* Implement tree model dump with a code generator.
* Split up generators.
* Implement graphviz generator.
* Use pattern matching.
* [Breaking] Return a Source in `to_graphviz` instead of Digraph in Python package.
Co-Authored-By: Philip Hyunsu Cho <chohyu01@cs.washington.edu>
* adding support for matrix slicing with query ID for cross-validation
* hail mary test of unrar installation for windows tests
* trying to modify tests to run in Github CI
* Remove dependency on wget and unrar
* Save error log from R test
* Relax assertion in test_training
* Use int instead of bool in C function interface
* Revise R interface
* Add XGDMatrixSliceDMatrixEx and keep old XGDMatrixSliceDMatrix for API compatibility
* Refactor CMake scripts.
* Remove CMake CUDA wrapper.
* Bump CMake version for CUDA.
* Use CMake to handle Doxygen.
* Split up CMakeList.
* Export install target.
* Use modern CMake.
* Remove build.sh
* Workaround for gpu_hist test.
* Use cmake 3.12.
* Revert machine.conf.
* Move CLI test to gpu.
* Small cleanup.
* Support using XGBoost as submodule.
* Fix windows
* Fix cpp tests on Windows
* Remove duplicated find_package.
* Upgrade gtest for clang-tidy.
* Use CMake to install GTest instead of mv.
* Don't enforce clang-tidy to return 0 due to errors in thrust.
* Add a small test for tidy itself.
* Reformat.
* Fix#3342 and h2oai/h2o4gpu#625: Save predictor parameters in model file
This allows pickled models to retain predictor attributes, such as
'predictor' (whether to use CPU or GPU) and 'n_gpu' (number of GPUs
to use). Related: h2oai/h2o4gpu#625Closes#3342.
TODO. Write a test.
* Fix lint
* Do not load GPU predictor into CPU-only XGBoost
* Add a test for pickling GPU predictors
* Make sample data big enough to pass multi GPU test
* Update test_gpu_predictor.cu
* Replaced std::vector with HostDeviceVector in MetaInfo and SparsePage.
- added distributions to HostDeviceVector
- using HostDeviceVector for labels, weights and base margings in MetaInfo
- using HostDeviceVector for offset and data in SparsePage
- other necessary refactoring
* Added const version of HostDeviceVector API calls.
- const versions added to calls that can trigger data transfers, e.g. DevicePointer()
- updated the code that uses HostDeviceVector
- objective functions now accept const HostDeviceVector<bst_float>& for predictions
* Updated src/linear/updater_gpu_coordinate.cu.
* Added read-only state for HostDeviceVector sync.
- this means no copies are performed if both host and devices access
the HostDeviceVector read-only
* Fixed linter and test errors.
- updated the lz4 plugin
- added ConstDeviceSpan to HostDeviceVector
- using device % dh::NVisibleDevices() for the physical device number,
e.g. in calls to cudaSetDevice()
* Fixed explicit template instantiation errors for HostDeviceVector.
- replaced HostDeviceVector<unsigned int> with HostDeviceVector<int>
* Fixed HostDeviceVector tests that require multiple GPUs.
- added a mock set device handler; when set, it is called instead of cudaSetDevice()
* Add basic Span class based on ISO++20.
* Use Span<Entry const> instead of Inst in SparsePage.
* Add DeviceSpan in HostDeviceVector, use it in regression obj.
* Fix#3545: XGDMatrixCreateFromCSCEx silently discards empty trailing rows
Description: The bug is triggered when
1. The data matrix has empty rows at the bottom. More precisely, the rows
`n-k+1`, `n-k+2`, ..., `n` of the matrix have missing values in all
dimensions (`n` number of instances, `k` number of trailing rows)
2. The data matrix is given as Compressed Sparse Column (CSC) format.
Diagnosis: When the CSC matrix is converted to Compressed Sparse Row (CSR)
format (this is common format used for DMatrix), the trailing empty rows
are silently ignored. More specifically, the row pointer (`offset`) of the
newly created CSR matrix does not take account of these rows.
Fix: Modify the row pointer.
* Add regression test
* Fail GPU CI after test failure
* Fix GPU linear tests
* Reduced number of GPU tests to speed up CI
* Remove static allocations of device memory
* Resolve illegal memory access for updater_fast_hist.cc
* Fix broken r tests dependency
* Update python install documentation for GPU
* add qid for https://github.com/dmlc/xgboost/issues/2748
* change names
* change spaces
* change qid to bst_uint type
* change qid type to size_t
* change qid first to SIZE_MAX
* change qid type from size_t to uint64_t
* update dmlc-core
* fix qids name error
* fix group_ptr_ error
* Style fix
* Add qid handling logic to SparsePage
* New MetaInfo format + backward compatibility fix
Old MetaInfo format (1.0) doesn't contain qid field. We still want to be able
to read from MetaInfo files saved in old format. Also, define a new format
(2.0) that contains the qid field. This way, we can distinguish files that
contain qid and those that do not.
* Update MetaInfo test
* Simply group assignment logic
* Explicitly set qid=nullptr in NativeDataIter
NativeDataIter's callback does not support qid field. Users of NativeDataIter
will need to call setGroup() function separately to set group information.
* Save qids_ in SaveBinary()
* Upgrade dmlc-core submodule
* Add a test for reading qid
* Add contributor
* Check the size of qids_
* Document qid format
* Use sparse page as singular CSR matrix representation
* Simplify dmatrix methods
* Reduce statefullness of batch iterators
* BREAKING CHANGE: Remove prob_buffer_row parameter. Users are instead recommended to sample their dataset as a preprocessing step before using XGBoost.
* Replaced std::vector-based interfaces with HostDeviceVector-based interfaces.
- replacement was performed in the learner, boosters, predictors,
updaters, and objective functions
- only interfaces used in training were replaced;
interfaces like PredictInstance() still use std::vector
- refactoring necessary for replacement of interfaces was also performed,
such as using HostDeviceVector in prediction cache
* HostDeviceVector-based interfaces for custom objective function example plugin.
In line 461, the "size_t offset = 0;" should be declared before any calculation, otherwise will cause compilation error.
```
I:\Libraries\xgboost\src\c_api\c_api.cc(416): error C2146: Missing ";" before "offset" [I:\Libraries\xgboost\build\objxgboost.vcxproj]
```
* Add interaction effects and cox loss
* Minimize whitespace changes
* Cox loss now no longer needs a pre-sorted dataset.
* Address code review comments
* Remove mem check, rename to pred_interactions, include bias
* Make lint happy
* More lint fixes
* Fix cox loss indexing
* Fix main effects and tests
* Fix lint
* Use half interaction values on the off-diagonals
* Fix lint again
* SHAP values for feature contributions
* Fix commenting error
* New polynomial time SHAP value estimation algorithm
* Update API to support SHAP values
* Fix merge conflicts with updates in master
* Correct submodule hashes
* Fix variable sized stack allocation
* Make lint happy
* Add docs
* Fix typo
* Adjust tolerances
* Remove unneeded def
* Fixed cpp test setup
* Updated R API and cleaned up
* Fixed test typo
* for MinGW, drop the 'lib' prefix from shared library name
* fix defines for 'g++ 4.8 or higher' to include g++ >= 5
* fix compile warnings
* [Appveyor] add MinGW with python; remove redundant jobs
* [Appveyor] also do python build for one of msvc jobs
* Add prediction of feature contributions
This implements the idea described at http://blog.datadive.net/interpreting-random-forests/
which tries to give insight in how a prediction is composed of its feature contributions
and a bias.
* Support multi-class models
* Calculate learning_rate per-tree instead of using the one from the first tree
* Do not rely on node.base_weight * learning_rate having the same value as the node mean value (aka leaf value, if it were a leaf); instead calculate them (lazily) on-the-fly
* Add simple test for contributions feature
* Check against param.num_nodes instead of checking for non-zero length
* Loop over all roots instead of only the first
This log appears to fire every time I ask the python package to make a prediction. It's the only log that fires from XGBoost. When we're getting predictions on millions of items a day in production, this log seems out of place.
* 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.
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.
* Add format to the params accepted by DumpModel
Currently, only the test format is supported when trying to dump
a model. The plan is to add more such formats like JSON which are
easy to read and/or parse by machines. And to make the interface
for this even more generic to allow other formats to be added.
Hence, we make some modifications to make these function generic
and accept a new parameter "format" which signifies the format of
the dump to be created.
* Fix typos and errors in docs
* plugin: Mention all the register macros available
Document the register macros currently available to the plugin
writers so they know what exactly can be extended using hooks.
* sparce_page_source: Use same arg name in .h and .cc
* gbm: Add JSON dump
The dump_format argument can be used to specify what type
of dump file should be created. Add functionality to dump
gblinear and gbtree into a JSON file.
The JSON file has an array, each item is a JSON object for the tree.
For gblinear:
- The item is the bias and weights vectors
For gbtree:
- The item is the root node. The root node has a attribute "children"
which holds the children nodes. This happens recursively.
* core.py: Add arg dump_format for get_dump()
