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2021-06-14[MRG] Batch/Lazy Log Sinkhorn Knopp on samples (#259)Huy Tran
* Add batch implementation of Sinkhorn * Reformat to pep8 and modify parameter * Fix error in batch size * Code review and add test * Fix accidental typo in test_empirical_sinkhorn * Remove whitespace * Edit config.yml
2021-06-01[MRG] POT numpy/torch/jax backends (#249)Rémi Flamary
* add numpy and torch backends * stat sets on functions * proper import * install recent torch on windows * install recent torch on windows * now testing all functions in backedn * add jax backedn * clenaup windowds * proper convert for jax backedn * pep8 * try again windows tests * test jax conversion * try proper widows tests * emd fuction ses backedn * better test partial OT * proper tests to_numpy and teplate Backend * pep8 * pep8 x2 * feaking sinkhorn works with torch * sinkhorn2 compatible * working ot.emd2 * important detach * it should work * jax autodiff emd * pep8 * no tast same for jax * new independat tests per backedn * freaking pep8 * add tests for gradients * deprecate ot.gpu * worging dist function * working dist * dist done in backedn * not in * remove indexing * change accuacy for jax * first pull backend * projection simplex * projection simplex * projection simplex * projection simplex no ci * projection simplex no ci * projection simplex no ci * pep8 * add backedn discusion to quickstart guide * projection simplex no ci * projection simplex no ci * projection simplex no ci * pep8 + better doc * proper links * corect doctest * big debug documentation * doctest again * doctest again bis * doctest again ter (last one or i kill myself) * backend test + doc proj simplex * correction test_utils * correction test_utils * correction cumsum * correction flip * correction flip v2 * more debug * more debug * more debug + pep8 * pep8 * argh * proj_simplex * backedn works for sort * proj simplex * jax sucks * update doc * Update test/test_utils.py Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update docs/source/quickstart.rst Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update docs/source/quickstart.rst Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update docs/source/quickstart.rst Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update docs/source/readme.rst Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update test/test_utils.py Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update ot/utils.py Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update docs/source/readme.rst Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update ot/lp/__init__.py Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * begin comment alex * comment alex part 2 * optimize test gromov * proj_simplex on vectors * add awesome gradient decsnt example on the weights * pep98 of course * proof read example by alex * pep8 again * encoding oos in translation * correct legend Co-authored-by: Nicolas Courty <ncourty@irisa.fr> Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org>
2021-04-19BUG/DOC FIX - Sinkhorn divergence used the wrong weights, and sinkhorn2 ↵AdrienCorenflos
didn't support epsilon_scaling method. (#235) * FIX: 1. Documentation of loss specific functions 2. Sinkhorn divergence weights handling 3. Sinkhorn2 does not support epsilon scaling, so I removed it (it *should* arguably support it, but this would require a refactoring of the sinkhorn iterates pretty much everywhere, maybe should be done in torch first?) * Had some PEP8 issues Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
2020-12-22[WIP] Update documentation "Why OT" section (#220)Rémi Flamary
* add some text + discussion sinkhorn * stating wrk on why POT * fix sphinx warnings + make html-noplot * discussion when not to use POT * add discussion which sinkhorn * edits on quickstart * more * remove warnings :any: * more * done * remove ref Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org>
2020-06-22Revert "[WIP] Update bregman.py : barycenter_sinkhorn function (#195)" (#196)Rémi Flamary
This reverts commit b2eae39e8a422b18ecc3fadc08bc909ee1dae55f.
2020-06-22[WIP] Update bregman.py : barycenter_sinkhorn function (#195)Rémi Flamary
* Update bregman.py * correct call to function Co-authored-by: FerdinandGns <56926826+FerdinandGns@users.noreply.github.com>
2020-04-24better doc per moduleRémi Flamary
2020-04-24better coverage options verbose and logRémi Flamary
2020-04-15fix soft labels, remove gammas from jcpotievred
2020-04-08added test barycenter + modif targetievred
2020-04-08remove laplace from jcpotievred
2020-04-07updievred
2020-04-07pep bregmanievred
2020-04-07pep bregmanievred
2020-04-02laplace v1ievred
2020-04-01fix test example add M to logievred
2020-03-31readme move to bregmanievred
2020-03-06Fix convolutional_barycenter kernel for non-symmetric imagesAlex Tong
Add authorship
2020-01-24add a warning for non installed Botteleneck moduleMokhtar Z. Alaya
2020-01-18cleanMokhtar Z. Alaya
2020-01-18cleanMokhtar Z. Alaya
2020-01-10improve docMokhtar Z. Alaya
2020-01-10improve docMokhtar Z. Alaya
2020-01-10update screenkhorn exampleMokhtar Z. Alaya
2020-01-10improve documentationMokhtar Z. Alaya
2020-01-08fix binary indexingMokhtar Z. Alaya
2020-01-08using binary indexing for definition the active setsMokhtar Z. Alaya
2020-01-07fix typos in documentationMokhtar Z. Alaya
2020-01-07fix definitions complementary active sets Ic, JcMokhtar Z. Alaya
2020-01-07replace reshape by numpy slicing in returnMokhtar Z. Alaya
2020-01-07fix default values for the budget argumentsMokhtar Z. Alaya
2020-01-07set default param. for LBFGS in the function's prototypeMokhtar Z. Alaya
2020-01-07replace @ operator by np.dotMokhtar Z. Alaya
2020-01-07delete "ArrayBox"-type test of dist. matrix MMokhtar Z. Alaya
2020-01-07improve documentation of screenkhornMokhtar Z. Alaya
add Exception at the beginning to check the installation of bottleneck module
2020-01-07close "bottleneck" tagMokhtar Z. Alaya
2020-01-06add screenkhorn: screening Sinkhorn algorithmMokhtar Z. Alaya
2019-10-19add weights arg in generic barycenter funcHicham Janati
2019-09-04improve docHicham Janati
2019-09-03style + make funcs publicHicham Janati
2019-08-28fix empirical sinkhorn doc-exampleHicham Janati
2019-08-28remove square in convergence checkHicham Janati
add unbalanced with stabilization add unbalanced tests with stabilization fix doctest examples add xvfb in travis remove explicit call xvfb in travis change alpha to reg_m minor flake8 remove redundant sink definitions + better doc and naming add stabilized unbalanced barycenter + add not converged warnings add test for stable barycenter add generic barycenter func + make method funcs private fix typo + add method test for barycenters fix doc examples + add xml to gitignore fix whitespace in example change logsumexp import - scipy deprecation warning fix doctest improve naming + add stable barycenter in bregman add test for stable bar + test the method arg in bregman
2019-07-23fix issue 94 + add testHicham Janati
2019-07-09trailing spacesAlexandre Gramfort
2019-07-09moreAlexandre Gramfort
2019-07-02Fix tolerance in doctestRomain Tavenard
2019-07-01Fixed all doctests assuming functions are working properly (actually tested ↵Romain Tavenard
in tests/)
2019-07-01Set numpy array formatting version to post-1.13Romain Tavenard
2019-07-01Fixed doctestsRomain Tavenard
2019-06-18fix func names + add more testsHicham Janati
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