Apache Spark - A unified analytics engine for large-scale data processing
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Joseph K. Bradley 980764f3c0 [SPARK-1405] [mllib] Latent Dirichlet Allocation (LDA) using EM
**This PR introduces an API + simple implementation for Latent Dirichlet Allocation (LDA).**

The [design doc for this PR](https://docs.google.com/document/d/1kSsDqTeZMEB94Bs4GTd0mvdAmduvZSSkpoSfn-seAzo) has been updated since I initially posted it.  In particular, see the API and Planning for the Future sections.

* Settle on a public API which may eventually include:
  * more inference algorithms
  * more options / functionality
* Have an initial easy-to-understand implementation which others may improve.
* This is NOT intended to support every topic model out there.  However, if there are suggestions for making this extensible or pluggable in the future, that could be nice, as long as it does not complicate the API or implementation too much.
* This may not be very scalable currently.  It will be important to check and improve accuracy.  For correctness of the implementation, please check against the Asuncion et al. (2009) paper in the design doc.

**Dependency: This makes MLlib depend on GraphX.**

Files and classes:
* LDA.scala (441 lines):
  * class LDA (main estimator class)
  * LDA.Document  (text + document ID)
* LDAModel.scala (266 lines)
  * abstract class LDAModel
  * class LocalLDAModel
  * class DistributedLDAModel
* LDAExample.scala (245 lines): script to run LDA + a simple (private) Tokenizer
* LDASuite.scala (144 lines)

Data/model representation and algorithm:
* Data/model: Uses GraphX, with term vertices + document vertices
* Algorithm: EM, following [Asuncion, Welling, Smyth, and Teh.  "On Smoothing and Inference for Topic Models."  UAI, 2009.](http://arxiv-web3.library.cornell.edu/abs/1205.2662v1)
* For more details, please see the description in the “DEVELOPERS NOTE” in LDA.scala

Please refer to the JIRA for more discussion + the [design doc for this PR](https://docs.google.com/document/d/1kSsDqTeZMEB94Bs4GTd0mvdAmduvZSSkpoSfn-seAzo)

Here, I list the main changes AFTER the design doc was posted.

Design decisions:
* logLikelihood() computes the log likelihood of the data and the current point estimate of parameters.  This is different from the likelihood of the data given the hyperparameters, which would be harder to compute.  I’d describe the current approach as more frequentist, whereas the harder approach would be more Bayesian.
* The current API takes Documents as token count vectors.  I believe there should be an extended API taking RDD[String] or RDD[Array[String]] in a future PR.  I have sketched this out in the design doc (as well as handier versions of getTopics returning Strings).
* Hyperparameters should be set differently for different inference/learning algorithms.  See Asuncion et al. (2009) in the design doc for a good demonstration.  I encourage good behavior via defaults and warning messages.

Items planned for future PRs:
* perplexity
* API taking Strings

* Should LDA be called LatentDirichletAllocation (and LDAModel be LatentDirichletAllocationModel)?
  * Pro: We may someday want LinearDiscriminantAnalysis.
  * Con: Very long names

* Should LDA reside in clustering?  Or do we want a sub-package?
  * mllib.topicmodel
  * mllib.clustering.topicmodel

* Does the API seem reasonable and extensible?

* Unit tests:
  * Should there be a test which checks a clustering results?  E.g., train on a small, fake dataset with 2 very distinct topics/clusters, and ensure LDA finds those 2 topics/clusters.  Does that sound useful or too flaky?

This has not been tested much for scaling.  I have run it on a laptop for 200 iterations on a 5MB dataset with 1000 terms and 5 topics.  Running it for 500 iterations made it fail because of GC problems.  I'm running larger scale tests & will put results here, but future PRs may need to improve the scaling.

* dlwh  for the initial implementation
  * + jegonzal  for some code in the initial implementation
* The many contributors towards topic model implementations in Spark which were referenced as a basis for this PR: akopich witgo yinxusen dlwh EntilZha jegonzal  IlyaKozlov
  * Note: The plan is to include this full list in the authors if this PR gets merged.  Please notify me if you prefer otherwise.

CC: mengxr

Authors:
  Joseph K. Bradley <joseph@databricks.com>
  Joseph Gonzalez <joseph.e.gonzalez@gmail.com>
  David Hall <david.lw.hall@gmail.com>
  Guoqiang Li <witgo@qq.com>
  Xiangrui Meng <meng@databricks.com>
  Pedro Rodriguez <pedro@snowgeek.org>
  Avanesov Valeriy <acopich@gmail.com>
  Xusen Yin <yinxusen@gmail.com>

Closes #2388
Closes #4047 from jkbradley/davidhall-lda and squashes the following commits:

77e8814 [Joseph K. Bradley] small doc fix
5c74345 [Joseph K. Bradley] cleaned up doc based on code review
589728b [Joseph K. Bradley] Updates per code review.  Main change was in LDAExample for faster vocab computation.  Also updated PeriodicGraphCheckpointerSuite.scala to clean up checkpoint files at end
e3980d2 [Joseph K. Bradley] cleaned up PeriodicGraphCheckpointerSuite.scala
74487e5 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into davidhall-lda
4ae2a7d [Joseph K. Bradley] removed duplicate graphx dependency in mllib/pom.xml
e391474 [Joseph K. Bradley] Removed LDATiming.  Added PeriodicGraphCheckpointerSuite.scala.  Small LDA cleanups.
e8d8acf [Joseph K. Bradley] Added catch for BreakIterator exception.  Improved preprocessing to reduce passes over data
1a231b4 [Joseph K. Bradley] fixed scalastyle
91aadfe [Joseph K. Bradley] Added Java-friendly run method to LDA. Added Java test suite for LDA. Changed LDAModel.describeTopics to return Java-friendly type
b75472d [Joseph K. Bradley] merged improvements from LDATiming into LDAExample.  Will remove LDATiming after done testing
993ca56 [Joseph K. Bradley] * Removed Document type in favor of (Long, Vector) * Changed doc ID restriction to be: id must be nonnegative and unique in the doc (instead of 0,1,2,...) * Add checks for valid ranges of eta, alpha * Rename “LearningState” to “EMOptimizer” * Renamed params: termSmoothing -> topicConcentration, topicSmoothing -> docConcentration   * Also added aliases alpha, beta
cb5a319 [Joseph K. Bradley] Added checkpointing to LDA * new class PeriodicGraphCheckpointer * params checkpointDir, checkpointInterval to LDA
43c1c40 [Joseph K. Bradley] small cleanup
0b90393 [Joseph K. Bradley] renamed LDA LearningState.collectTopicTotals to globalTopicTotals
77a2c85 [Joseph K. Bradley] Moved auto term,topic smoothing computation to get*Smoothing methods.  Changed word to term in some places.  Updated LDAExample to use default smoothing amounts.
fb1e7b5 [Xiangrui Meng] minor
08d59a3 [Xiangrui Meng] reset spacing
9fe0b95 [Xiangrui Meng] optimize aggregateMessages
cec0a9c [Xiangrui Meng] * -> *=
6cb11b0 [Xiangrui Meng] optimize computePTopic
9eb3d02 [Xiangrui Meng] + -> +=
892530c [Xiangrui Meng] use axpy
45cc7f2 [Xiangrui Meng] mapPart -> flatMap
ce53be9 [Joseph K. Bradley] fixed example name
75749e7 [Joseph K. Bradley] scala style fix
9f2a492 [Joseph K. Bradley] Unit tests and fixes for LDA, now ready for PR
377ebd9 [Joseph K. Bradley] separated LDA models into own file.  more cleanups before PR
2d40006 [Joseph K. Bradley] cleanups before PR
2891e89 [Joseph K. Bradley] Prepped LDA main class for PR, but some cleanups remain
0cb7187 [Joseph K. Bradley] Added 3 files from dlwh LDA implementation
2015-02-02 23:57:37 -08:00
assembly [SPARK-4809] Rework Guava library shading. 2015-01-28 00:29:29 -08:00
bagel [SPARK-4048] Enhance and extend hadoop-provided profile. 2015-01-08 17:15:13 -08:00
bin [SPARK-3996]: Shade Jetty in Spark deliverables 2015-02-01 21:13:57 -08:00
build [SPARK-5188][BUILD] make-distribution.sh should support curl, not only wget to get Tachyon 2015-01-28 12:43:22 -08:00
conf [SPARK-5422] Add support for sending Graphite metrics via UDP 2015-01-31 23:41:05 -08:00
core [SPARK-5414] Add SparkFirehoseListener class for consuming all SparkListener events 2015-02-02 23:35:07 -08:00
data/mllib SPARK-2363. Clean MLlib's sample data files 2014-07-13 19:27:43 -07:00
dev SPARK-5542: Decouple publishing, packaging, and tagging in release script 2015-02-02 21:00:30 -08:00
docker [SPARK-1342] Scala 2.10.4 2014-04-01 18:35:50 -07:00
docs [Doc] Minor: Fixes several formatting issues 2015-02-02 21:14:21 -08:00
ec2 [SPARK-5434] [EC2] Preserve spaces in EC2 path 2015-01-28 12:56:03 -08:00
examples [SPARK-1405] [mllib] Latent Dirichlet Allocation (LDA) using EM 2015-02-02 23:57:37 -08:00
external [SPARK-5154] [PySpark] [Streaming] Kafka streaming support in Python 2015-02-02 19:16:27 -08:00
extras [SPARK-5155] Build fails with spark-ganglia-lgpl profile 2015-02-01 17:53:56 -08:00
graphx [SPARK-5534] [graphx] Graph getStorageLevel fix 2015-02-02 17:02:29 -08:00
mllib [SPARK-1405] [mllib] Latent Dirichlet Allocation (LDA) using EM 2015-02-02 23:57:37 -08:00
network [SPARK-3996]: Shade Jetty in Spark deliverables 2015-02-01 21:13:57 -08:00
project [SPARK-5536] replace old ALS implementation by the new one 2015-02-02 23:49:09 -08:00
python [SPARK-5536] replace old ALS implementation by the new one 2015-02-02 23:49:09 -08:00
repl Spark 3883: SSL support for HttpServer and Akka 2015-02-02 17:27:26 -08:00
sbin [SPARK-5176] The thrift server does not support cluster mode 2015-02-01 17:57:31 -08:00
sbt Adde LICENSE Header to build/mvn, build/sbt and sbt/sbt 2014-12-29 10:48:53 -08:00
sql [SPARK-5501][SPARK-5420][SQL] Write support for the data source API 2015-02-02 23:30:44 -08:00
streaming SPARK-3996: Add jetty servlet and continuations. 2015-02-02 21:01:36 -08:00
tools SPARK-4159 [CORE] Maven build doesn't run JUnit test suites 2015-01-06 12:02:08 -08:00
yarn SPARK-3996: Add jetty servlet and continuations. 2015-02-02 21:01:36 -08:00
.gitattributes [SPARK-3870] EOL character enforcement 2014-10-31 12:39:52 -07:00
.gitignore [SPARK-4501][Core] - Create build/mvn to automatically download maven/zinc/scalac 2014-12-27 13:26:38 -08:00
.rat-excludes [HOTFIX] Fix RAT exclusion for known_translations file 2014-12-16 23:00:25 -08:00
CONTRIBUTING.md [Docs] minor grammar fix 2014-09-17 12:33:09 -07:00
LICENSE SPARK-3926 [CORE] Reopened: result of JavaRDD collectAsMap() is not serializable 2014-12-08 16:13:03 -08:00
make-distribution.sh [SPARK-5188][BUILD] make-distribution.sh should support curl, not only wget to get Tachyon 2015-01-28 12:43:22 -08:00
NOTICE SPARK-1827. LICENSE and NOTICE files need a refresh to contain transitive dependency info 2014-05-14 09:38:33 -07:00
pom.xml SPARK-3996: Add jetty servlet and continuations. 2015-02-02 21:01:36 -08:00
README.md [Docs] Fix Building Spark link text 2015-02-02 12:33:49 -08:00
scalastyle-config.xml [Core] Upgrading ScalaStyle version to 0.5 and removing SparkSpaceAfterCommentStartChecker. 2014-10-16 02:05:44 -04:00
tox.ini [SPARK-3073] [PySpark] use external sort in sortBy() and sortByKey() 2014-08-26 16:57:40 -07:00

Apache Spark

Spark is a fast and general cluster computing system for Big Data. It provides high-level APIs in Scala, Java, and Python, and an optimized engine that supports general computation graphs for data analysis. It also supports a rich set of higher-level tools including Spark SQL for SQL and structured data processing, MLlib for machine learning, GraphX for graph processing, and Spark Streaming for stream processing.

http://spark.apache.org/

Online Documentation

You can find the latest Spark documentation, including a programming guide, on the project web page and project wiki. This README file only contains basic setup instructions.

Building Spark

Spark is built using Apache Maven. To build Spark and its example programs, run:

mvn -DskipTests clean package

(You do not need to do this if you downloaded a pre-built package.) More detailed documentation is available from the project site, at "Building Spark".

Interactive Scala Shell

The easiest way to start using Spark is through the Scala shell:

./bin/spark-shell

Try the following command, which should return 1000:

scala> sc.parallelize(1 to 1000).count()

Interactive Python Shell

Alternatively, if you prefer Python, you can use the Python shell:

./bin/pyspark

And run the following command, which should also return 1000:

>>> sc.parallelize(range(1000)).count()

Example Programs

Spark also comes with several sample programs in the examples directory. To run one of them, use ./bin/run-example <class> [params]. For example:

./bin/run-example SparkPi

will run the Pi example locally.

You can set the MASTER environment variable when running examples to submit examples to a cluster. This can be a mesos:// or spark:// URL, "yarn-cluster" or "yarn-client" to run on YARN, and "local" to run locally with one thread, or "local[N]" to run locally with N threads. You can also use an abbreviated class name if the class is in the examples package. For instance:

MASTER=spark://host:7077 ./bin/run-example SparkPi

Many of the example programs print usage help if no params are given.

Running Tests

Testing first requires building Spark. Once Spark is built, tests can be run using:

./dev/run-tests

Please see the guidance on how to run all automated tests.

A Note About Hadoop Versions

Spark uses the Hadoop core library to talk to HDFS and other Hadoop-supported storage systems. Because the protocols have changed in different versions of Hadoop, you must build Spark against the same version that your cluster runs.

Please refer to the build documentation at "Specifying the Hadoop Version" for detailed guidance on building for a particular distribution of Hadoop, including building for particular Hive and Hive Thriftserver distributions. See also "Third Party Hadoop Distributions" for guidance on building a Spark application that works with a particular distribution.

Configuration

Please refer to the Configuration guide in the online documentation for an overview on how to configure Spark.