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* add entropic fgw + fgw bary + srgw + srfgw with tests
* add exemples for entropic srgw - srfgw solvers
* add PPA solvers for GW/FGW + complete previous commits
* update readme
* add tests
* add examples + tests + warning in entropic solvers + releases
* reduce testing runtimes for test_gromov
* fix conflicts
* optional marginals
* improve coverage
* gromov doc harmonization
* fix pep8
* complete optional marginal for entropic srfgw
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Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
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* alpha differentiable
* autopep and update gradient test
* debug test gradient
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Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
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* make alpha diferentiable
* update release file
* debug tensorflow to_numpy
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* maj gw/ srgw/ generic cg solver
* correct pep8 on current state
* fix bug previous tests
* fix pep8
* fix bug srGW constC in loss and gradient
* fix doc html
* fix doc html
* start updating test_optim.py
* update tests gromov and optim - plus fix gromov dependencies
* add symmetry feature to entropic gw
* add symmetry feature to entropic gw
* add exemple for sr(F)GW matchings
* small stuff
* remove (reg,M) from line-search/ complete srgw tests with backend
* remove backend repetitions / rename fG to costG/ fix innerlog to True
* fix pep8
* take comments into account / new nx parameters still to test
* factor (f)gw2 + test new backend parameters in ot.gromov + harmonize stopping criterions
* split gromov.py in ot/gromov/ + update test_gromov with helper_backend functions
* manual documentaion gromov
* remove circular autosummary
* trying stuff
* debug documentation
* alphabetic ordering of module
* merge into branch
* add note in entropic gw solvers
* fix exemples/gromov doc
* add fixed issue to releases.md
* fix bugs of gw_entropic and armijo to run on gpu
* add pr to releases.md
* fix pep8
* fix call to backend in line_search_armijo
* correct docstring generic_conditional_gradient
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Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
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gromov-wasserstein solvers (#431)
* maj gw/ srgw/ generic cg solver
* correct pep8 on current state
* fix bug previous tests
* fix pep8
* fix bug srGW constC in loss and gradient
* fix doc html
* fix doc html
* start updating test_optim.py
* update tests gromov and optim - plus fix gromov dependencies
* add symmetry feature to entropic gw
* add symmetry feature to entropic gw
* add exemple for sr(F)GW matchings
* small stuff
* remove (reg,M) from line-search/ complete srgw tests with backend
* remove backend repetitions / rename fG to costG/ fix innerlog to True
* fix pep8
* take comments into account / new nx parameters still to test
* factor (f)gw2 + test new backend parameters in ot.gromov + harmonize stopping criterions
* split gromov.py in ot/gromov/ + update test_gromov with helper_backend functions
* manual documentaion gromov
* remove circular autosummary
* trying stuff
* debug documentation
* alphabetic ordering of module
* merge into branch
* add note in entropic gw solvers
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Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
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* remove all cpu submodule and tests
* speedup tests gromov
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* First draft
* Add matrix inverse and square root to backend
* Eigen decomposition for older versions of pytorch (1.8.1 and older)
* Corrected eigen decomposition for pytorch 1.8.1 and older
* Spectral theorem is a thing
* Optimization
* small optimization
* More functions converted
* pep8
* remove a warning and prepare torch meshgrid for future torch release (which will change default indexing)
* dots and pep8
* Meshgrid corrected for older version and prepared for future versions changes
* New backend functions
* Base transport
* LinearTransport
* All transport classes + pep8
* PR added to release file
* Jcpot barycenter test
* unbalanced with backend
* pep8
* bug solve
* test of domain adaptation with backends
* solve bug for tic toc & macos
* solving scipy deprecation warning
* solving scipy deprecation warning attempt2
* solving scipy deprecation warning attempt3
* A warning is triggered when a float->int conversion is detected
* bug solve
* docs
* release file updated
* Better handling of float->int conversion in EMD
* Corrected test for is_floating_point
* docs
* release file updated
* cupy does not allow implicit cast
* fromnumpy
* added test
* test da tf jax
* test unbalanced with no provided histogram
* using type_as argument in unif function correctly
* pep8
* transport plan cast in emd changed behaviour, now trying to cast as histogram's dtype, defaulting to cost matrix
Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
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* Resolves gromov wasserstein backward bug
* release file updated
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* add fgw dictionary learning feature
* add fgw dictionary learning feature
* plot gromov wasserstein dictionary learning
* Update __init__.py
* fix pep8 errors exact E501 line too long
* fix last pep8 issues
* add unitary tests for (F)GW dictionary learning without using autodifferentiable functions
* correct tests for (F)GW dictionary learning without using autodiff
* correct tests for (F)GW dictionary learning without using autodiff
* fix docs and notations
* answer to review: improve tests, docs, examples + make node weights optional
* fix pep8 and examples
* improve docs + tests + thumbnail
* make example faster
* improve ex
* update README.md
* make GDL tests faster
Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
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* First batch of tf methods (to be continued)
* Second batch of method (yet to debug)
* tensorflow for cpu
* add tf requirement
* pep8 + bug
* small changes
* attempt to solve pymanopt bug with tf2
* attempt #2
* attempt #3
* attempt 4
* docstring
* correct pep8 violation introduced in merge conflicts resolution
* attempt 5
* attempt 6
* just a random try
* Revert "just a random try"
This reverts commit 8223e768bfe33635549fb66cca2267514a60ebbf.
* GPU tests for tensorflow
* pep8
* attempt to solve issue with m2r2
* Remove transpose backend method
* first draft of benchmarker (need to correct time measurement)
* prettier bench table
* Bitsize and prettier device methods
* prettified table bench
* Bug corrected (results were mixed up in the final table)
* Better perf counter (for GPU support)
* pep8
* EMD bench
* solve bug if no GPU available
* pep8
* warning about tensorflow numpy api being required in the backend.py docstring
* Bug solve in backend docstring
* not covering code which requires a GPU
* Tensorflow gradients manipulation tested
* Number of warmup runs is now customizable
* typo
* Remove some warnings while building docs
* Change prettier_device to device_type in backend
* Correct JAX mistakes preventing to see the CPU if a GPU is present
* Attempt to solve JAX bug in case no GPU is found
* Reworked benchmarks order and results storage & clear GPU after usage by benchmark
* Add bench to backend docstring
* better benchs
* remove useless stuff
* Better device_type
* Now using MYST_PARSER and solving links issue in the README.md / online docs
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* Fix issue 317
* Update with docs and tests
Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
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* Cupy backend
* pep8 + bug
* working even if cupy not installed
* attempt to force codecov to ignore cupy because no gpu can be used for testing on github
* docstring
* readme
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* First draft : making pytest use gpu for torch testing
* bug solve
* Revert "bug solve"
This reverts commit 29b013abd162f8693128f26d8129186b79923609.
* Revert "First draft : making pytest use gpu for torch testing"
This reverts commit 2778175bcc338016c704efa4187d132fe5162e3a.
* sliced
* sliced
* ot 1dsolver
* bregman
* better print
* jax works with sinkhorn, sinkhorn_log and sinkhornn_stabilized, no need to skip them
* gromov & entropic gromov
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* grmov differentable
* new stuff
* test gromov gradients
* fgwdifferentiable
* fgw tested
* correc name test
* add awesome example with gromov optimizatrion
* pep8+ typos
* damn pep8
* thunbnail
* remove prints
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* bregman: small correction
* gromov backend first draft
* Removing decorators
* Reworked casting method
* Bug solve
* Removing casting
* Bug solve
* toarray renamed todense ; expand_dims removed
* Warning (jax not supporting sparse matrix) moved
* Mistake corrected
* test backend
* Sparsity test for older versions of pytorch
* Trying pytorch/1.10
* Attempt to correct torch sparse bug
* Backend version of gromov tests
* Random state introduced for remaining gromov functions
* review changes
* code coverage
* Docs (first draft, to be continued)
* Gromov docs
* Prettified docs
* mistake corrected in the docs
* little change
Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
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* adda sinkhorn log and working sinkhorn2 function
* more tests pass
* more tests pass
* it works but not by default yet
* remove warningd
* update circleci doc
* update circleci doc
* new sinkhorn implemeted but not by default
* better
* doctest pass
* test doctest
* new test utils
* remove pep8 errors
* remove pep8 errors
* doc new implementtaion with log
* test sinkhorn 2
* doc for log implementation
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* Add two new algorithms to solve Gromov Wasserstein: Sampled Gromov Wasserstein and Pointwise Gromov Wasserstein.
* Correct some lines in SaGroW and PoGroW to follow pep8 guide.
* Change nb_samples name. Use rdm state. Change symmetric check.
* Change names of len(p) and len(q) in SaGroW and PoGroW.
* Re-add some deleted lines in the comments of gromov.py
Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
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* speedup tests
* add color to tests and timings
* add test unbalanced
* stupid missing -
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* 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>
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merge pot
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function
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function
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