scikit-network 0.32.1__cp39-cp39-win_amd64.whl → 0.33.1__cp39-cp39-win_amd64.whl
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- {scikit_network-0.32.1.dist-info → scikit_network-0.33.1.dist-info}/AUTHORS.rst +0 -1
- scikit_network-0.33.1.dist-info/METADATA +120 -0
- {scikit_network-0.32.1.dist-info → scikit_network-0.33.1.dist-info}/RECORD +66 -66
- {scikit_network-0.32.1.dist-info → scikit_network-0.33.1.dist-info}/WHEEL +1 -1
- sknetwork/__init__.py +1 -1
- sknetwork/classification/diffusion.py +4 -3
- sknetwork/classification/knn.py +4 -3
- sknetwork/classification/metrics.py +3 -3
- sknetwork/classification/pagerank.py +1 -1
- sknetwork/classification/propagation.py +7 -6
- sknetwork/classification/vote.cp39-win_amd64.pyd +0 -0
- sknetwork/classification/vote.cpp +684 -677
- sknetwork/clustering/leiden.py +2 -1
- sknetwork/clustering/leiden_core.cp39-win_amd64.pyd +0 -0
- sknetwork/clustering/leiden_core.cpp +713 -702
- sknetwork/clustering/louvain.py +6 -6
- sknetwork/clustering/louvain_core.cp39-win_amd64.pyd +0 -0
- sknetwork/clustering/louvain_core.cpp +713 -702
- sknetwork/clustering/metrics.py +1 -1
- sknetwork/clustering/tests/test_kcenters.py +5 -37
- sknetwork/clustering/tests/test_louvain.py +6 -0
- sknetwork/data/__init__.py +1 -1
- sknetwork/data/base.py +7 -2
- sknetwork/data/load.py +18 -21
- sknetwork/data/models.py +15 -15
- sknetwork/data/parse.py +19 -17
- sknetwork/data/tests/test_API.py +3 -3
- sknetwork/data/tests/test_base.py +2 -2
- sknetwork/data/tests/test_toy_graphs.py +33 -33
- sknetwork/data/toy_graphs.py +35 -43
- sknetwork/embedding/base.py +3 -0
- sknetwork/embedding/louvain_embedding.py +0 -26
- sknetwork/embedding/svd.py +0 -4
- sknetwork/embedding/tests/test_louvain_embedding.py +9 -4
- sknetwork/embedding/tests/test_svd.py +6 -0
- sknetwork/gnn/gnn_classifier.py +1 -1
- sknetwork/hierarchy/louvain_hierarchy.py +10 -6
- sknetwork/hierarchy/metrics.py +3 -3
- sknetwork/hierarchy/paris.cp39-win_amd64.pyd +0 -0
- sknetwork/hierarchy/paris.cpp +2651 -2027
- sknetwork/hierarchy/paris.pyx +4 -3
- sknetwork/hierarchy/tests/test_metrics.py +4 -4
- sknetwork/linalg/diteration.cp39-win_amd64.pyd +0 -0
- sknetwork/linalg/diteration.cpp +684 -677
- sknetwork/linalg/push.cp39-win_amd64.pyd +0 -0
- sknetwork/linalg/push.cpp +1769 -1153
- sknetwork/linalg/sparse_lowrank.py +1 -1
- sknetwork/ranking/betweenness.cp39-win_amd64.pyd +0 -0
- sknetwork/ranking/betweenness.cpp +563 -557
- sknetwork/regression/diffusion.py +6 -4
- sknetwork/topology/cliques.cp39-win_amd64.pyd +0 -0
- sknetwork/topology/cliques.cpp +1729 -1110
- sknetwork/topology/core.cp39-win_amd64.pyd +0 -0
- sknetwork/topology/core.cpp +1755 -1139
- sknetwork/topology/cycles.py +1 -1
- sknetwork/topology/minheap.cp39-win_amd64.pyd +0 -0
- sknetwork/topology/minheap.cpp +687 -677
- sknetwork/topology/triangles.cp39-win_amd64.pyd +0 -0
- sknetwork/topology/triangles.cpp +437 -432
- sknetwork/topology/weisfeiler_lehman_core.cp39-win_amd64.pyd +0 -0
- sknetwork/topology/weisfeiler_lehman_core.cpp +684 -677
- sknetwork/utils/__init__.py +1 -1
- sknetwork/utils/values.py +5 -3
- sknetwork/visualization/graphs.py +1 -1
- scikit_network-0.32.1.dist-info/METADATA +0 -511
- {scikit_network-0.32.1.dist-info → scikit_network-0.33.1.dist-info}/LICENSE +0 -0
- {scikit_network-0.32.1.dist-info → scikit_network-0.33.1.dist-info}/top_level.txt +0 -0
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Metadata-Version: 2.1
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Name: scikit-network
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Version: 0.33.1
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Summary: Graph algorithms
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Author: Scikit-network team
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Maintainer-email: Thomas Bonald <bonald@enst.fr>
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License: BSD License
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Project-URL: Repository, https://github.com/sknetwork-team/scikit-network
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Project-URL: Documentation, https://scikit-network.readthedocs.io/
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Project-URL: Changelog, https://github.com/sknetwork-team/scikit-network/blob/master/HISTORY.rst
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Keywords: sknetwork
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Classifier: Development Status :: 3 - Alpha
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Classifier: Intended Audience :: Developers
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Classifier: Intended Audience :: Information Technology
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Classifier: Intended Audience :: Education
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Classifier: Intended Audience :: Science/Research
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Classifier: License :: OSI Approved :: BSD License
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Classifier: Natural Language :: English
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Classifier: Programming Language :: Cython
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Classifier: Programming Language :: Python :: 3.9
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Classifier: Programming Language :: Python :: 3.10
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Classifier: Programming Language :: Python :: 3.11
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Classifier: Programming Language :: Python :: 3.12
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Requires-Python: >=3.9
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Description-Content-Type: text/x-rst
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License-File: LICENSE
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License-File: AUTHORS.rst
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Requires-Dist: numpy >=1.22.4
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Requires-Dist: scipy >=1.7.3
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Provides-Extra: test
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Requires-Dist: pytest ; extra == 'test'
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Requires-Dist: pluggy >=0.7.1 ; extra == 'test'
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.. image:: https://perso.telecom-paristech.fr/bonald/logo_sknetwork.png
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:align: right
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:width: 150px
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:alt: logo sknetwork
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.. image:: https://img.shields.io/pypi/v/scikit-network.svg
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:target: https://pypi.python.org/pypi/scikit-network
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.. image:: https://github.com/sknetwork-team/scikit-network/actions/workflows/ci_checks.yml/badge.svg
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:target: https://github.com/sknetwork-team/scikit-network/actions/workflows/ci_checks.yml
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.. image:: https://readthedocs.org/projects/scikit-network/badge/?version=latest
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:target: https://scikit-network.readthedocs.io/en/latest/?badge=latest
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:alt: Documentation Status
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.. image:: https://codecov.io/gh/sknetwork-team/scikit-network/branch/master/graph/badge.svg
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:target: https://codecov.io/gh/sknetwork-team/scikit-network
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.. image:: https://img.shields.io/pypi/pyversions/scikit-network.svg
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:target: https://pypi.python.org/pypi/scikit-network
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Free software library in Python for machine learning on graphs:
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* Memory-efficient representation of graphs as sparse matrices in scipy_ format
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* Fast algorithms
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* Simple API inspired by scikit-learn_
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.. _scipy: https://www.scipy.org
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.. _scikit-learn: https://scikit-learn.org/
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Resources
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---------
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* Free software: BSD license
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* GitHub: https://github.com/sknetwork-team/scikit-network
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* Documentation: https://scikit-network.readthedocs.io
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Quick start
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-----------
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Install scikit-network:
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.. code-block:: console
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$ pip install scikit-network
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Import scikit-network::
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import sknetwork
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Overview
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--------
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An overview of the package is presented in this `notebook <https://scikit-network.readthedocs.io/en/latest/tutorials/overview/index.html>`_.
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Documentation
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-------------
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The documentation is structured as follows:
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* `Getting started <https://scikit-network.readthedocs.io/en/latest/first_steps.html>`_: First steps to install, import and use scikit-network.
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* `User manual <https://scikit-network.readthedocs.io/en/latest/reference/data.html>`_: Description of each function and object of scikit-network.
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* `Tutorials <https://scikit-network.readthedocs.io/en/latest/tutorials/data/index.html>`_: Application of the main tools to toy examples.
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* `Examples <https://scikit-network.readthedocs.io/en/latest/use_cases/text.html>`_: Examples combining several tools on specific use cases.
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* `About <https://scikit-network.readthedocs.io/en/latest/authors.html>`_: Authors, history of the library, how to contribute, index of functions and objects.
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Citing
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------
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If you want to cite scikit-network, please refer to the publication in
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the `Journal of Machine Learning Research <https://jmlr.org>`_:
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@article{JMLR:v21:20-412,
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author = {Thomas Bonald and Nathan de Lara and Quentin Lutz and Bertrand Charpentier},
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title = {Scikit-network: Graph Analysis in Python},
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journal = {Journal of Machine Learning Research},
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year = {2020},
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volume = {21},
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number = {185},
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pages = {1-6},
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url = {http://jmlr.org/papers/v21/20-412.html}
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}
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sknetwork/topology/triangles.cpp,sha256=KAyCp274y03wMzVxjwHsq15u0VlQ4cOI85QYN1ujmio,352670
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sknetwork/topology/weisfeiler_lehman_core.cpp,sha256=1oc1YPT0n6bdMpGhGn9_02irQ4QRN2zKxhYLP9ZVGYw,1024487
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sknetwork/topology/weisfeiler_lehman_core.pyx,sha256=lpUV1BpxtedsGBfOl19b8OFXCIbyaAA4ZYlW6BzSxbw,3148
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sknetwork/topology/tests/__init__.py,sha256=84T-xv8JCFeA9D7Rxw9gy3_dNAoE8CY1k1pYcuG8K3s,26
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sknetwork/topology/tests/test_cliques.py,sha256=vdRMDmF8AKkIWE-LnU2yGzk1wzwzq9PdggpeS-8wfRw,866
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sknetwork/topology/tests/test_structure.py,sha256=BIJuO39ROQRA-xipUfk8PajHQ0Uk9EY6C-c3JYkmBSg,4033
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sknetwork/topology/tests/test_triangles.py,sha256=5AYxNQ8DkKTvpShWEWV-v1r7WZx1DuylChcEmVF0yTk,1313
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sknetwork/topology/tests/test_wl.py,sha256=vesYcnlJHPphk2RJLzKJH9N6aYpPeKLFJko1E8kBdtc,2290
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sknetwork/utils/__init__.py,sha256=
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sknetwork/utils/__init__.py,sha256=ZF_Xx7FhOeHOsqmiBpwO1_bmGj2uoE6knq47oMpMN70,332
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sknetwork/utils/check.py,sha256=LWUkHwDzr9Z9IyT7AIsrQyDrRAMjO2bzWyFsv_P9Ask,13295
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sknetwork/utils/format.py,sha256=g_cfUlETJp7AppCiVKG2VZPexH-H9rVNGF4hXh2rshM,8987
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sknetwork/utils/membership.py,sha256=kan9WuytJCyBAZi0CfM0SJEf527XB4WAYMkIctD5D9w,2244
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sknetwork/utils/neighbors.py,sha256=-EwBXigM3mn2qvVTi_aPmG0XifDMojZgsMQ9_A8cLkk,3466
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sknetwork/utils/tfidf.py,sha256=vvISEaZJa7RZrNNgQEAHgMH2rJToARuNWcVjnA8u7po,993
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sknetwork/utils/values.py,sha256=
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sknetwork/utils/values.py,sha256=fqD2iGRwzPG44Vy6c1Us8koggqkWkRGSENZfJonJ2Uw,2671
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sknetwork/utils/tests/__init__.py,sha256=JQuARG8Ycb5apL6PUy_wuEHsLjmEZFOPQUKWRgTMdCY,23
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sknetwork/utils/tests/test_check.py,sha256=LxYAubg6YZ0RHYFz_R3byNtw3EQ6hsHxPPI3QgP1DLg,6954
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sknetwork/utils/tests/test_format.py,sha256=NJrRBI-kFF8dYFmTwuFF7VUnHS6Mz75DG-RB-iGk8ag,2308
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sknetwork/visualization/__init__.py,sha256=Ww8O1hby1xf_mtRgFftc9srMzvbFgWOzj_khKkqq9Mg,220
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sknetwork/visualization/colors.py,sha256=NhyMQeetfH16khnJD2gD_uZJkBD3JQDV0K3Jzacamqw,2543
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sknetwork/visualization/dendrograms.py,sha256=HtubynuGsJ5b7bD5I8dIKL5UqhqynmqOhw_wJt6VGUA,10178
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sknetwork/visualization/graphs.py,sha256=
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sknetwork/visualization/graphs.py,sha256=vLsuL2AUyrc8B5nxM2K713QPRjf7i1PRaoRXYbY44L4,42215
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sknetwork/visualization/tests/__init__.py,sha256=hrso2pNVzMWn4D2pRyWA_xAMib-xacKjm-rf91MyGGk,31
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sknetwork/visualization/tests/test_dendrograms.py,sha256=e0u3qL9SlWlrQiVAeCVXxq7P6-mU0GaCz3FBu6cm_HA,2519
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sknetwork/visualization/tests/test_graphs.py,sha256=FPZcgGj9asTjOvtkXpENYjeE8xtwh1ES4XYWcYe56Jo,9597
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scikit_network-0.33.1.dist-info/LICENSE,sha256=BJ1Hth1QjBmjIfHcp1sVxlkEqHYM58Vn5bcpYcggMZE,1656
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scikit_network-0.33.1.dist-info/METADATA,sha256=dvTU-9SmoSsqZhmqCCwHwbQgB08J4wdyQWJKQ-rYhYs,4524
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scikit_network-0.33.1.dist-info/WHEEL,sha256=vq7bX_I37ZJK2gZz_HGA8eCPjBDKQSfb_9FNjesTNkk,99
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scikit_network-0.33.1.dist-info/top_level.txt,sha256=fkwspWQ9B3csqb5ENEOoVciRY6XftnMuz4MvTDQeSsg,10
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scikit_network-0.33.1.dist-info/RECORD,,
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sknetwork/__init__.py
CHANGED
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@@ -55,7 +55,7 @@ class DiffusionClassifier(BaseClassifier):
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55
55
|
>>> labels_true = graph.labels
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56
56
|
>>> labels = {0: labels_true[0], 33: labels_true[33]}
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57
57
|
>>> labels_pred = diffusion.fit_predict(adjacency, labels)
|
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58
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-
>>>
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58
|
+
>>> float(round(np.mean(labels_pred == labels_true), 2))
|
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59
59
|
0.97
|
|
60
60
|
|
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61
61
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References
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|
@@ -74,8 +74,9 @@ class DiffusionClassifier(BaseClassifier):
|
|
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74
74
|
self.scale = scale
|
|
75
75
|
|
|
76
76
|
def fit(self, input_matrix: Union[sparse.csr_matrix, np.ndarray],
|
|
77
|
-
labels: Optional[Union[dict,
|
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78
|
-
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77
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+
labels: Optional[Union[dict, list, np.ndarray]] = None,
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78
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+
labels_row: Optional[Union[dict, list, np.ndarray]] = None,
|
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79
|
+
labels_col: Optional[Union[dict, list, np.ndarray]] = None, force_bipartite: bool = False) \
|
|
79
80
|
-> 'DiffusionClassifier':
|
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80
81
|
"""Compute the solution to the Dirichlet problem (temperatures at equilibrium).
|
|
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82
|
|
sknetwork/classification/knn.py
CHANGED
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@@ -55,7 +55,7 @@ class NNClassifier(BaseClassifier):
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55
55
|
>>> labels_true = graph.labels
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56
56
|
>>> labels = {0: labels_true[0], 33: labels_true[33]}
|
|
57
57
|
>>> labels_pred = classifier.fit_predict(adjacency, labels)
|
|
58
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-
>>>
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58
|
+
>>> float(round(np.mean(labels_pred == labels_true), 2))
|
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59
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0.82
|
|
60
60
|
"""
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61
61
|
def __init__(self, n_neighbors: int = 3, embedding_method: Optional[BaseEmbedding] = None, normalize: bool = True):
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@@ -97,8 +97,9 @@ class NNClassifier(BaseClassifier):
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97
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return probs, labels
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def fit(self, input_matrix: Union[sparse.csr_matrix, np.ndarray], labels: Union[np.ndarray, dict] = None,
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101
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-
labels_row: Union[np.ndarray,
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100
|
+
def fit(self, input_matrix: Union[sparse.csr_matrix, np.ndarray], labels: Union[np.ndarray, list, dict] = None,
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101
|
+
labels_row: Union[np.ndarray, list, dict] = None,
|
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102
|
+
labels_col: Union[np.ndarray, list, dict] = None) -> 'NNClassifier':
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|
102
103
|
"""Node classification by k-nearest neighbors in the embedding space.
|
|
103
104
|
|
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104
105
|
Parameters
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|
@@ -34,7 +34,7 @@ def get_accuracy_score(labels_true: np.ndarray, labels_pred: np.ndarray) -> floa
|
|
|
34
34
|
>>> import numpy as np
|
|
35
35
|
>>> labels_true = np.array([0, 0, 1, 1])
|
|
36
36
|
>>> labels_pred = np.array([0, 0, 0, 1])
|
|
37
|
-
>>> get_accuracy_score(labels_true, labels_pred)
|
|
37
|
+
>>> float(round(get_accuracy_score(labels_true, labels_pred), 2))
|
|
38
38
|
0.75
|
|
39
39
|
"""
|
|
40
40
|
check_vector_format(labels_true, labels_pred)
|
|
@@ -105,7 +105,7 @@ def get_f1_score(labels_true: np.ndarray, labels_pred: np.ndarray, return_precis
|
|
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105
105
|
>>> import numpy as np
|
|
106
106
|
>>> labels_true = np.array([0, 0, 1, 1])
|
|
107
107
|
>>> labels_pred = np.array([0, 0, 0, 1])
|
|
108
|
-
>>>
|
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108
|
+
>>> float(round(get_f1_score(labels_true, labels_pred), 2))
|
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109
109
|
0.67
|
|
110
110
|
"""
|
|
111
111
|
values = set(labels_true[labels_true >= 0]) | set(labels_pred[labels_pred >= 0])
|
|
@@ -188,7 +188,7 @@ def get_average_f1_score(labels_true: np.ndarray, labels_pred: np.ndarray, avera
|
|
|
188
188
|
>>> import numpy as np
|
|
189
189
|
>>> labels_true = np.array([0, 0, 1, 1])
|
|
190
190
|
>>> labels_pred = np.array([0, 0, 0, 1])
|
|
191
|
-
>>>
|
|
191
|
+
>>> float(round(get_average_f1_score(labels_true, labels_pred), 2))
|
|
192
192
|
0.73
|
|
193
193
|
"""
|
|
194
194
|
if average == 'micro':
|
|
@@ -51,7 +51,7 @@ class PageRankClassifier(RankClassifier):
|
|
|
51
51
|
>>> labels_true = graph.labels
|
|
52
52
|
>>> labels = {0: labels_true[0], 33: labels_true[33]}
|
|
53
53
|
>>> labels_pred = pagerank.fit_predict(adjacency, labels)
|
|
54
|
-
>>> np.round(np.mean(labels_pred == labels_true), 2)
|
|
54
|
+
>>> float(np.round(np.mean(labels_pred == labels_true), 2))
|
|
55
55
|
0.97
|
|
56
56
|
|
|
57
57
|
References
|
|
@@ -58,7 +58,7 @@ class Propagation(BaseClassifier):
|
|
|
58
58
|
>>> labels_true = graph.labels
|
|
59
59
|
>>> labels = {0: labels_true[0], 33: labels_true[33]}
|
|
60
60
|
>>> labels_pred = propagation.fit_predict(adjacency, labels)
|
|
61
|
-
>>> np.round(np.mean(labels_pred == labels_true), 2)
|
|
61
|
+
>>> float(np.round(np.mean(labels_pred == labels_true), 2))
|
|
62
62
|
0.94
|
|
63
63
|
|
|
64
64
|
References
|
|
@@ -91,19 +91,20 @@ class Propagation(BaseClassifier):
|
|
|
91
91
|
labels = labels[index_seed]
|
|
92
92
|
return index_seed.astype(np.int32), index_remain.astype(np.int32), labels.astype(np.int32)
|
|
93
93
|
|
|
94
|
-
def fit(self, input_matrix: Union[sparse.csr_matrix, np.ndarray], labels: Union[np.ndarray, dict] = None,
|
|
95
|
-
labels_row: Union[np.ndarray,
|
|
94
|
+
def fit(self, input_matrix: Union[sparse.csr_matrix, np.ndarray], labels: Union[np.ndarray, list, dict] = None,
|
|
95
|
+
labels_row: Union[np.ndarray, list, dict] = None,
|
|
96
|
+
labels_col: Union[np.ndarray, list, dict] = None) -> 'Propagation':
|
|
96
97
|
"""Node classification by label propagation.
|
|
97
98
|
|
|
98
99
|
Parameters
|
|
99
100
|
----------
|
|
100
101
|
input_matrix : sparse.csr_matrix, np.ndarray
|
|
101
102
|
Adjacency matrix or biadjacency matrix of the graph.
|
|
102
|
-
labels :
|
|
103
|
+
labels : array, list or dict
|
|
103
104
|
Known labels. Negative values ignored.
|
|
104
|
-
labels_row :
|
|
105
|
+
labels_row : array, list or dict
|
|
105
106
|
Known labels of rows, for bipartite graphs.
|
|
106
|
-
labels_col :
|
|
107
|
+
labels_col : array, list or dict
|
|
107
108
|
Known labels of columns, for bipartite graphs.
|
|
108
109
|
|
|
109
110
|
Returns
|
|
Binary file
|