[MRG] Semi-relaxed (fused) gromov-wasserstein divergence and improvem…

…ents of gromov-wasserstein solvers (PythonOT#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 --------- Co-authored-by: Rémi Flamary <[email protected]>
wasahaiah · Mar 9, 2023 · a5930d3 · a5930d3
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diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md
@@ -36,7 +36,7 @@ The contributors to this library are:
 * [Tanguy Kerdoncuff](https://hv0nnus.github.io/) (Sampled Gromov Wasserstein)
 * [Minhui Huang](https://mhhuang95.github.io) (Projection Robust Wasserstein Distance)
 * [Nathan Cassereau](https://github.com/ncassereau-idris) (Backends)
-* [Cédric Vincent-Cuaz](https://github.com/cedricvincentcuaz) (Graph Dictionary Learning)
+* [Cédric Vincent-Cuaz](https://github.com/cedricvincentcuaz) (Graph Dictionary Learning, semi-relaxed FGW)
 * [Eloi Tanguy](https://github.com/eloitanguy) (Generalized Wasserstein Barycenters)
 * [Camille Le Coz](https://www.linkedin.com/in/camille-le-coz-8593b91a1/) (EMD2 debug)
 * [Eduardo Fernandes Montesuma](https://eddardd.github.io/my-personal-blog/) (Free support sinkhorn barycenter)

diff --git a/README.md b/README.md
@@ -42,6 +42,7 @@ POT provides the following generic OT solvers (links to examples):
 * [Wasserstein distance on the circle](https://pythonot.github.io/auto_examples/plot_compute_wasserstein_circle.html) [44, 45]
 * [Spherical Sliced Wasserstein](https://pythonot.github.io/auto_examples/sliced-wasserstein/plot_variance_ssw.html) [46]
 * [Graph Dictionary Learning solvers](https://pythonot.github.io/auto_examples/gromov/plot_gromov_wasserstein_dictionary_learning.html) [38].
+* [Semi-relaxed (Fused) Gromov-Wasserstein divergences](https://pythonot.github.io/auto_examples/gromov/plot_semirelaxed_fgw.html) [48].
 * [Several backends](https://pythonot.github.io/quickstart.html#solving-ot-with-multiple-backends) for easy use of POT with  [Pytorch](https://pytorch.org/)/[jax](https://github.com/google/jax)/[Numpy](https://numpy.org/)/[Cupy](https://cupy.dev/)/[Tensorflow](https://www.tensorflow.org/) arrays.
 
 POT provides the following Machine Learning related solvers:
@@ -300,4 +301,8 @@ Dictionary Learning](https://arxiv.org/pdf/2102.06555.pdf), International Confer
 
 [45] Hundrieser, Shayan, Marcel Klatt, and Axel Munk. [The statistics of circular optimal transport.](https://arxiv.org/abs/2103.15426) Directional Statistics for Innovative Applications: A Bicentennial Tribute to Florence Nightingale. Singapore: Springer Nature Singapore, 2022. 57-82.
 
-[46] Bonet, C., Berg, P., Courty, N., Septier, F., Drumetz, L., & Pham, M. T. (2023). [Spherical Sliced-Wasserstein](https://openreview.net/forum?id=jXQ0ipgMdU). International Conference on Learning Representations.
+[46] Bonet, C., Berg, P., Courty, N., Septier, F., Drumetz, L., & Pham, M. T. (2023). [Spherical Sliced-Wasserstein](https://openreview.net/forum?id=jXQ0ipgMdU). International Conference on Learning Representations.
+
+[47] Chowdhury, S., & Mémoli, F. (2019). [The gromov–wasserstein distance between networks and stable network invariants](https://academic.oup.com/imaiai/article/8/4/757/5627736). Information and Inference: A Journal of the IMA, 8(4), 757-787.
+
+[48] Cédric Vincent-Cuaz, Rémi Flamary, Marco Corneli, Titouan Vayer, Nicolas Courty (2022). [Semi-relaxed Gromov-Wasserstein divergence and applications on graphs](https://openreview.net/pdf?id=RShaMexjc-x). International Conference on Learning Representations (ICLR), 2022.
diff --git a/RELEASES.md b/RELEASES.md
@@ -3,7 +3,9 @@
 ## 0.8.3dev
 
 #### New features
-
+- Added feature to (Fused) Gromov-Wasserstein solvers herited from `ot.optim` to support relative and absolute loss variations as stopping criterions (PR #431)
+- Added feature to (Fused) Gromov-Wasserstein solvers to handle asymmetric matrices (PR #431)
+- Added semi-relaxed (Fused) Gromov-Wasserstein solvers in `ot.gromov` + examples (PR #431)
 - Added the spherical sliced-Wasserstein discrepancy in `ot.sliced.sliced_wasserstein_sphere` and `ot.sliced.sliced_wasserstein_sphere_unif` + examples (PR #434)
 - Added the Wasserstein distance on the circle in ``ot.lp.solver_1d.wasserstein_circle`` (PR #434)
 - Added the Wasserstein distance on the circle (for p>=1) in `ot.lp.solver_1d.binary_search_circle` + examples (PR #434)

diff --git a/docs/cache_nbrun b/docs/cache_nbrun
diff --git a/docs/source/_templates/module.rst b/docs/source/_templates/module.rst
@@ -2,6 +2,7 @@
 {{ underline }}
 
 .. automodule:: {{ fullname }}
+   :members:
 
    {% block functions %}
    {% if functions %}
@@ -12,6 +13,7 @@
    {% for item in functions %}
 
    .. autofunction:: {{ item }}
+
 
    .. include:: backreferences/{{fullname}}.{{item}}.examples
 

diff --git a/docs/source/all.rst b/docs/source/all.rst
@@ -13,29 +13,33 @@ API and modules
    :toctree: gen_modules/
    :template: module.rst
 
-   lp
+
    backend
    bregman
-   smooth
-   gromov
-   optim
    da
-   dr
-   utils
    datasets
+   dr
+   factored
+   gaussian
+   gromov
+   lp
+   optim
+   partial
    plot
-   stochastic
-   unbalanced
    regpath
-   partial
    sliced
+   smooth
+   stochastic
+   unbalanced
+   utils
    weak
-   factored
-   gaussian
+
 
-.. autosummary::
-   :toctree: ../modules/generated/
-   :template: module.rst
+Main :py:mod:`ot` functions
+--------------
 
 .. automodule:: ot
    :members:
+
+
+
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -119,7 +119,7 @@ def __getattr__(cls, name):
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
@@ -341,6 +341,9 @@ def __getattr__(cls, name):
 # If true, do not generate a @detailmenu in the "Top" node's menu.
 #texinfo_no_detailmenu = False
 
+autodoc_default_options = {'autosummary': True,
+                           'autosummary_imported_members': True}
+
 
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {'python': ('https://docs.python.org/3', None),

diff --git a/examples/gromov/plot_gromov.py b/examples/gromov/plot_gromov.py
@@ -3,7 +3,6 @@
 ==========================
 Gromov-Wasserstein example
 ==========================
-
 This example is designed to show how to use the Gromov-Wassertsein distance
 computation in POT.
 """