umap

What's Changed

• Setting random state could still lead to stochastic results by @dannywhuang in https://github.com/lmcinnes/umap/pull/1081
• Change release tag structure and switch to real PyPI by @gclendenning in https://github.com/lmcinnes/umap/pull/1085
• Add Keras 3 support to ParametricUMAP by @fchollet in https://github.com/lmcinnes/umap/pull/1101
• Finish refactoring ParametricUMAP by @fchollet in https://github.com/lmcinnes/umap/pull/1105
• Add torch support to ParametricUMAP by @fchollet in https://github.com/lmcinnes/umap/pull/1104
• Bit hamming by @lmcinnes in https://github.com/lmcinnes/umap/pull/1107

New Contributors

• @dannywhuang made their first contribution in https://github.com/lmcinnes/umap/pull/1081
• @fchollet made their first contribution in https://github.com/lmcinnes/umap/pull/1101

Full Changelog: https://github.com/lmcinnes/umap/compare/release-0.5.5...release-0.5.6

What's Changed

• fix interactive plot if hover_data but no tools is provided by @timoleistner in https://github.com/lmcinnes/umap/pull/1058
• Fixed bug causing digits data bokeh plot in tutorial to break by @Liqs-v2 in https://github.com/lmcinnes/umap/pull/1067
• Make tbb requirement optional by @mithaler in https://github.com/lmcinnes/umap/pull/1066
• Fix pkg_resources deprecation warning by @laclouis5 in https://github.com/lmcinnes/umap/pull/1072

New Contributors

• @timoleistner made their first contribution in https://github.com/lmcinnes/umap/pull/1058
• @Liqs-v2 made their first contribution in https://github.com/lmcinnes/umap/pull/1067
• @mithaler made their first contribution in https://github.com/lmcinnes/umap/pull/1066
• @laclouis5 made their first contribution in https://github.com/lmcinnes/umap/pull/1072

Full Changelog: https://github.com/lmcinnes/umap/compare/0.5.4...release-0.5.5

What's Changed

• Add numerically stable cross entropy loss by @jgraving in https://github.com/lmcinnes/umap/pull/856
• Fix AlignedUMAP.update by @hndgzkn in https://github.com/lmcinnes/umap/pull/861
• Fixed numerical issue in make_epochs_per_sample by @GregDemand in https://github.com/lmcinnes/umap/pull/875
• Fix in1d() return type issue by @GregDemand in https://github.com/lmcinnes/umap/pull/877
• Fix use of relation_dicts in expand_relations by @GregDemand in https://github.com/lmcinnes/umap/pull/880
• Fix indexing issue with relations array by @GregDemand in https://github.com/lmcinnes/umap/pull/882
• Added uniqueness flag to intersect1d by @SkBlaz in https://github.com/lmcinnes/umap/pull/896
• Fix typos in docstrings by @sky-2002 in https://github.com/lmcinnes/umap/pull/903
• consistency between install_requires and requirements.txt by @jlmelville in https://github.com/lmcinnes/umap/pull/908
• Search index is optional for precomputed_knn by @jlmelville in https://github.com/lmcinnes/umap/pull/909
• Fix doc build (a bit) by @jlmelville in https://github.com/lmcinnes/umap/pull/910
• Fix the doc build by @jlmelville in https://github.com/lmcinnes/umap/pull/913
• PCA initialization option by @jlmelville in https://github.com/lmcinnes/umap/pull/911
• Allow points to be passed to umap.plot.points by @dribnet in https://github.com/lmcinnes/umap/pull/912
• feature: add ability to specify tools to interactive charts so richer exploration with images and other content is possible by @suneeta-mall in https://github.com/lmcinnes/umap/pull/858
• tighten test_umap_trustworthiness_random_init bound by @austereantelope in https://github.com/lmcinnes/umap/pull/850
• tighten test_umap_sparse_trustworthiness bound by @austereantelope in https://github.com/lmcinnes/umap/pull/851
• Get intermediate results at different epochs by @matthieuheitz in https://github.com/lmcinnes/umap/pull/696
• Update penguins doc by @jlmelville in https://github.com/lmcinnes/umap/pull/914
• ignore force approximation with precomputed knn by @jlmelville in https://github.com/lmcinnes/umap/pull/927
• Update deprecated matplotlib colormap registry by @yannikschaelte in https://github.com/lmcinnes/umap/pull/929
• Esm metagenomic atlas to Interactive Visualizations by @BioGeek in https://github.com/lmcinnes/umap/pull/936
• get_feature_names_out for UMAP + tests by @CarloLepelaars in https://github.com/lmcinnes/umap/pull/939
• Updated densMAP citation in README by @hhcho in https://github.com/lmcinnes/umap/pull/945
• sklearn parwise distances doesn't support np.matrix anymore by @lmcinnes in https://github.com/lmcinnes/umap/pull/946
• Minor performance improvements by @rohan-shah-nearmap in https://github.com/lmcinnes/umap/pull/948
• Anticipate stricter asarray handling in numpy by @lmcinnes in https://github.com/lmcinnes/umap/pull/952
• Aligned umap issues by @GregDemand in https://github.com/lmcinnes/umap/pull/958
• Update densmap_demo.rst by @aizardar in https://github.com/lmcinnes/umap/pull/973
• Allow UMAP to accept data with nan or inf values by @SamKlier in https://github.com/lmcinnes/umap/pull/977
• new spectral initialization option: a truncated SVD-warmed lobpcg by @jlmelville in https://github.com/lmcinnes/umap/pull/924
• fix: fix numpy.int and numpy.float deprecation to be compatible with numpy >= 1.20.0 by @TTTPOB in https://github.com/lmcinnes/umap/pull/1010
• Docs | Add missing space in precomputed_k-nn.rst by @Odessit007 in https://github.com/lmcinnes/umap/pull/1014
• Docs | Fix typo in supervised.rst by @Odessit007 in https://github.com/lmcinnes/umap/pull/1013
• Update README.rst by @dsblank in https://github.com/lmcinnes/umap/pull/1016
• Fix docstring formatting of init parameter of UMAP class by @felixdivo in https://github.com/lmcinnes/umap/pull/1019
• Plotting Fix: fixing capitalization for Bokeh plotting for version 3.1.1 compatibility by @msakarvadia in https://github.com/lmcinnes/umap/pull/1023
• Issue warning if setting n_jobs and random_state by @crypdick in https://github.com/lmcinnes/umap/pull/1002
• docs : Fix formatting in UMAP class documentation by @Hamza-nabil in https://github.com/lmcinnes/umap/pull/992
• docs: minor typos fix by @0xTiger in https://github.com/lmcinnes/umap/pull/983
• [TYPO] Update precomputed_k-nn.rst by @cakiki in https://github.com/lmcinnes/umap/pull/922
• Bug fix round pre0.5.4 by @lmcinnes in https://github.com/lmcinnes/umap/pull/1038
• Fix unit tests by @hamelin in https://github.com/lmcinnes/umap/pull/1031
• fix relations_dictionary problems which prevents from correctly updating aligned_umap by @hndgzkn in https://github.com/lmcinnes/umap/pull/863
• Drop requirements.txt, embrace setup.py for deps by @hamelin in https://github.com/lmcinnes/umap/pull/1044
• Fix unit tests involving spectral initialization by @hamelin in https://github.com/lmcinnes/umap/pull/1043
• Drop dependency on TBB on non-Intel deployments by @hamelin in https://github.com/lmcinnes/umap/pull/1045
• Add azure devops pipeline to push to PyPI by @gclendenning in https://github.com/lmcinnes/umap/pull/1053

New Contributors

• @jgraving made their first contribution in https://github.com/lmcinnes/umap/pull/856
• @hndgzkn made their first contribution in https://github.com/lmcinnes/umap/pull/861
• @GregDemand made their first contribution in https://github.com/lmcinnes/umap/pull/875
• @SkBlaz made their first contribution in https://github.com/lmcinnes/umap/pull/896
• @sky-2002 made their first contribution in https://github.com/lmcinnes/umap/pull/903
• @dribnet made their first contribution in https://github.com/lmcinnes/umap/pull/912
• @suneeta-mall made their first contribution in https://github.com/lmcinnes/umap/pull/858
• @matthieuheitz made their first contribution in https://github.com/lmcinnes/umap/pull/696
• @yannikschaelte made their first contribution in https://github.com/lmcinnes/umap/pull/929
• @BioGeek made their first contribution in https://github.com/lmcinnes/umap/pull/936
• @CarloLepelaars made their first contribution in https://github.com/lmcinnes/umap/pull/939
• @rohan-shah-nearmap made their first contribution in https://github.com/lmcinnes/umap/pull/948
• @aizardar made their first contribution in https://github.com/lmcinnes/umap/pull/973
• @SamKlier made their first contribution in https://github.com/lmcinnes/umap/pull/977
• @TTTPOB made their first contribution in https://github.com/lmcinnes/umap/pull/1010
• @Odessit007 made their first contribution in https://github.com/lmcinnes/umap/pull/1014
• @dsblank made their first contribution in https://github.com/lmcinnes/umap/pull/1016
• @msakarvadia made their first contribution in https://github.com/lmcinnes/umap/pull/1023
• @crypdick made their first contribution in https://github.com/lmcinnes/umap/pull/1002
• @Hamza-nabil made their first contribution in https://github.com/lmcinnes/umap/pull/992
• @0xTiger made their first contribution in https://github.com/lmcinnes/umap/pull/983
• @cakiki made their first contribution in https://github.com/lmcinnes/umap/pull/922
• @hamelin made their first contribution in https://github.com/lmcinnes/umap/pull/1031
• @gclendenning made their first contribution in https://github.com/lmcinnes/umap/pull/1053

Full Changelog: https://github.com/lmcinnes/umap/compare/0.5.3...0.5.4

What's Changed

• Use labels in AlignedUMAP if provided by @gclen in https://github.com/lmcinnes/umap/pull/802
• Properly escape invalid escape sequences. by @brilee in https://github.com/lmcinnes/umap/pull/807
• Update parametric_umap.rst by @timsainb in https://github.com/lmcinnes/umap/pull/811
• homtopically -> homotopically by @faisito in https://github.com/lmcinnes/umap/pull/820
• covert -> convert by @faisito in https://github.com/lmcinnes/umap/pull/819
• super minor grammar by @faisito in https://github.com/lmcinnes/umap/pull/818
• Add Mutual-NN Description by @adalmia96 in https://github.com/lmcinnes/umap/pull/822
• Loss needs to be handled independently now as well by @lmcinnes in https://github.com/lmcinnes/umap/pull/808
• Fix header for Mutual NN Doc by @adalmia96 in https://github.com/lmcinnes/umap/pull/823
• Add missing links for graph layout methods by @jlmelville in https://github.com/lmcinnes/umap/pull/829
• tighten test_umap_trustworthiness_fast_approx bound by @austereantelope in https://github.com/lmcinnes/umap/pull/832

New Contributors

• @brilee made their first contribution in https://github.com/lmcinnes/umap/pull/807
• @faisito made their first contribution in https://github.com/lmcinnes/umap/pull/820
• @adalmia96 made their first contribution in https://github.com/lmcinnes/umap/pull/822
• @austereantelope made their first contribution in https://github.com/lmcinnes/umap/pull/832

Full Changelog: https://github.com/lmcinnes/umap/compare/0.5.2...0.5.3

Various bug fixes for transform, update, etc.
Support for passing pre-defined knn-graphs as input.

A few minor fixes, including a bug fix against the upcoming numba 0.53

Adds support for ParametricUMAP, DensMAP, AlignedUMAP and more.

Fix some issues with the latest scipy sparse lil_matrix handling.

The is a release candidate for the new 0.4 version of UMAP which introduces a number of new features and various improvements and bug fixes.

Remove object mode jit decorators that now cause warnings in numba.

There was a bug in the layout algorithm for small data sets. That has now been resolved. Pushing a patch release to keep everyone up to date with working code.