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Recent Releases of cebra

cebra - v0.6.0a2

What's Changed

This release adds functionality to run inference on datasets that do not fully fit into memory (batched inference, #168 ) and adds support to train unified encoders across multiple sessions in a dataset (#251 ).

🚧 A preprint is pending "Unified CEBRA Encoders for Integrating Neural Recordings via Behavioral Alignment" by Célia Benquet (@CeliaBenquet ), Hossein Mirzaei (@hsirm) , Steffen Schneider (@stes), Mackenzie W. Mathis (@MMathisLab ).

💻 A DEMO Notebook is available at: https://cebra.ai/docs/demos.html

  • Fix quantizedembeddingnorm undefined when normalize=False by @CeliaBenquet in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/249
  • Batched inference CEBRA & padding at the Solver level by @CeliaBenquet in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/168
  • Add unified CEBRA encoder: pytorch implementation by @CeliaBenquet in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/251
  • Release 0.6.0a2 by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/256

Full Changelog: https://github.com/AdaptiveMotorControlLab/CEBRA/compare/v0.6.0a1...v0.6.0a2

- Python
Published by stes 9 months ago

cebra - v0.6.0a1

What's Changed

  • Add xCEBRA implementation (AISTATS 2025) by @stes @gonlairo et al. & @mmathislab in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/225
  • - this code accompanies https://openreview.net/forum?id=aGrCXoTB4P
  • Upgrade docs build by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/241
  • Allow indexing of the cebra docs by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/242
  • Fix broken docs coverage workflows by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/246
  • Update conf.py by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/237
  • Update docs.yml to build from main by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/248
  • Update installation.rst --> add link to docker hub by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/247

Full Changelog: https://github.com/AdaptiveMotorControlLab/CEBRA/compare/v0.5.0...v0.6.0a1

- Python
Published by MMathisLab 10 months ago

cebra - v0.5.0

What's Changed

  • Fix pandas intersphinx mapping; fix test setup by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/136
  • Implementation for discrete multisession by @introspective-swallow in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/135
  • Update imports in pivae from keras to tensorflow.keras by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/164
  • Upgrade dependencies and fix testsuite by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/172
  • Add device as arg to TensorDataset by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/170
  • Update installation.rst by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/163
  • Add OS indepdent paths for monkey, hippocampus and synthetic data by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/169
  • Change pytorch version in docs to stable by @CeliaBenquet in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/176
  • Fix tests for upgraded dependencies by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/184
  • Add ruff for linting the codebase by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/167
  • Extend type checking to all float datatypes by @CeliaBenquet in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/166
  • Fix linting issues by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/185
  • Set default offset to an Offset object by @icarosadero in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/180
  • Add additional tests for TensorDataset by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/187
  • Fix linting errors in tests by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/188
  • Fix scikit-learn reference in conda environment files by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/195
  • Add support for new sklearn_tags by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/205
  • Update workflows to actions/setup-python@v5, actions/cache@v4 by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/212
  • Fix deprecation warning forceallfinite -> ensureallfinite for sklearn>=1.6 by @icarosadero in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/206
  • Add tests to check legacy model loading by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/214
  • Add improved goodness of fit implementation by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/190
  • Support numpy 2, upgrade tests to support torch 2.6 by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/221
  • Release 0.5.0rc1 by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/189
  • Fix pypi action by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/222
  • Update base.py by @icarosadero in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/224
  • Change max consistency value to 100 instead of 99 by @CeliaBenquet in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/227
  • Update assets.py --> force check for parent dir by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/230
  • User docs minor edit by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/229
  • General Doc refresher by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/232
  • render plotly in our docs, show code/doc version by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/231
  • Update layout.html by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/233
  • Update conf.py by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/234
  • Refactoring setup.cfg by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/228
  • Home page landing update by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/235
  • v0.5.0 by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/238

New Contributors

  • @introspective-swallow made their first contribution in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/135
  • @icarosadero made their first contribution in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/180

Full Changelog: https://github.com/AdaptiveMotorControlLab/CEBRA/compare/v0.4.0...v0.5.0

- Python
Published by stes 10 months ago

cebra - v0.5.0rc1

What's Changed

  • Fix pandas intersphinx mapping; fix test setup by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/136
  • Implementation for discrete multisession by @introspective-swallow in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/135
  • Update imports in pivae from keras to tensorflow.keras by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/164
  • Upgrade dependencies and fix testsuite by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/172
  • Add device as arg to TensorDataset by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/170
  • Update installation.rst by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/163
  • Add OS indepdent paths for monkey, hippocampus and synthetic data by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/169
  • Change pytorch version in docs to stable by @CeliaBenquet in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/176
  • Fix tests for upgraded dependencies by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/184
  • Add ruff for linting the codebase by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/167
  • Extend type checking to all float datatypes by @CeliaBenquet in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/166
  • Fix linting issues by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/185
  • Set default offset to an Offset object by @icarosadero in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/180
  • Add additional tests for TensorDataset by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/187
  • Fix linting errors in tests by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/188
  • Fix scikit-learn reference in conda environment files by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/195
  • Add support for new sklearn_tags by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/205
  • Update workflows to actions/setup-python@v5, actions/cache@v4 by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/212
  • Fix deprecation warning forceallfinite -> ensureallfinite for sklearn>=1.6 by @icarosadero in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/206
  • Add tests to check legacy model loading by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/214
  • Add improved goodness of fit implementation by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/190
  • Support numpy 2, upgrade tests to support torch 2.6 by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/221
  • Release 0.5.0rc1 by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/189

New Contributors

  • @introspective-swallow made their first contribution in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/135
  • @icarosadero made their first contribution in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/180

Full Changelog: https://github.com/AdaptiveMotorControlLab/CEBRA/compare/v0.4.0...v0.5.0rc1

- Python
Published by MMathisLab about 1 year ago

cebra - v0.4.0

What's Changed

Starting with v0.4.0, CEBRA is released under an Apache 2.0 license.

  • Add missing error raising and test for adapt on Multissession by @CeliaBenquet in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/114
  • Change license to Apache 2.0 by @MMathisLab and @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/117
  • Apply updated license headers by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/118
  • Update setup.cfg license classifier by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/119
  • Update README.md by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/120
  • Pass showlegend/template kwargs to plotly by @nastya236 in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/122

Full Changelog: https://github.com/AdaptiveMotorControlLab/CEBRA/compare/v0.3.1...v0.4.0

- Python
Published by stes about 2 years ago

cebra - v0.3.1

What's Changed

  • Auto-import plotly integration by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/96
  • Update usage.rst by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/98
  • Simplify plotly docstring example by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/102
  • Restructure API docs for integrations by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/103
  • Release v0.3.1rc1 by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/104
  • Fix windows tests by @gonlairo in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/90
  • Add torch API usage example by @timonmerk in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/99
  • Update icon link for dandi demo data by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/113
  • Update cebrapaperm1.yml and cebra.yml by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/112
  • Release 0.3.1 by @MMathisLab and @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/110

New Contributors

  • @timonmerk made their first contribution in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/99

Full Changelog: https://github.com/AdaptiveMotorControlLab/CEBRA/compare/v0.3.0...v0.3.1

- Python
Published by stes about 2 years ago

cebra - v0.3.0

What's Changed

  • Update usage.rst docs by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/21
  • Remove subsample default in OrthogonalProcrustesAlignment, improve tests by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/28
  • Remove grid_search_models/ after running tests by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/26
  • Fix action workflow definitions for external contributors by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/31
  • For docs build, limit scikit-learn version by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/37
  • Temporarily disable PR comment to report doc coverage by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/38
  • Update repo link on landing page by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/36
  • Fix typo in pi_vae.py by @eltociear in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/20
  • Automatically download the rat-hippocampus dataset by @gonlairo in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/35
  • Fix dtypes handled in the labels of the decoders by @CeliaBenquet in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/30
  • Temporarily disable test runs on dev repo by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/40
  • Add ... pattern to copybutton config by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/41
  • Expose n_bins argument from align_embeddings by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/25
  • Add pre-commit config to standardize files by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/42
  • Fix Device in Multisession Training by @gonlairo in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/44
  • Support More Data Types in the sklearn Dataset and Decoder by @gonlairo in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/43
  • Improve device support and add support for Apple Silicon chipset (mps) by @gonlairo in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/34
  • Add NLB tools pypi package back as dataset dependency by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/50
  • Add missing mark in test_datasets.py by @gonlairo in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/52
  • Add Matplotlib ImportError when using compare_models() by @gonlairo in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/53
  • Fix test failures due to http rate limit by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/62
  • Autodownload monkey reaching data by @gonlairo in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/59
  • add demo link to homepage by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/64
  • Fix type bug in to() method by @sofiagilardini in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/55
  • Release 0.3.0rc1 by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/66
  • Autodownload synthetic data by @gonlairo in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/68
  • Add thumbnail for openscope notebook by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/71
  • Improve saving and loading of models by @gonlairo in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/69
  • Update installation.rst by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/80
  • Improve documentation for local docs build by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/70
  • Extend Delta distribution to multiple dimensions by @gonlairo in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/76
  • Fix broadcasting in InfoNCE loss by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/86
  • Enhance ModuleNotFoundError messages by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/85
  • Add OS independent paths for Allen dataset by @gonlairo in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/88
  • Fix consistency labels ordering and simplify by @CeliaBenquet in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/87
  • Inspired by @obarnstedt work at Lindoscope workshop we added interactive plots using plotly by @nastya236 in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/82
  • Release v0.3.0rc2 by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/67
  • Pin tables <= 3.8 by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/91
  • Release v0.3.0 by @stes in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/92

Contributors

  • @nastya236 made their first contribution in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/82
  • @eltociear made their first contribution in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/20
  • @gonlairo made their first contribution in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/35
  • @CeliaBenquet made their first contribution in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/30
  • @sofiagilardini made their first contribution in https://github.com/AdaptiveMotorControlLab/CEBRA/pull/55

Full Changelog: https://github.com/AdaptiveMotorControlLab/CEBRA/compare/v0.2.0...v0.3.0

- Python
Published by stes over 2 years ago