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* [SPARK-6336] LBFGS should document what convergenceTol meanslewuathe2015-03-171-0/+4
| | | | | | | | | | | | LBFGS uses convergence tolerance. This value should be written in document as an argument. Author: lewuathe <lewuathe@me.com> Closes #5033 from Lewuathe/SPARK-6336 and squashes the following commits: e738b33 [lewuathe] Modify text to be more natural ac03c3a [lewuathe] Modify documentations 6ccb304 [lewuathe] [SPARK-6336] LBFGS should document what convergenceTol means
* [SPARK-4711] [mllib] [docs] Programming guide advice on choosing optimizerJoseph K. Bradley2014-12-041-6/+11
| | | | | | | | | | | | | | I have heard requests for the docs to include advice about choosing an optimization method. The programming guide could include a brief statement about this (so the user does not have to read the whole optimization section). CC: mengxr Author: Joseph K. Bradley <joseph@databricks.com> Closes #3569 from jkbradley/lr-doc and squashes the following commits: 654aeb5 [Joseph K. Bradley] updated section header for mllib-optimization 5035ad0 [Joseph K. Bradley] updated based on review 94f6dec [Joseph K. Bradley] Updated linear methods and optimization docs with quick advice on choosing an optimization method
* [SPARK-1484][MLLIB] Warn when running an iterative algorithm on uncached data.Aaron Staple2014-09-251-0/+1
| | | | | | | | | | | | | | | | | | | Add warnings to KMeans, GeneralizedLinearAlgorithm, and computeSVD when called with input data that is not cached. KMeans is implemented iteratively, and I believe that GeneralizedLinearAlgorithm’s current optimizers are iterative and its future optimizers are also likely to be iterative. RowMatrix’s computeSVD is iterative against an RDD when run in DistARPACK mode. ALS and DecisionTree are iterative as well, but they implement RDD caching internally so do not require a warning. I added a warning to GeneralizedLinearAlgorithm rather than inside its optimizers, where the iteration actually occurs, because internally GeneralizedLinearAlgorithm maps its input data to an uncached RDD before passing it to an optimizer. (In other words, the warning would be printed for every GeneralizedLinearAlgorithm run, regardless of whether its input is cached, if the warning were in GradientDescent or other optimizer.) I assume that use of an uncached RDD by GeneralizedLinearAlgorithm is intentional, and that the mapping there (adding label, intercepts and scaling) is a lightweight operation. Arguably a user calling an optimizer such as GradientDescent will be knowledgable enough to cache their data without needing a log warning, so lack of a warning in the optimizers may be ok. Some of the documentation examples making use of these iterative algorithms did not cache their training RDDs (while others did). I updated the examples to always cache. I also fixed some (unrelated) minor errors in the documentation examples. Author: Aaron Staple <aaron.staple@gmail.com> Closes #2347 from staple/SPARK-1484 and squashes the following commits: bd49701 [Aaron Staple] Address review comments. ab2d4a4 [Aaron Staple] Disable warnings on python code path. a7a0f99 [Aaron Staple] Change code comments per review comments. 7cca1dc [Aaron Staple] Change warning message text. c77e939 [Aaron Staple] [SPARK-1484][MLLIB] Warn when running an iterative algorithm on uncached data. 3b6c511 [Aaron Staple] Minor doc example fixes.
* [SPARK-1945][MLLIB] Documentation Improvements for Spark 1.0Michael Giannakopoulos2014-07-201-1/+95
| | | | | | | | | | | | | | | | | | | | | | Standalone application examples are added to 'mllib-linear-methods.md' file written in Java. This commit is related to the issue [Add full Java Examples in MLlib docs](https://issues.apache.org/jira/browse/SPARK-1945). Also I changed the name of the sigmoid function from 'logit' to 'f'. This is because the logit function is the inverse of sigmoid. Thanks, Michael Author: Michael Giannakopoulos <miccagiann@gmail.com> Closes #1311 from miccagiann/master and squashes the following commits: 8ffe5ab [Michael Giannakopoulos] Update code so as to comply with code standards. f7ad5cc [Michael Giannakopoulos] Merge remote-tracking branch 'upstream/master' 38d92c7 [Michael Giannakopoulos] Adding PCA, SVD and LBFGS examples in Java. Performing minor updates in the already committed examples so as to eradicate the call of 'productElement' function whenever is possible. cc0a089 [Michael Giannakopoulos] Modyfied Java examples so as to comply with coding standards. b1141b2 [Michael Giannakopoulos] Added Java examples for Clustering and Collaborative Filtering [mllib-clustering.md & mllib-collaborative-filtering.md]. 837f7a8 [Michael Giannakopoulos] Merge remote-tracking branch 'upstream/master' 15f0eb4 [Michael Giannakopoulos] Java examples included in 'mllib-linear-methods.md' file.
* SPARK-2363. Clean MLlib's sample data filesSean Owen2014-07-131-1/+1
| | | | | | | | | | | | | | | | (Just made a PR for this, mengxr was the reporter of:) MLlib has sample data under serveral folders: 1) data/mllib 2) data/ 3) mllib/data/* Per previous discussion with Matei Zaharia, we want to put them under `data/mllib` and clean outdated files. Author: Sean Owen <sowen@cloudera.com> Closes #1394 from srowen/SPARK-2363 and squashes the following commits: 54313dd [Sean Owen] Move ML example data from /mllib/data/ and /data/ into /data/mllib/
* MLlib documentation fixAnatoli Fomenko2014-06-161-4/+4
| | | | | | | | | | | | | | | | | Synchronized mllib-optimization.md with Spark Scaladoc: removed reference to GradientDescent.runMiniBatchSGD method This is a temporary fix to remove a link from http://spark.apache.org/docs/latest/mllib-optimization.html to GradientDescent.runMiniBatchSGD which is not in the current online GradientDescent Scaladoc. FIXME: revert this commit after GradientDescent Scaladoc is updated. See images for details. ![mllib-docs-fix-1](https://cloud.githubusercontent.com/assets/1375501/3294410/ccf19bb8-f5a8-11e3-93f1-f593016209eb.png) ![mllib-docs-fix-2](https://cloud.githubusercontent.com/assets/1375501/3294411/d0b59a7e-f5a8-11e3-8fc8-329c177ef8c8.png) Author: Anatoli Fomenko <fa@apache.org> Closes #1098 from afomenko/master and squashes the following commits: 5cb0758 [Anatoli Fomenko] MLlib documentation fix
* [SPARK-1566] consolidate programming guide, and general doc updatesMatei Zaharia2014-05-301-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This is a fairly large PR to clean up and update the docs for 1.0. The major changes are: * A unified programming guide for all languages replaces language-specific ones and shows language-specific info in tabs * New programming guide sections on key-value pairs, unit testing, input formats beyond text, migrating from 0.9, and passing functions to Spark * Spark-submit guide moved to a separate page and expanded slightly * Various cleanups of the menu system, security docs, and others * Updated look of title bar to differentiate the docs from previous Spark versions You can find the updated docs at http://people.apache.org/~matei/1.0-docs/_site/ and in particular http://people.apache.org/~matei/1.0-docs/_site/programming-guide.html. Author: Matei Zaharia <matei@databricks.com> Closes #896 from mateiz/1.0-docs and squashes the following commits: 03e6853 [Matei Zaharia] Some tweaks to configuration and YARN docs 0779508 [Matei Zaharia] tweak ef671d4 [Matei Zaharia] Keep frames in JavaDoc links, and other small tweaks 1bf4112 [Matei Zaharia] Review comments 4414f88 [Matei Zaharia] tweaks d04e979 [Matei Zaharia] Fix some old links to Java guide a34ed33 [Matei Zaharia] tweak 541bb3b [Matei Zaharia] miscellaneous changes fcefdec [Matei Zaharia] Moved submitting apps to separate doc 61d72b4 [Matei Zaharia] stuff 181f217 [Matei Zaharia] migration guide, remove old language guides e11a0da [Matei Zaharia] Add more API functions 6a030a9 [Matei Zaharia] tweaks 8db0ae3 [Matei Zaharia] Added key-value pairs section 318d2c9 [Matei Zaharia] tweaks 1c81477 [Matei Zaharia] New section on basics and function syntax e38f559 [Matei Zaharia] Actually added programming guide to Git a33d6fe [Matei Zaharia] First pass at updating programming guide to support all languages, plus other tweaks throughout 3b6a876 [Matei Zaharia] More CSS tweaks 01ec8bf [Matei Zaharia] More CSS tweaks e6d252e [Matei Zaharia] Change color of doc title bar to differentiate from 0.9.0
* [WIP][SPARK-1871][MLLIB] Improve MLlib guide for v1.0Xiangrui Meng2014-05-181-5/+6
| | | | | | | | | | | | | | | | | | | | | | | | Some improvements to MLlib guide: 1. [SPARK-1872] Update API links for unidoc. 2. [SPARK-1783] Added `page.displayTitle` to the global layout. If it is defined, use it instead of `page.title` for title display. 3. Add more Java/Python examples. Author: Xiangrui Meng <meng@databricks.com> Closes #816 from mengxr/mllib-doc and squashes the following commits: ec2e407 [Xiangrui Meng] format scala example for ALS cd9f40b [Xiangrui Meng] add a paragraph to summarize distributed matrix types 4617f04 [Xiangrui Meng] add python example to loadLibSVMFile and fix Java example d6509c2 [Xiangrui Meng] [SPARK-1783] update mllib titles 561fdc0 [Xiangrui Meng] add a displayTitle option to global layout 195d06f [Xiangrui Meng] add Java example for summary stats and minor fix 9f1ff89 [Xiangrui Meng] update java api links in mllib-basics 7dad18e [Xiangrui Meng] update java api links in NB 3a0f4a6 [Xiangrui Meng] api/pyspark -> api/python 35bdeb9 [Xiangrui Meng] api/mllib -> api/scala e4afaa8 [Xiangrui Meng] explicity state what might change
* L-BFGS DocumentationDB Tsai2014-05-121-4/+116
| | | | | | | | | | | | | | Documentation for L-BFGS, and an example of training binary L2 logistic regression using L-BFGS. Author: DB Tsai <dbtsai@alpinenow.com> Closes #702 from dbtsai/dbtsai-lbfgs-doc and squashes the following commits: 0712215 [DB Tsai] Update 38fdfa1 [DB Tsai] Removed extra empty line 5745b64 [DB Tsai] Update again e9e418e [DB Tsai] Update 7381521 [DB Tsai] L-BFGS Documentation
* [SPARK-1506][MLLIB] Documentation improvements for MLlib 1.0Xiangrui Meng2014-04-221-13/+12
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Preview: http://54.82.240.23:4000/mllib-guide.html Table of contents: * Basics * Data types * Summary statistics * Classification and regression * linear support vector machine (SVM) * logistic regression * linear linear squares, Lasso, and ridge regression * decision tree * naive Bayes * Collaborative Filtering * alternating least squares (ALS) * Clustering * k-means * Dimensionality reduction * singular value decomposition (SVD) * principal component analysis (PCA) * Optimization * stochastic gradient descent * limited-memory BFGS (L-BFGS) Author: Xiangrui Meng <meng@databricks.com> Closes #422 from mengxr/mllib-doc and squashes the following commits: 944e3a9 [Xiangrui Meng] merge master f9fda28 [Xiangrui Meng] minor 9474065 [Xiangrui Meng] add alpha to ALS examples 928e630 [Xiangrui Meng] initialization_mode -> initializationMode 5bbff49 [Xiangrui Meng] add imports to labeled point examples c17440d [Xiangrui Meng] fix python nb example 28f40dc [Xiangrui Meng] remove localhost:4000 369a4d3 [Xiangrui Meng] Merge branch 'master' into mllib-doc 7dc95cc [Xiangrui Meng] update linear methods 053ad8a [Xiangrui Meng] add links to go back to the main page abbbf7e [Xiangrui Meng] update ALS argument names 648283e [Xiangrui Meng] level down statistics 14e2287 [Xiangrui Meng] add sample libsvm data and use it in guide 8cd2441 [Xiangrui Meng] minor updates 186ab07 [Xiangrui Meng] update section names 6568d65 [Xiangrui Meng] update toc, level up lr and svm 162ee12 [Xiangrui Meng] rename section names 5c1e1b1 [Xiangrui Meng] minor 8aeaba1 [Xiangrui Meng] wrap long lines 6ce6a6f [Xiangrui Meng] add summary statistics to toc 5760045 [Xiangrui Meng] claim beta cc604bf [Xiangrui Meng] remove classification and regression 92747b3 [Xiangrui Meng] make section titles consistent e605dd6 [Xiangrui Meng] add LIBSVM loader f639674 [Xiangrui Meng] add python section to migration guide c82ffb4 [Xiangrui Meng] clean optimization 31660eb [Xiangrui Meng] update linear algebra and stat 0a40837 [Xiangrui Meng] first pass over linear methods 1fc8271 [Xiangrui Meng] update toc 906ed0a [Xiangrui Meng] add a python example to naive bayes 5f0a700 [Xiangrui Meng] update collaborative filtering 656d416 [Xiangrui Meng] update mllib-clustering 86e143a [Xiangrui Meng] remove data types section from main page 8d1a128 [Xiangrui Meng] move part of linear algebra to data types and add Java/Python examples d1b5cbf [Xiangrui Meng] merge master 72e4804 [Xiangrui Meng] one pass over tree guide 64f8995 [Xiangrui Meng] move decision tree guide to a separate file 9fca001 [Xiangrui Meng] add first version of linear algebra guide 53c9552 [Xiangrui Meng] update dependencies f316ec2 [Xiangrui Meng] add migration guide f399f6c [Xiangrui Meng] move linear-algebra to dimensionality-reduction 182460f [Xiangrui Meng] add guide for naive Bayes 137fd1d [Xiangrui Meng] re-organize toc a61e434 [Xiangrui Meng] update mllib's toc
* [SPARK-1439, SPARK-1440] Generate unified Scaladoc across projects and JavadocsMatei Zaharia2014-04-211-4/+4
| | | | | | | | | | | | | | | | | | | | | | I used the sbt-unidoc plugin (https://github.com/sbt/sbt-unidoc) to create a unified Scaladoc of our public packages, and generate Javadocs as well. One limitation is that I haven't found an easy way to exclude packages in the Javadoc; there is a SBT task that identifies Java sources to run javadoc on, but it's been very difficult to modify it from outside to change what is set in the unidoc package. Some SBT-savvy people should help with this. The Javadoc site also lacks package-level descriptions and things like that, so we may want to look into that. We may decide not to post these right now if it's too limited compared to the Scala one. Example of the built doc site: http://people.csail.mit.edu/matei/spark-unified-docs/ Author: Matei Zaharia <matei@databricks.com> This patch had conflicts when merged, resolved by Committer: Patrick Wendell <pwendell@gmail.com> Closes #457 from mateiz/better-docs and squashes the following commits: a63d4a3 [Matei Zaharia] Skip Java/Scala API docs for Python package 5ea1f43 [Matei Zaharia] Fix links to Java classes in Java guide, fix some JS for scrolling to anchors on page load f05abc0 [Matei Zaharia] Don't include java.lang package names 995e992 [Matei Zaharia] Skip internal packages and class names with $ in JavaDoc a14a93c [Matei Zaharia] typo 76ce64d [Matei Zaharia] Add groups to Javadoc index page, and a first package-info.java ed6f994 [Matei Zaharia] Generate JavaDoc as well, add titles, update doc site to use unified docs acb993d [Matei Zaharia] Add Unidoc plugin for the projects we want Unidoced
* Merge pull request #566 from martinjaggi/copy-MLlib-d.Martin Jaggi2014-02-091-19/+145
| | | | | | | | | | | | | | | | | | | | | | | | | | | | new MLlib documentation for optimization, regression and classification new documentation with tex formulas, hopefully improving usability and reproducibility of the offered MLlib methods. also did some minor changes in the code for consistency. scala tests pass. this is the rebased branch, i deleted the old PR jira: https://spark-project.atlassian.net/browse/MLLIB-19 Author: Martin Jaggi <m.jaggi@gmail.com> Closes #566 and squashes the following commits: 5f0f31e [Martin Jaggi] line wrap at 100 chars 4e094fb [Martin Jaggi] better description of GradientDescent 1d6965d [Martin Jaggi] remove broken url ea569c3 [Martin Jaggi] telling what updater actually does 964732b [Martin Jaggi] lambda R() in documentation a6c6228 [Martin Jaggi] better comments in SGD code for regression b32224a [Martin Jaggi] new optimization documentation d5dfef7 [Martin Jaggi] new classification and regression documentation b07ead6 [Martin Jaggi] correct scaling for MSE loss ba6158c [Martin Jaggi] use d for the number of features bab2ed2 [Martin Jaggi] renaming LeastSquaresGradient
* Merge pull request #552 from martinjaggi/master. Closes #552.Martin Jaggi2014-02-081-0/+40
tex formulas in the documentation using mathjax. and spliting the MLlib documentation by techniques see jira https://spark-project.atlassian.net/browse/MLLIB-19 and https://github.com/shivaram/spark/compare/mathjax Author: Martin Jaggi <m.jaggi@gmail.com> == Merge branch commits == commit 0364bfabbfc347f917216057a20c39b631842481 Author: Martin Jaggi <m.jaggi@gmail.com> Date: Fri Feb 7 03:19:38 2014 +0100 minor polishing, as suggested by @pwendell commit dcd2142c164b2f602bf472bb152ad55bae82d31a Author: Martin Jaggi <m.jaggi@gmail.com> Date: Thu Feb 6 18:04:26 2014 +0100 enabling inline latex formulas with $.$ same mathjax configuration as used in math.stackexchange.com sample usage in the linear algebra (SVD) documentation commit bbafafd2b497a5acaa03a140bb9de1fbb7d67ffa Author: Martin Jaggi <m.jaggi@gmail.com> Date: Thu Feb 6 17:31:29 2014 +0100 split MLlib documentation by techniques and linked from the main mllib-guide.md site commit d1c5212b93c67436543c2d8ddbbf610fdf0a26eb Author: Martin Jaggi <m.jaggi@gmail.com> Date: Thu Feb 6 16:59:43 2014 +0100 enable mathjax formula in the .md documentation files code by @shivaram commit d73948db0d9bc36296054e79fec5b1a657b4eab4 Author: Martin Jaggi <m.jaggi@gmail.com> Date: Thu Feb 6 16:57:23 2014 +0100 minor update on how to compile the documentation
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