The coresets from zalanborsos

Coresets

This library contains the implementation coreset generation for k-Means and (Bayesian) Gaussian mixture models. It also offers the extended versions of the corresponding algorithms that support weighted data sets.

To get started, take a look at:

examples/intro.ipynb

Setup

pip install -r requirements.txt
python setup.py build_ext --inplace

Running tests

In project root run:

python -m pytest tests/

References

The implementation of the library is based on the following works:

Bachem, O., Lucic, M., & Krause, A. (2017). Practical coreset constructions for machine learning. arXiv preprint arXiv:1703.06476.

Bachem, O., Lucic, M., & Krause, A. (2017). Scalable and distributed clustering via lightweight coresets. arXiv preprint arXiv:1702.08248.

Lucic, M., Faulkner, M., Krause, A., & Feldman, D. (2018). Training Gaussian Mixture Models at Scale via Coresets. Journal of Machine Learning Research, 18, Art-No.

Borsos, Z., Bachem, O., & Krause, A. Variational Inference for DPGMM with Coresets. (2017). Advances in Approximate Bayesian Inference

k_means import from scikit-learn not found in test

I have scikit_learn installed, but the tests fail:

Traceback:
../../importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_mixtures.py:6: in <module>
    from algorithms import WeightedGaussianMixture, WeightedBayesianGaussianMixture
algorithms/__init__.py:3: in <module>
    from algorithms.weighted_kmeans import WeightedKMeans
algorithms/weighted_kmeans.py:2: in <module>
    from sklearn.cluster.k_means_ import _init_centroids
E   ModuleNotFoundError: No module named 'sklearn.cluster.k_means_'
__________________________________________ ERROR collecting tests/test_sensitivity.py __________________________________________
ImportError while importing test module '/home/icb/karin.hrovatin/miniconda3/envs/subsampling/lib/python3.8/site-packages/coresets/tests/test_sensitivity.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../../importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_sensitivity.py:7: in <module>
    from coresets import *
coresets/__init__.py:4: in <module>
    from coresets.k_means_coreset import KMeansLightweightCoreset, KMeansCoreset, KMeansUniformCoreset
coresets/k_means_coreset.py:1: in <module>
    from sklearn.cluster.k_means_ import _init_centroids
E   ModuleNotFoundError: No module named 'sklearn.cluster.k_means_'
________________________________________ ERROR collecting tests/test_weighted_kmeans.py ________________________________________
ImportError while importing test module '/home/icb/karin.hrovatin/miniconda3/envs/subsampling/lib/python3.8/site-packages/coresets/tests/test_weighted_kmeans.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../../importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_weighted_kmeans.py:5: in <module>
    from algorithms import weighted_kmeans
algorithms/__init__.py:3: in <module>
    from algorithms.weighted_kmeans import WeightedKMeans
algorithms/weighted_kmeans.py:2: in <module>
    from sklearn.cluster.k_means_ import _init_centroids
E   ModuleNotFoundError: No module named 'sklearn.cluster.k_means_'
=================================================== short test summary info ====================================================
ERROR tests/test_k_means_coresets.py
ERROR tests/test_mixtures.py
ERROR tests/test_sensitivity.py
ERROR tests/test_weighted_kmeans.py
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 4 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
====================================================== 4 errors in 1.35s =======================================================
(subsampling) [karin.hrovatin@icb-lisa coresets]$ pip freeze|grep scikit-learn
scikit-learn==0.24.1

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