2941 Commits

Author SHA1 Message Date
Matthew Drury
edc356f7ec Add monotonic tutorial. (#1870) 2016-12-14 20:17:19 -06:00
Ian
167864da75 python package tree plotting support fmap (#1856)
* to_graphviz and plot_tree support fmap

* [python-package] add model_plot docstring
2016-12-13 07:36:17 -06:00
Liam Huang
49bdb5c97f fix typo in comment. (#1850) 2016-12-11 19:49:04 +01:00
Vadim Khotilovich
b21e658a02 [R-package] JSON dump format and a couple of bugfixes (#1855)
* [R-package] JSON tree dump interface

* [R-package] precision bugfix in xgb.attributes

* [R-package] bugfix for cb.early.stop called from xgb.cv

* [R-package] a bit more clarity on labels checking in xgb.cv

* [R-package] test JSON dump for gblinear as well

* whitespace lint
2016-12-11 19:48:39 +01:00
AbdealiJK
0268dedeea config.mk: Set TEST_COVER to 0 by default (#1853)
Set the TEST_COVER to 0 by default so it uses optimization
-O3 when compiling.
2016-12-11 19:48:15 +01:00
Ruimin Wang
d9584ab82e refactor duplicate evaluation implementation (#1852) 2016-12-08 20:33:40 -08:00
RAMitchell
2b6aa7736f Add benchmarks, fix GCC build (#1848) 2016-12-08 18:59:10 +01:00
Xin Yin
e7fbc8591f [jvm-packages] Scala implementation of the Rabit tracker. (#1612)
* [jvm-packages] Scala implementation of the Rabit tracker.

A Scala implementation of RabitTracker that is interface-interchangable with the
Java implementation, ported from `tracker.py` in the
[dmlc-core project](https://github.com/dmlc/dmlc-core).

* [jvm-packages] Updated Akka dependency in pom.xml.

* Refactored the RabitTracker directory structure.

* Fixed premature stopping of connection handler.

Added a new finite state "AwaitingPortNumber" to explicitly wait for the
worker to send the port, and close the connection. Stopping the actor
prematurely sends a TCP RST to the worker, causing the worker to crash
on AssertionError.

* Added interface IRabitTracker so that user can switch implementations.

* Default timeout duration changes.

* Dependency for Akka tests.

* Removed the main function of RabitTracker.

* A skeleton for testing Akka-based Rabit tracker.

* waitFor() in RabitTracker no longer throws exceptions.

* Completed unit test for the 'start' command of Rabit tracker.

* Preliminary support for Rabit Allreduce via JNI (no prepare function support yet.)

* Fixed the default timeout duration.

* Use Java container to avoid serialization issues due to intermediate wrappers.

* Added tests for Allreduce/model training using Scala Rabit tracker.

* Added spill-over unit test for the Scala Rabit tracker.

* Fixed a typo.

* Overhaul of RabitTracker interface per code review.

  - Removed methods start() waitFor() (no arguments) from IRabitTracker.
  - The timeout in start(timeout) is now worker connection timeout, as tcp
    socket binding timeout is less intuitive.
  - Dropped time unit from start(...) and waitFor(...) methods; the default
    time unit is millisecond.
  - Moved random port number generation into the RabitTrackerHandler.
  - Moved all Rabit-related classes to package ml.dmlc.xgboost4j.scala.rabit.

* More code refactoring and comments.

* Unified timeout constants. Readable tracker status code.

* Add comments to indicate that allReduce is for tests only. Removed all other variants.

* Removed unused imports.

* Simplified signatures of training methods.

 - Moved TrackerConf into parameter map.
 - Changed GeneralParams so that TrackerConf becomes a standalone parameter.
 - Updated test cases accordingly.

* Changed monitoring strategies.

* Reverted monitoring changes.

* Update test case for Rabit AllReduce.

* Mix in UncaughtExceptionHandler into IRabitTracker to prevent tracker from hanging due to exceptions thrown by workers.

* More comprehensive test cases for exception handling and worker connection timeout.

* Handle executor loss due to unknown cause: the newly spawned executor will attempt to connect to the tracker. Interrupt tracker in such case.

* Per code-review, removed training timeout from TrackerConf. Timeout logic must be implemented explicitly and externally in the driver code.

* Reverted scalastyle-config changes.

* Visibility scope change. Interface tweaks.

* Use match pattern to handle tracker_conf parameter.

* Minor clarification in JNI code.

* Clearer intent in match pattern to suppress warnings.

* Removed Future from constructor. Block in start() and waitFor() instead.

* Revert inadvertent comment changes.

* Removed debugging information.

* Updated test cases that are a bit finicky.

* Added comments on the reasoning behind the unit tests for testing Rabit tracker robustness.
2016-12-07 06:35:42 -08:00
Simon DENEL
7078c41dad Changing omp_get_num_threads to omp_get_max_threads (#1831)
* Updating dmlc-core

* Changing omp_get_num_threads to omp_get_max_threads
2016-12-04 11:26:45 -08:00
AbdealiJK
47ba2de7d4 tests/cpp: Add tests for multiclass_metric.cc 2016-12-04 11:25:57 -08:00
AbdealiJK
a7e20555a3 tests/cpp: Add tests for rank_metrics.cc 2016-12-04 11:25:57 -08:00
AbdealiJK
5912e051b1 rank_metric.cc: Use GetWeight in EvalAMS
The GetWeight is a wrapper which sets the correct weight
if the weights vector is not provided. Hence accessing the default
weights vector is not recommended.
2016-12-04 11:25:57 -08:00
AbdealiJK
4a2ef130a7 tests/cpp: Add test for elementwise_metric.cc 2016-12-04 11:25:57 -08:00
AbdealiJK
03abd47f49 tests/cpp: Add tests for Metric RMSE 2016-12-04 11:25:57 -08:00
AbdealiJK
582c373274 tests/cpp: Add tests for metric.cc 2016-12-04 11:25:57 -08:00
AbdealiJK
cc859420ba tests/cpp: Add tests for TweedieRegression 2016-12-04 11:25:57 -08:00
AbdealiJK
fa865564f6 tests/cpp: Add tests for GammaRegression 2016-12-04 11:25:57 -08:00
AbdealiJK
401e4b5220 tests/cpp: Add tests for PoissonRegression 2016-12-04 11:25:57 -08:00
AbdealiJK
d41aab4f61 tests/cpp: Add tests for regression_obj.cc
Test the objective functions in regression_obj.cc

tests/cpp: Add tests for objective.cc and RegLossObj
2016-12-04 11:25:57 -08:00
AbdealiJK
fd99d39372 tests/cpp: Add tests for SplitEntry 2016-12-04 11:25:57 -08:00
AbdealiJK
62e3468603 tests/cpp: Add tests for param.h 2016-12-04 11:25:57 -08:00
AbdealiJK
d6407c3746 tests/cpp: Add tests for SparsePageDMatrix
The SparsePageDMatrix or external memory DMatrix reads data from the
file IO rather than load it into RAM.
2016-12-04 11:25:57 -08:00
AbdealiJK
c3629c91d3 tests/cpp: Add tests for SimpleCSRSource
Test the binary format saved and read by a SimpleDMatrix, which is
internally the SimpleCSRSource.
2016-12-04 11:25:57 -08:00
AbdealiJK
be0f55d563 tests/cpp: Add tests for SimpleDMatrix 2016-12-04 11:25:57 -08:00
AbdealiJK
ef7fe06cf8 tests/cpp/test_metainfo: Add tests to save and load 2016-12-04 11:25:57 -08:00
AbdealiJK
8eb69e0677 travis: Add code coverage on success
Update the code coverage of the project on codecov for easy viewing.

Also the gcov on travis uses a different version which cannot
find the directory of the given files, and it needs to be specified
in the -o flag. Hence now we loop over the list of files and
run them independently.
2016-12-04 11:25:57 -08:00
AbdealiJK
61a9b3a49e travis: Run CPP tests 2016-12-04 11:25:57 -08:00
AbdealiJK
006f9e0760 Makefile: Add CPP code coverage 2016-12-04 11:25:57 -08:00
AbdealiJK
1f2ad36bad Add make commands for tests
This adds the make commands required to build and run tests.
2016-12-04 11:25:57 -08:00
AbdealiJK
b045ccd764 data.cc: Remove redundant ftype variable 2016-12-04 11:25:57 -08:00
JohnStott
1683e07461 Fix issue introduced from correction to log2 (#1837)
https://github.com/dmlc/xgboost/pull/1642
2016-12-04 11:11:56 -08:00
Vadim Khotilovich
a44032d095 [CORE] The update process for a tree model, and its application to feature importance (#1670)
* [CORE] allow updating trees in an existing model

* [CORE] in refresh updater, allow keeping old leaf values and update stats only

* [R-package] xgb.train mod to allow updating trees in an existing model

* [R-package] added check for nrounds when is_update

* [CORE] merge parameter declaration changes; unify their code style

* [CORE] move the update-process trees initialization to Configure; rename default process_type to 'default'; fix the trees and trees_to_update sizes comparison check

* [R-package] unit tests for the update process type

* [DOC] documentation for process_type parameter; improved docs for updater, Gamma and Tweedie; added some parameter aliases; metrics indentation and some were non-documented

* fix my sloppy merge conflict resolutions

* [CORE] add a TreeProcessType enum

* whitespace fix
2016-12-04 09:33:52 -08:00
Nat Wilson
4398fbbe4a fix typo on documentation page (#1836)
replaces "Lanuages" -> "Languages"
2016-12-03 14:41:30 -08:00
Tong He
2f3958a455 Fix for CRAN Submission (#1826)
* fix cran check

* change required R version because of utils::globalVariables

* temporary commit, monotone not working

* fix test

* fix doc

* fix doc

* fix cran note and warning

* improve checks

* fix urls
2016-12-02 20:19:03 -08:00
xgdgsc
27ca50e2c2 change contribution link to open issues (#1834) 2016-12-02 11:03:03 -08:00
ccphillippi
dd477ac903 Move feature_importances_ to base XGBModel for XGBRegressor access (#1591) 2016-12-01 10:17:37 -08:00
AbdealiJK
6f16f0ef58 Use bst_float consistently throughout (#1824)
* Fix various typos

* Add override to functions that are overridden

gcc gives warnings about functions that are being overridden by not
being marked as oveirridden. This fixes it.

* Use bst_float consistently

Use bst_float for all the variables that involve weight,
leaf value, gradient, hessian, gain, loss_chg, predictions,
base_margin, feature values.

In some cases, when due to additions and so on the value can
take a larger value, double is used.

This ensures that type conversions are minimal and reduces loss of
precision.
2016-11-30 10:02:10 -08:00
Dr. Kashif Rasul
da2556f58a fixed some typos (#1814) 2016-11-25 16:34:57 -05:00
RAMitchell
be2f28ec08 Update build instructions, improve memory usage (#1811) 2016-11-25 09:43:22 -08:00
Yuan (Terry) Tang
80c8515457 Bump up the date of R package (#1813) 2016-11-25 03:20:18 -05:00
Jivan Roquet
0c19d4b029 [python-package] Provide a learning_rates parameter to xgb.cv() (#1770)
* Allow using learning_rates parameter when doing CV

- Create a new `callback_cv` method working when called from `xgb.cv()`
- Rename existing `callback` into `callback_train` and make it the default callback
- Get the logic out of the callbacks and place it into a common helper

* Add a learning_rates parameter to cv()

* lint

* remove caller explicit reference

* callback is aware of its calling context

* remove caller argument

* remove learning_rates param

* restore learning_rates for training, but deprecated

* lint

* lint line too long

* quick example for predefined callbacks
2016-11-24 09:49:07 -08:00
Alexey Grigorev
80e70c56b9 [jvm-packages] xgboost4j: publishing sources along with bins (#1797)
* xgboost4j: publishing sources along with bins

* description about building maven artifacts

* publishing scala source to local m2 as well
2016-11-21 15:02:57 -05:00
Ruimin Wang
d80cec3384 [jvm-pacakges] the first parameter in getModelDump should be featuremap path not model path (#1788)
* fix the model dump in xgboost4j example

* Modify the dump model part of scala version

* add the forgotten modelInfos
2016-11-21 08:52:26 -05:00
AbdealiJK
97371ff7e5 c_api.cc: Bring back silent argument (#1794)
In ecb3a271bed151252fb048528ce5a90ad75bb68f the silent argument
in XGDMatrixCreateFromFile of c_api.cc was always overridden to
be false. This disabled the functionality to hide log messages.

This commit reverts that part to enable the hiding of log messages.
2016-11-20 22:04:36 -08:00
Nan Zhu
965091c4bb [jvm-packages] update methods in test cases to be consistent (#1780)
* add back train method but mark as deprecated

* fix scalastyle error

* change class to object in examples

* fix compilation error

* update methods in test cases to be consistent

* add blank lines

* fix
2016-11-20 22:49:18 -05:00
XianXing Zhang
ce708c8e7f [jvm-packages] Leverage the Spark ml API to read DataFrame from files in LibSVM format. (#1785) 2016-11-20 21:28:03 -05:00
Yuan (Terry) Tang
ca0069b708 Fix typo - eval_metric in param should be dictionary (#1791) 2016-11-20 18:52:41 -06:00
Yuan (Terry) Tang
090b37e85d Bumped up err assert in glm test (#1792) 2016-11-20 18:23:19 -06:00
Nan Zhu
5217e53156 stylistic fix (#1789)
* stylistic fix

* try multiple repos

* fix

* fix
2016-11-19 22:03:10 -05:00
Tianqi Chen
060a0ac396 Update setup.sh 2016-11-19 17:57:47 -08:00