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Recent Releases of nemos

nemos - NeMoS 0.2.3

Release Highlights

  • New Bernoulli observation model: Added support for modeling binary outcomes in GLMs using a Bernoulli distribution.
  • Enhanced pynapple integration: When using pynapple, the GLM's predict method now returns firing rates with the same metadata as the input spike counts, enabling seamless filtering and downstream processing.
  • New CustomBasis class: Allows users to define a fully functional NeMoS basis from a list of custom functions, for greater flexibility in model design.

What's Changed

  • Updates current injection tutorial by @billbrod in https://github.com/flatironinstitute/nemos/pull/324
  • String obs model by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/335
  • Pre commit by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/340
  • Add Bernoulli observation model and refactor GLM tests by @sjvenditto in https://github.com/flatironinstitute/nemos/pull/329
  • Attach Metadata on predict by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/339
  • Add string initialization for Bernoulli by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/341
  • Drop NaNs in GLM.initialize_state by @bagibence in https://github.com/flatironinstitute/nemos/pull/342
  • Custom Basis Class by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/328
  • Plot dirctive docstring by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/343
  • Development by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/344

Full Changelog: https://github.com/flatironinstitute/nemos/compare/0.2.2...0.2.3

- Python
Published by BalzaniEdoardo 10 months ago

nemos - 0.2.2

Simplified Composite Basis Handling

  • Simplified handling of composite basis with basis labels.
  • Simplified model simplified selection using basis labels.

See this documentation page to learn more!

What's Changed

  • updated checkout version by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/299
  • Negative axis by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/301
  • Update README.md by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/303
  • Update CONTRIBUTING.md by @arnabiswas in https://github.com/flatironinstitute/nemos/pull/304
  • set version dynamically by @billbrod in https://github.com/flatironinstitute/nemos/pull/297
  • Dynamic version fix by @billbrod in https://github.com/flatironinstitute/nemos/pull/308
  • Fix contributing install instruction by @sjvenditto in https://github.com/flatironinstitute/nemos/pull/309
  • add nih support by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/312
  • Update raised cosine width docs and error message by @billbrod in https://github.com/flatironinstitute/nemos/pull/310
  • Label get param by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/306
  • Speed up recursions by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/307
  • Simplify API basis by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/318
  • Cleanup unused funcs by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/332
  • Development by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/331

New Contributors 🚀

  • @arnabiswas made their first contribution in https://github.com/flatironinstitute/nemos/pull/304
  • @sjvenditto made their first contribution in https://github.com/flatironinstitute/nemos/pull/309

Full Changelog: https://github.com/flatironinstitute/nemos/compare/0.2.1...0.2.210e2d8a70b30b97bdba486254f98517ceabf01e1f9

- Python
Published by BalzaniEdoardo 11 months ago

nemos - 0.2.1

Bugfix on the repr utility function.

What's Changed

  • Hotfix repr by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/296

Full Changelog: https://github.com/flatironinstitute/nemos/compare/0.2.0...0.2.1

- Python
Published by BalzaniEdoardo about 1 year ago

nemos - 0.2.0

Overview

  • New basis API. Distinct basis objects for "Conv" and "Eval" mode of operation.
  • Basis compute_features accepts multi-dimensional inputs for both "Conv" and "Eval" bases.
  • Added IdentityEval bases for including custom inputs in composite bases.
  • Added HistoryConv bases to include the raw history of an input as a predictor.
  • New module for applying identifiability constraints to a model matrix.
  • New SVRG solver with optimized parameters.
  • New documentation website based on sphinx PyData theme.
  • Improved basis documentation: new how-to guides and summary of the available bases.
  • Added examples in docstrings of user-facing methods and functions.
  • Coefficient splitting method of basis.

What's Changed

  • Update python versions by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/211
  • Add (Prox-)SVRG as a solver for GLMs by @bagibence in https://github.com/flatironinstitute/nemos/pull/184
  • fix ident constraint by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/214
  • Swap parameter order to match sklearn scorer by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/215
  • Use pooch by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/216
  • add try/except for seaborn and ipython by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/218
  • improved code refs by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/219
  • Change names and simplify landing page by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/223
  • set up javascript animation by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/230
  • renaming files in dev notes by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/231
  • Development by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/233
  • Add support section by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/234
  • Doctest by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/232
  • reordered cards by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/237
  • Move overview by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/227
  • prevent absolute links to docs (except badge) by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/238
  • Fix sklearn test by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/240
  • Bugfix basis properties by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/241
  • Revert "Bugfix basis properties" by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/244
  • Bugfix basis properties by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/245
  • fixed warns in test_convergence.py by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/242
  • Fix warns test convolution by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/246
  • Development by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/239
  • Splits tox into multiple jobs by @billbrod in https://github.com/flatironinstitute/nemos/pull/250
  • require sample axis to be axis=0 by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/254
  • Initialization by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/252
  • Added glm.py examples in docstrings by @pranmod01 in https://github.com/flatironinstitute/nemos/pull/249
  • Automatic step sizes for SVRG by @bagibence in https://github.com/flatironinstitute/nemos/pull/207
  • added linting tests to tox.ini and linted by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/258
  • Started basis examples by @pranmod01 in https://github.com/flatironinstitute/nemos/pull/253
  • fixed abs links by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/262
  • Start facilitating coefficient splitting by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/247
  • Sphinx by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/264
  • Basis refactor pr1 by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/273
  • Document basis by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/274
  • Multi dim eval basis by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/275
  • Set shape basis method by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/276
  • Improve transformer api by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/280
  • Identity basis by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/282
  • added decorator to simulate by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/287
  • PopulationGLM sklearn clone by @billbrod in https://github.com/flatironinstitute/nemos/pull/291
  • fix splitbyfeature bug by @billbrod in https://github.com/flatironinstitute/nemos/pull/289
  • Adds repr for our custom classes by @billbrod in https://github.com/flatironinstitute/nemos/pull/286
  • Development by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/293
  • Bugfix init composite basis by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/294
  • New release by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/295

New Contributors

  • @pranmod01 made their first contribution in https://github.com/flatironinstitute/nemos/pull/249

Full Changelog: https://github.com/flatironinstitute/nemos/compare/0.1.6...0.2.0

- Python
Published by BalzaniEdoardo about 1 year ago

nemos - 0.1.6

NeMoS New Release

In this new release: - Simplified API for GLM: You can now set regularization using a string. All regularization and solver hyperparameters can be passed during GLM initialization. python import nemos as nmo model = nmo.glm.GLM(regularizer="Ridge", regularizer_strength=0.1) - New TransformerBasis API: All Basis attributes are now available in TransformerBasis, facilitating inspection and cross-validation. See the updated tutorial in the API guide. python import nemos as nmo transformer_basis = nmo.basis.RaisedCosineBasisLinear(10).to_transformer() print(transformer_basis.n_basis_funcs) # prints 10 - Bounds for Basis: Added support for specifying bounds for the range of values covered by a basis function.

What's Changed

  • quickfix by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/175
  • improved docstrings by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/182
  • run ci only for non-draft prs by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/192
  • Refactoring regularizer and solver by @clewis7 in https://github.com/flatironinstitute/nemos/pull/183
  • add tests for checking get_params() by @clewis7 in https://github.com/flatironinstitute/nemos/pull/200
  • Provide a range for basis by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/191
  • update contributing guide by @clewis7 in https://github.com/flatironinstitute/nemos/pull/198
  • fix convergence tests by @clewis7 in https://github.com/flatironinstitute/nemos/pull/206
  • Update TransformerBasis and Basis to work with scikit-learn pipelining and CV by @bagibence in https://github.com/flatironinstitute/nemos/pull/169
  • fixed basis call docstrings by @BalzaniEdoardo in https://github.com/flatironinstitute/nemos/pull/209

New Contributors

  • @clewis7 made their first contribution in https://github.com/flatironinstitute/nemos/pull/183 🚀 🚀 🚀
  • @bagibence made their first contribution in https://github.com/flatironinstitute/nemos/pull/169 🚀 🚀 🚀

Full Changelog: https://github.com/flatironinstitute/nemos/compare/0.1.5...0.1.6

- Python
Published by BalzaniEdoardo over 1 year ago

nemos - NeMoS version 0.1.5

New with this release: - GammaObservations model, for fitting Gamma-GLMs. - GLMs'updateandinitialize_solver` methods for batching

- Python
Published by BalzaniEdoardo over 1 year ago

nemos - NeMoS version 0.1.4

New with this release:

  • GammaObservations model, for fitting Gamma-GLMs.

  • GLMs' update and initialize_solver methods for batching

- Python
Published by BalzaniEdoardo over 1 year ago

nemos - Compatiblity with `pynapple>=0.6.5`

This update make sure that nemos is compatible with pynapple>=0.6.5.

- Python
Published by BalzaniEdoardo almost 2 years ago

nemos - `nemos` for GLM and `PopulationGLM`

Release of the package tested for python 3.9, 3.10, and 3.11. Current modules include basis.py for feature construction and glm for single neuron and population GLM modeling.

- Python
Published by BalzaniEdoardo almost 2 years ago

nemos - `nemos` first release

First working release of nemos.

- Python
Published by BalzaniEdoardo almost 2 years ago

nemos - First release nemos

nemos first release

- Python
Published by BalzaniEdoardo almost 2 years ago

nemos - Reserve package name on PyPI

This is an alpha version of the code. We are releasing this version with the aim of reserving the package name on PyPI

- Python
Published by BalzaniEdoardo over 2 years ago