARK-10138.
* [SPARK-9900] [MLLIB] User guide for Association RulesFeynman Liang2015-08-181-1/+1
| | | | | | | | Updates FPM user guide to include Association Rules. Author: Feynman Liang <fliang@databricks.com> Closes #8207 from feynmanliang/SPARK-9900-arules.
* [SPARK-9661] [MLLIB] minor clean-up of SPARK-9661Xiangrui Meng2015-08-141-17/+23
| | | | | | | | Some minor clean-ups after SPARK-9661. See my inline comments. MechCoder jkbradley Author: Xiangrui Meng <meng@databricks.com> Closes #8190 from mengxr/SPARK-9661-fix.
* [SPARK-9661] [MLLIB] [ML] Java compatibilityMechCoder2015-08-132-0/+46
| | | | | | | | | | | | I skimmed through the docs for various instance of Object and replaced them with Java compaible versions of the same. 1. Some methods in LDAModel. 2. runMiniBatchSGD 3. kolmogorovSmirnovTest Author: MechCoder <manojkumarsivaraj334@gmail.com> Closes #8126 from MechCoder/java_incop.
* [SPARK-9789] [ML] Added logreg threshold param backJoseph K. Bradley2015-08-121-5/+2
| | | | | | | | | | Reinstated LogisticRegression.threshold Param for binary compatibility. Param thresholds overrides threshold, if set. CC: mengxr dbtsai feynmanliang Author: Joseph K. Bradley <joseph@databricks.com> Closes #8079 from jkbradley/logreg-reinstate-threshold.
* [SPARK-9112] [ML] Implement Stats for LogisticRegressionMechCoder2015-08-061-0/+9
| | | | | | | | | | | | | | | | | | | I have added support for stats in LogisticRegression. The API is similar to that of LinearRegression with LogisticRegressionTrainingSummary and LogisticRegressionSummary I have some queries and asked them inline. Author: MechCoder <manojkumarsivaraj334@gmail.com> Closes #7538 from MechCoder/log_reg_stats and squashes the following commits: 2e9f7c7 [MechCoder] Change defs into lazy vals d775371 [MechCoder] Clean up class inheritance 9586125 [MechCoder] Add abstraction to handle Multiclass Metrics 40ad8ef [MechCoder] minor 640376a [MechCoder] remove unnecessary dataframe stuff and add docs 80d9954 [MechCoder] Added tests fbed861 [MechCoder] DataFrame support for metrics 70a0fc4 [MechCoder] [SPARK-9112] [ML] Implement Stats for LogisticRegression
* [SPARK-8069] [ML] Add multiclass thresholds for ProbabilisticClassifierHolden Karau2015-08-041-2/+7
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This PR replaces the old "threshold" with a generalized "thresholds" Param. We keep getThreshold,setThreshold for backwards compatibility for binary classification. Note that the primary author of this PR is holdenk Author: Holden Karau <holden@pigscanfly.ca> Author: Joseph K. Bradley <joseph@databricks.com> Closes #7909 from jkbradley/holdenk-SPARK-8069-add-cutoff-aka-threshold-to-random-forest and squashes the following commits: 3952977 [Joseph K. Bradley] fixed pyspark doc test 85febc8 [Joseph K. Bradley] made python unit tests a little more robust 7eb1d86 [Joseph K. Bradley] small cleanups 6cc2ed8 [Joseph K. Bradley] Fixed remaining merge issues. 0255e44 [Joseph K. Bradley] Many cleanups for thresholds, some more tests 7565a60 [Holden Karau] fix pep8 style checks, add a getThreshold method similar to our LogisticRegression.scala one for API compat be87f26 [Holden Karau] Convert threshold to thresholds in the python code, add specialized support for Array[Double] to shared parems codegen, etc. 6747dad [Holden Karau] Override raw2prediction for ProbabilisticClassifier, fix some tests 25df168 [Holden Karau] Fix handling of thresholds in LogisticRegression c02d6c0 [Holden Karau] No default for thresholds 5e43628 [Holden Karau] CR feedback and fixed the renamed test f3fbbd1 [Holden Karau] revert the changes to random forest :( 51f581c [Holden Karau] Add explicit types to public methods, fix long line f7032eb [Holden Karau] Fix a java test bug, remove some unecessary changes adf15b4 [Holden Karau] rename the classifier suite test to ProbabilisticClassifierSuite now that we only have it in Probabilistic 398078a [Holden Karau] move the thresholding around a bunch based on the design doc 4893bdc [Holden Karau] Use numtrees of 3 since previous result was tied (one tree for each) and the switch from different max methods picked a different element (since they were equal I think this is ok) 638854c [Holden Karau] Add a scala RandomForestClassifierSuite test based on corresponding python test e09919c [Holden Karau] Fix return type, I need more coffee.... 8d92cac [Holden Karau] Use ClassifierParams as the head 3456ed3 [Holden Karau] Add explicit return types even though just test a0f3b0c [Holden Karau] scala style fixes 6f14314 [Holden Karau] Since hasthreshold/hasthresholds is in root classifier now ffc8dab [Holden Karau] Update the sharedParams 0420290 [Holden Karau] Allow us to override the get methods selectively 978e77a [Holden Karau] Move HasThreshold into classifier params and start defining the overloaded getThreshold/getThresholds functions 1433e52 [Holden Karau] Revert "try and hide threshold but chainges the API so no dice there" 1f09a2e [Holden Karau] try and hide threshold but chainges the API so no dice there efb9084 [Holden Karau] move setThresholds only to where its used 6b34809 [Holden Karau] Add a test with thresholding for the RFCS 74f54c3 [Holden Karau] Fix creation of vote array 1986fa8 [Holden Karau] Setting the thresholds only makes sense if the underlying class hasn't overridden predict, so lets push it down. 2f44b18 [Holden Karau] Add a global default of null for thresholds param f338cfc [Holden Karau] Wait that wasn't a good idea, Revert "Some progress towards unifying threshold and thresholds" 634b06f [Holden Karau] Some progress towards unifying threshold and thresholds 85c9e01 [Holden Karau] Test passes again... little fnur 099c0f3 [Holden Karau] Move thresholds around some more (set on model not trainer) 0f46836 [Holden Karau] Start adding a classifiersuite f70eb5e [Holden Karau] Fix test compile issues a7d59c8 [Holden Karau] Move thresholding into Classifier trait 5d999d2 [Holden Karau] Some more progress, start adding a test (maybe try and see if we can find a better thing to use for the base of the test) 1fed644 [Holden Karau] Use thresholds to scale scores in random forest classifcation 31d6bf2 [Holden Karau] Start threading the threshold info through 0ef228c [Holden Karau] Add hasthresholds
* [SPARK-9534] [BUILD] Enable javac lint for scalac parity; fix a lot of build ↵Sean Owen2015-08-041-7/+7
| | | | | | | | | | | | | | warnings, 1.5.0 edition Enable most javac lint warnings; fix a lot of build warnings. In a few cases, touch up surrounding code in the process. I'll explain several of the changes inline in comments. Author: Sean Owen <sowen@cloudera.com> Closes #7862 from srowen/SPARK-9534 and squashes the following commits: ea51618 [Sean Owen] Enable most javac lint warnings; fix a lot of build warnings. In a few cases, touch up surrounding code in the process.
* [SPARK-5133] [ML] Added featureImportance to RandomForestClassifier and ↵Joseph K. Bradley2015-08-032-0/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | Regressor Added featureImportance to RandomForestClassifier and Regressor. This follows the scikit-learn implementation here: [https://github.com/scikit-learn/scikit-learn/blob/a95203b249c1cf392f86d001ad999e29b2392739/sklearn/tree/_tree.pyx#L3341] CC: yanboliang Would you mind taking a look? Thanks! Author: Joseph K. Bradley <joseph@databricks.com> Author: Feynman Liang <fliang@databricks.com> Closes #7838 from jkbradley/dt-feature-importance and squashes the following commits: 72a167a [Joseph K. Bradley] fixed unit test 86cea5f [Joseph K. Bradley] Modified RF featuresImportances to return Vector instead of Map 5aa74f0 [Joseph K. Bradley] finally fixed unit test for real 33df5db [Joseph K. Bradley] fix unit test 42a2d3b [Joseph K. Bradley] fix unit test fe94e72 [Joseph K. Bradley] modified feature importance unit tests cc693ee [Feynman Liang] Add classifier tests 79a6f87 [Feynman Liang] Compare dense vectors in test 21d01fc [Feynman Liang] Added failing SKLearn test ac0b254 [Joseph K. Bradley] Added featureImportance to RandomForestClassifier/Regressor. Need to add unit tests
* [SPARK-9527] [MLLIB] add PrefixSpanModel and make PrefixSpan Java friendlyXiangrui Meng2015-08-021-0/+67
| | | | | | | | | | | | | | | 1. Use `PrefixSpanModel` to wrap the frequent sequences. 2. Define `FreqSequence` to wrap each frequent sequence, which contains a Java-friendly method `javaSequence` 3. Overload `run` for Java users. 4. Added a unit test in Java to check Java compatibility. zhangjiajin feynmanliang Author: Xiangrui Meng <meng@databricks.com> Closes #7869 from mengxr/SPARK-9527 and squashes the following commits: 4345594 [Xiangrui Meng] add PrefixSpanModel and make PrefixSpan Java friendly
* [SPARK-9214] [ML] [PySpark] support ml.NaiveBayes for PythonYanbo Liang2015-07-301-2/+2
| | | | | | | | | | | | | | support ml.NaiveBayes for Python Author: Yanbo Liang <ybliang8@gmail.com> Closes #7568 from yanboliang/spark-9214 and squashes the following commits: 5ee3fd6 [Yanbo Liang] fix typos 3ecd046 [Yanbo Liang] fix typos f9c94d1 [Yanbo Liang] change lambda_ to smoothing and fix other issues 180452a [Yanbo Liang] fix typos 7dda1f4 [Yanbo Liang] support ml.NaiveBayes for Python
* [SPARK-6793] [MLLIB] OnlineLDAOptimizer LDA perplexityFeynman Liang2015-07-291-1/+5
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | Implements `logPerplexity` in `OnlineLDAOptimizer`. Also refactors inference code into companion object to enable future reuse (e.g. `predict` method). Author: Feynman Liang <fliang@databricks.com> Closes #7705 from feynmanliang/SPARK-6793-perplexity and squashes the following commits: 6da2c99 [Feynman Liang] Remove get* from LDAModel public API 8381da6 [Feynman Liang] Code review comments 17f7000 [Feynman Liang] Documentation typo fixes 2f452a4 [Feynman Liang] Remove auxillary DistributedLDAModel constructor a275914 [Feynman Liang] Prevent empty counts calls to variationalInference 06d02d9 [Feynman Liang] Remove deprecated LocalLDAModel constructor afecb46 [Feynman Liang] Fix regression bug in sstats accumulator 5a327a0 [Feynman Liang] Code review quick fixes 998c03e [Feynman Liang] Fix style 1cbb67d [Feynman Liang] Fix access modifier bug 4362daa [Feynman Liang] Organize imports 4f171f7 [Feynman Liang] Fix indendation 2f049ce [Feynman Liang] Fix failing save/load tests 7415e96 [Feynman Liang] Pick changes from big PR 11e7c33 [Feynman Liang] Merge remote-tracking branch 'apache/master' into SPARK-6793-perplexity f8adc48 [Feynman Liang] Add logPerplexity, refactor variationalBound into a method cd521d6 [Feynman Liang] Refactor methods into companion class 7f62a55 [Feynman Liang] --amend c62cb1e [Feynman Liang] Outer product for stats, revert Range slicing aead650 [Feynman Liang] Range slice, in-place update, reduce transposes
* [SPARK-9268] [ML] Removed varargs annotation from Params.setDefault taking ↵Joseph K. Bradley2015-07-221-3/+0
| | | | | | | | | | | | | | | | multiple params Removed varargs annotation from Params.setDefault taking multiple params. Though varargs is technically correct, it often requires that developers do clean assembly, rather than (not clean) assembly, which is a nuisance during development. CC: mengxr Author: Joseph K. Bradley <joseph@databricks.com> Closes #7604 from jkbradley/params-setdefault-varargs and squashes the following commits: 6016dc6 [Joseph K. Bradley] removed varargs annotation from Params.setDefault taking multiple params
* [SPARK-7879] [MLLIB] KMeans API for spark.ml PipelinesYu ISHIKAWA2015-07-171-0/+72
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | I Implemented the KMeans API for spark.ml Pipelines. But it doesn't include clustering abstractions for spark.ml (SPARK-7610). It would fit for another issues. And I'll try it later, since we are trying to add the hierarchical clustering algorithms in another issue. Thanks. [SPARK-7879] KMeans API for spark.ml Pipelines - ASF JIRA https://issues.apache.org/jira/browse/SPARK-7879 Author: Yu ISHIKAWA <yuu.ishikawa@gmail.com> Closes #6756 from yu-iskw/SPARK-7879 and squashes the following commits: be752de [Yu ISHIKAWA] Add assertions a14939b [Yu ISHIKAWA] Fix the dashed line's length in pyspark.ml.rst 4c61693 [Yu ISHIKAWA] Remove the test about whether "features" and "prediction" columns exist or not in Python fb2417c [Yu ISHIKAWA] Use getInt, instead of get f397be4 [Yu ISHIKAWA] Switch the comparisons. ca78b7d [Yu ISHIKAWA] Add the Scala docs about the constraints of each parameter. effc650 [Yu ISHIKAWA] Using expertSetParam and expertGetParam c8dc6e6 [Yu ISHIKAWA] Remove an unnecessary test 19a9d63 [Yu ISHIKAWA] Include spark.ml.clustering to python tests 1abb19c [Yu ISHIKAWA] Add the statements about spark.ml.clustering into pyspark.ml.rst f8338bc [Yu ISHIKAWA] Add the placeholders in Python 4a03003 [Yu ISHIKAWA] Test for contains in Python 6566c8b [Yu ISHIKAWA] Use `get`, instead of `apply` 288e8d5 [Yu ISHIKAWA] Using `contains` to check the column names 5a7d574 [Yu ISHIKAWA] Renamce `validateInitializationMode` to `validateInitMode` and remove throwing exception 97cfae3 [Yu ISHIKAWA] Fix the type of return value of `KMeans.copy` e933723 [Yu ISHIKAWA] Remove the default value of seed from the Model class 978ee2c [Yu ISHIKAWA] Modify the docs of KMeans, according to mllib's KMeans 2ec80bc [Yu ISHIKAWA] Fit on 1 line e186be1 [Yu ISHIKAWA] Make a few variables, setters and getters be expert ones b2c205c [Yu ISHIKAWA] Rename the method `getInitializationSteps` to `getInitSteps` and `setInitializationSteps` to `setInitSteps` in Scala and Python f43f5b4 [Yu ISHIKAWA] Rename the method `getInitializationMode` to `getInitMode` and `setInitializationMode` to `setInitMode` in Scala and Python 3cb5ba4 [Yu ISHIKAWA] Modify the description about epsilon and the validation 4fa409b [Yu ISHIKAWA] Add a comment about the default value of epsilon 2f392e1 [Yu ISHIKAWA] Make some variables `final` and Use `IntParam` and `DoubleParam` 19326f8 [Yu ISHIKAWA] Use `udf`, instead of callUDF 4d2ad1e [Yu ISHIKAWA] Modify the indentations 0ae422f [Yu ISHIKAWA] Add a test for `setParams` 4ff7913 [Yu ISHIKAWA] Add "ml.clustering" to `javacOptions` in SparkBuild.scala 11ffdf1 [Yu ISHIKAWA] Use `===` and the variable 220a176 [Yu ISHIKAWA] Set a random seed in the unit testing 92c3efc [Yu ISHIKAWA] Make the points for a test be fewer c758692 [Yu ISHIKAWA] Modify the parameters of KMeans in Python 6aca147 [Yu ISHIKAWA] Add some unit testings to validate the setter methods 687cacc [Yu ISHIKAWA] Alias mllib.KMeans as MLlibKMeans in KMeansSuite.scala a4dfbef [Yu ISHIKAWA] Modify the last brace and indentations 5bedc51 [Yu ISHIKAWA] Remve an extra new line 444c289 [Yu ISHIKAWA] Add the validation for `runs` e41989c [Yu ISHIKAWA] Modify how to validate `initStep` 7ea133a [Yu ISHIKAWA] Change how to validate `initMode` 7991e15 [Yu ISHIKAWA] Add a validation for `k` c2df35d [Yu ISHIKAWA] Make `predict` private 93aa2ff [Yu ISHIKAWA] Use `withColumn` in `transform` d3a79f7 [Yu ISHIKAWA] Remove the inhefited docs e9532e1 [Yu ISHIKAWA] make `parentModel` of KMeansModel private 8559772 [Yu ISHIKAWA] Remove the `paramMap` parameter of KMeans 6684850 [Yu ISHIKAWA] Rename `initializationSteps` to `initSteps` 99b1b96 [Yu ISHIKAWA] Rename `initializationMode` to `initMode` 79ea82b [Yu ISHIKAWA] Modify the parameters of KMeans docs 6569bcd [Yu ISHIKAWA] Change how to set the default values with `setDefault` 20a795a [Yu ISHIKAWA] Change how to set the default values with `setDefault` 11c2a12 [Yu ISHIKAWA] Limit the imports badb481 [Yu ISHIKAWA] Alias spark.mllib.{KMeans, KMeansModel} f80319a [Yu ISHIKAWA] Rebase mater branch and add copy methods 85d92b1 [Yu ISHIKAWA] Add `KMeans.setPredictionCol` aa9469d [Yu ISHIKAWA] Fix a python test suite error caused by python 3.x c2d6bcb [Yu ISHIKAWA] ADD Java test suites of the KMeans API for spark.ml Pipeline 598ed2e [Yu ISHIKAWA] Implement the KMeans API for spark.ml Pipelines in Python 63ad785 [Yu ISHIKAWA] Implement the KMeans API for spark.ml Pipelines in Scala
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