PERF: pyemd to POT for EMD computation in wmdistance (#3327)

* PERF: switch from pyemd to POT for EMD computation * Adapt citations * Adapt dependency * Adapt tests * Update cache for gallery Co-authored-by: TLouf <loufthomas@gmail.com>
piskvorky · Nov 3, 2022 · fdf40eb · fdf40eb
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diff --git a/.travis.yml b/.travis.yml
@@ -26,7 +26,7 @@ env:
         # them here for now.  They'll get picked up by the multibuild stuff
         # running in multibuild/common_utils.sh.
         #
-      - TEST_DEPENDS="pytest mock cython nmslib pyemd testfixtures python-levenshtein==0.12.0 visdom==0.1.8.9 scikit-learn"
+      - TEST_DEPENDS="pytest mock cython nmslib POT testfixtures python-levenshtein==0.12.0 visdom==0.1.8.9 scikit-learn"
 
 matrix:
       #

diff --git a/docs/notebooks/WMD_tutorial.ipynb b/docs/notebooks/WMD_tutorial.ipynb
@@ -30,7 +30,7 @@
     "\n",
     "## Running this notebook\n",
     "\n",
-    "You can download this [iPython Notebook](http://ipython.org/notebook.html), and run it on your own computer, provided you have installed Gensim, PyEMD, NLTK, and downloaded the necessary data.\n",
+    "You can download this [iPython Notebook](http://ipython.org/notebook.html), and run it on your own computer, provided you have installed Gensim, POT, NLTK, and downloaded the necessary data.\n",
     "\n",
     "The notebook was run on an Ubuntu machine with an Intel core i7-4770 CPU 3.40GHz (8 cores) and 32 GB memory. Running the entire notebook on this machine takes about 3 minutes.\n",
     "\n",
@@ -524,8 +524,7 @@
    "source": [
     "## References\n",
     "\n",
-    "1. Ofir Pele and Michael Werman, *A linear time histogram metric for improved SIFT matching*, 2008.\n",
-    "* Ofir Pele and Michael Werman, *Fast and robust earth mover's distances*, 2009.\n",
+    "1. * Rémi Flamary et al. *POT: Python Optimal Transport*, 2021.\n",
     "* Matt Kusner et al. *From Embeddings To Document Distances*, 2015.\n",
     "* Thomas Mikolov et al. *Efficient Estimation of Word Representations in Vector Space*, 2013."
    ]

diff --git a/docs/notebooks/soft_cosine_tutorial.ipynb b/docs/notebooks/soft_cosine_tutorial.ipynb
@@ -30,7 +30,7 @@
     ">\n",
     "\n",
     "## Running this notebook\n",
-    "You can download this [Jupyter notebook](http://jupyter.org/), and run it on your own computer, provided you have installed the `gensim`, `jupyter`, `sklearn`, `pyemd`, and `wmd` Python packages.\n",
+    "You can download this [Jupyter notebook](http://jupyter.org/), and run it on your own computer, provided you have installed the `gensim`, `jupyter`, `sklearn`, `POT`, and `wmd` Python packages.\n",
     "\n",
     "The notebook was run on an Ubuntu machine with an Intel core i7-6700HQ CPU 3.10GHz (4 cores) and 16 GB memory. Assuming all resources required by the notebook have already been downloaded, running the entire notebook on this machine takes about 30 minutes."
    ]
@@ -357,7 +357,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!pip install pyemd"
+    "!pip install POT"
    ]
   },
   {
@@ -404,7 +404,7 @@
     "    return similarities\n",
     "\n",
     "def wmd_gensim(query, documents):\n",
-    "    # Compute Word Mover's Distance as implemented in PyEMD by William Mayner\n",
+    "    # Compute Word Mover's Distance as implemented in POT\n",
     "    # between the query and the documents.\n",
     "    index = WmdSimilarity(documents, w2v_model)\n",
     "    similarities = index[query]\n",
@@ -532,26 +532,26 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-     "Dataset | Strategy | MAP score | Elapsed time (sec)\n",
-     ":---|:---|:---|---:\n",
-     "2016-test|softcossim|78.52 ±11.18|6.00 ±0.79\n",
-     "2016-test|**Winner (UH-PRHLT-primary)**|76.70 ±0.00|\n",
-     "2016-test|cossim|76.45 ±10.40|0.64 ±0.08\n",
-     "2016-test|wmd-gensim|76.23 ±11.42|5.37 ±0.64\n",
-     "2016-test|**Baseline 1 (IR)**|74.75 ±0.00|\n",
-     "2016-test|wmd-relax|71.05 ±11.06|1.11 ±0.09\n",
-     "2016-test|**Baseline 2 (random)**|46.98 ±0.00|\n",
-     "\n",
-     "\n",
-     "Dataset | Strategy | MAP score | Elapsed time (sec)\n",
-     ":---|:---|:---|---:\n",
-     "2017-test|**Winner (SimBow-primary)**|47.22 ±0.00|\n",
-     "2017-test|softcossim|45.88 ±16.22|7.08 ±1.49\n",
-     "2017-test|cossim|44.38 ±14.71|0.74 ±0.10\n",
-     "2017-test|wmd-gensim|44.06 ±15.92|6.20 ±0.87\n",
-     "2017-test|wmd-relax|43.52 ±16.30|1.30 ±0.18\n",
-     "2017-test|**Baseline 1 (IR)**|41.85 ±0.00|\n",
-     "2017-test|**Baseline 2 (random)**|29.81 ±0.00|"
+    "Dataset | Strategy | MAP score | Elapsed time (sec)\n",
+    ":---|:---|:---|---:\n",
+    "2016-test|softcossim|78.52 ±11.18|6.00 ±0.79\n",
+    "2016-test|**Winner (UH-PRHLT-primary)**|76.70 ±0.00|\n",
+    "2016-test|cossim|76.45 ±10.40|0.64 ±0.08\n",
+    "2016-test|wmd-gensim|76.23 ±11.42|5.37 ±0.64\n",
+    "2016-test|**Baseline 1 (IR)**|74.75 ±0.00|\n",
+    "2016-test|wmd-relax|71.05 ±11.06|1.11 ±0.09\n",
+    "2016-test|**Baseline 2 (random)**|46.98 ±0.00|\n",
+    "\n",
+    "\n",
+    "Dataset | Strategy | MAP score | Elapsed time (sec)\n",
+    ":---|:---|:---|---:\n",
+    "2017-test|**Winner (SimBow-primary)**|47.22 ±0.00|\n",
+    "2017-test|softcossim|45.88 ±16.22|7.08 ±1.49\n",
+    "2017-test|cossim|44.38 ±14.71|0.74 ±0.10\n",
+    "2017-test|wmd-gensim|44.06 ±15.92|6.20 ±0.87\n",
+    "2017-test|wmd-relax|43.52 ±16.30|1.30 ±0.18\n",
+    "2017-test|**Baseline 1 (IR)**|41.85 ±0.00|\n",
+    "2017-test|**Baseline 2 (random)**|29.81 ±0.00|"
    ]
   },
   {

diff --git a/docs/src/auto_examples/core/index.rst b/docs/src/auto_examples/core/index.rst
@@ -0,0 +1,98 @@
+
+
+.. _sphx_glr_auto_examples_core:
+
+Core Tutorials: New Users Start Here!
+-------------------------------------
+
+If you're new to gensim, we recommend going through all core tutorials in order.
+Understanding this functionality is vital for using gensim effectively.
+
+
+
+.. raw:: html
+
+    <div class="sphx-glr-thumbnails">
+
+
+.. raw:: html
+
+    <div class="sphx-glr-thumbcontainer" tooltip="This tutorial introduces Documents, Corpora, Vectors and Models: the basic concepts and terms n...">
+
+.. only:: html
+
+  .. image:: /auto_examples/core/images/thumb/sphx_glr_run_core_concepts_thumb.png
+    :alt: Core Concepts
+
+  :ref:`sphx_glr_auto_examples_core_run_core_concepts.py`
+
+.. raw:: html
+
+      <div class="sphx-glr-thumbnail-title">Core Concepts</div>
+    </div>
+
+
+.. raw:: html
+
+    <div class="sphx-glr-thumbcontainer" tooltip="Demonstrates transforming text into a vector space representation.">
+
+.. only:: html
+
+  .. image:: /auto_examples/core/images/thumb/sphx_glr_run_corpora_and_vector_spaces_thumb.png
+    :alt: Corpora and Vector Spaces
+
+  :ref:`sphx_glr_auto_examples_core_run_corpora_and_vector_spaces.py`
+
+.. raw:: html
+
+      <div class="sphx-glr-thumbnail-title">Corpora and Vector Spaces</div>
+    </div>
+
+
+.. raw:: html
+
+    <div class="sphx-glr-thumbcontainer" tooltip="Introduces transformations and demonstrates their use on a toy corpus.">
+
+.. only:: html
+
+  .. image:: /auto_examples/core/images/thumb/sphx_glr_run_topics_and_transformations_thumb.png
+    :alt: Topics and Transformations
+
+  :ref:`sphx_glr_auto_examples_core_run_topics_and_transformations.py`
+
+.. raw:: html
+
+      <div class="sphx-glr-thumbnail-title">Topics and Transformations</div>
+    </div>
+
+
+.. raw:: html
+
+    <div class="sphx-glr-thumbcontainer" tooltip="Demonstrates querying a corpus for similar documents.">
+
+.. only:: html
+
+  .. image:: /auto_examples/core/images/thumb/sphx_glr_run_similarity_queries_thumb.png
+    :alt: Similarity Queries
+
+  :ref:`sphx_glr_auto_examples_core_run_similarity_queries.py`
+
+.. raw:: html
+
+      <div class="sphx-glr-thumbnail-title">Similarity Queries</div>
+    </div>
+
+
+.. raw:: html
+
+    </div>
+
+
+.. toctree::
+   :hidden:
+
+   /auto_examples/core/run_core_concepts
+   /auto_examples/core/run_corpora_and_vector_spaces
+   /auto_examples/core/run_topics_and_transformations
+   /auto_examples/core/run_similarity_queries
+
diff --git a/docs/src/auto_examples/howtos/index.rst b/docs/src/auto_examples/howtos/index.rst
@@ -0,0 +1,97 @@
+
+
+.. _sphx_glr_auto_examples_howtos:
+
+How-to Guides: Solve a Problem
+------------------------------
+
+These **goal-oriented guides** demonstrate how to **solve a specific problem** using gensim.
+
+
+
+.. raw:: html
+
+    <div class="sphx-glr-thumbnails">
+
+
+.. raw:: html
+
+    <div class="sphx-glr-thumbcontainer" tooltip="Demonstrates simple and quick access to common corpora and pretrained models.">
+
+.. only:: html
+
+  .. image:: /auto_examples/howtos/images/thumb/sphx_glr_run_downloader_api_thumb.png
+    :alt: How to download pre-trained models and corpora
+
+  :ref:`sphx_glr_auto_examples_howtos_run_downloader_api.py`
+
+.. raw:: html
+
+      <div class="sphx-glr-thumbnail-title">How to download pre-trained models and corpora</div>
+    </div>
+
+
+.. raw:: html
+
+    <div class="sphx-glr-thumbcontainer" tooltip="How to author documentation for Gensim.">
+
+.. only:: html
+
+  .. image:: /auto_examples/howtos/images/thumb/sphx_glr_run_doc_thumb.png
+    :alt: How to Author Gensim Documentation
+
+  :ref:`sphx_glr_auto_examples_howtos_run_doc.py`
+
+.. raw:: html
+
+      <div class="sphx-glr-thumbnail-title">How to Author Gensim Documentation</div>
+    </div>
+
+
+.. raw:: html
+
+    <div class="sphx-glr-thumbcontainer" tooltip="Shows how to reproduce results of the &quot;Distributed Representation of Sentences and Documents&quot; p...">
+
+.. only:: html
+
+  .. image:: /auto_examples/howtos/images/thumb/sphx_glr_run_doc2vec_imdb_thumb.png
+    :alt: How to reproduce the doc2vec 'Paragraph Vector' paper
+
+  :ref:`sphx_glr_auto_examples_howtos_run_doc2vec_imdb.py`
+
+.. raw:: html
+
+      <div class="sphx-glr-thumbnail-title">How to reproduce the doc2vec 'Paragraph Vector' paper</div>
+    </div>
+
+
+.. raw:: html
+
+    <div class="sphx-glr-thumbcontainer" tooltip="Demonstrates how you can visualize and compare trained topic models.">
+
+.. only:: html
+
+  .. image:: /auto_examples/howtos/images/thumb/sphx_glr_run_compare_lda_thumb.png
+    :alt: How to Compare LDA Models
+
+  :ref:`sphx_glr_auto_examples_howtos_run_compare_lda.py`
+
+.. raw:: html
+
+      <div class="sphx-glr-thumbnail-title">How to Compare LDA Models</div>
+    </div>
+
+
+.. raw:: html
+
+    </div>
+
+
+.. toctree::
+   :hidden:
+
+   /auto_examples/howtos/run_downloader_api
+   /auto_examples/howtos/run_doc
+   /auto_examples/howtos/run_doc2vec_imdb
+   /auto_examples/howtos/run_compare_lda
+
diff --git a/docs/src/auto_examples/index.rst b/docs/src/auto_examples/index.rst
@@ -152,35 +152,35 @@ Learning-oriented lessons that introduce a particular gensim feature, e.g. a mod
 
 .. raw:: html
 
-    <div class="sphx-glr-thumbcontainer" tooltip="Introduces Gensim&#x27;s EnsembleLda model">
+    <div class="sphx-glr-thumbcontainer" tooltip="Introduces Gensim&#x27;s fastText model and demonstrates its use on the Lee Corpus.">
 
 .. only:: html
 
-  .. image:: /auto_examples/tutorials/images/thumb/sphx_glr_run_ensemblelda_thumb.png
-    :alt: Ensemble LDA
+  .. image:: /auto_examples/tutorials/images/thumb/sphx_glr_run_fasttext_thumb.png
+    :alt: FastText Model
 
-  :ref:`sphx_glr_auto_examples_tutorials_run_ensemblelda.py`
+  :ref:`sphx_glr_auto_examples_tutorials_run_fasttext.py`
 
 .. raw:: html
 
-      <div class="sphx-glr-thumbnail-title">Ensemble LDA</div>
+      <div class="sphx-glr-thumbnail-title">FastText Model</div>
     </div>
 
 
 .. raw:: html
 
-    <div class="sphx-glr-thumbcontainer" tooltip="Introduces Gensim&#x27;s fastText model and demonstrates its use on the Lee Corpus.">
+    <div class="sphx-glr-thumbcontainer" tooltip="Introduces Gensim&#x27;s EnsembleLda model">
 
 .. only:: html
 
-  .. image:: /auto_examples/tutorials/images/thumb/sphx_glr_run_fasttext_thumb.png
-    :alt: FastText Model
+  .. image:: /auto_examples/tutorials/images/thumb/sphx_glr_run_ensemblelda_thumb.png
+    :alt: Ensemble LDA
 
-  :ref:`sphx_glr_auto_examples_tutorials_run_fasttext.py`
+  :ref:`sphx_glr_auto_examples_tutorials_run_ensemblelda.py`
 
 .. raw:: html
 
-      <div class="sphx-glr-thumbnail-title">FastText Model</div>
+      <div class="sphx-glr-thumbnail-title">Ensemble LDA</div>
     </div>
 
 
@@ -220,7 +220,7 @@ Learning-oriented lessons that introduce a particular gensim feature, e.g. a mod
 
 .. raw:: html
 
-    <div class="sphx-glr-thumbcontainer" tooltip="Demonstrates using Gensim&#x27;s implemenation of the SCM.">
+    <div class="sphx-glr-thumbcontainer" tooltip="Demonstrates using Gensim&#x27;s implemenation of the WMD.">
 
 .. only:: html
 
@@ -237,7 +237,7 @@ Learning-oriented lessons that introduce a particular gensim feature, e.g. a mod
 
 .. raw:: html
 
-    <div class="sphx-glr-thumbcontainer" tooltip="Demonstrates using Gensim&#x27;s implemenation of the WMD.">
+    <div class="sphx-glr-thumbcontainer" tooltip="Demonstrates using Gensim&#x27;s implemenation of the SCM.">
 
 .. only:: html