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Recent Releases of swyft

swyft - v0.4.5

What's Changed

Updates: * Modularisation of SwyftModule * Restructuring of configure_optimizers and configure_callbacks * New default is AdamW with early stopping * Alternatives with AdamW and OneCycleLR and ReduceLROnPlateau exist as well * Automatic reloading of best model at the end of training is default * Extended plot options * Add smooth_prior flag for interpolating likelihoods * Renaming of plotting routines (plotposterior, plotcorner, plot_pair) * Update example notebook * Bug fix for labels in corner plot by @anchal-009 in https://github.com/undark-lab/swyft/pull/136

New Contributors

  • @anchal-009 made their first contribution in https://github.com/undark-lab/swyft/pull/136
  • Co-authored-by: NoemiAM noemi.anaumontel@gmail.com

Full Changelog: https://github.com/undark-lab/swyft/compare/v0.4.4...v0.4.5

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cweniger over 2 years ago

swyft - v0.4.4

Overview

  • Included updated author list (AUTHOR file) and update LICENSE information
  • Add torch conjugate gradient to dependencies (for forthcoming applications)
  • Add list of Swyft publications and events to docs
  • pytorch-lighthing 2.0 compatibility not fully established (pending until 2.0 has feature parity with 1.9)
  • Add swyft.getclassprobs for extracting classification results from ratio estimators
  • Add LogRatioEstimator_Gaussian, a Gaussian ratio estimator for arbitrary dimensions
  • Deprecate LogRatioEstimator1dimGaussian (worked only with 1dim features and 1dim parameters)
  • Rewritten logratios aggregator in swyft.Module to be more resilient
  • Add AuxLoss, which just enables to add arbitrary extra losses (e.g. related to regularisation) to the training object
  • Enable Spectral embedding for parameters in LogRatioEstimator_Ndim for high fidelity posteriors
  • Add LogRatioEstimator_Autoregressive, an autoregressive neural ratio estimator module

What's Changed

  • Documentation updates (citations, changelog) by @cweniger in https://github.com/undark-lab/swyft/pull/125
  • Update setup.cfg - pytorch-lightning <=1.9.5 by @cweniger in https://github.com/undark-lab/swyft/pull/126
  • Merge dev branch by @cweniger in https://github.com/undark-lab/swyft/pull/128
  • Updates AUTHORS and LICENSE files by @cweniger in https://github.com/undark-lab/swyft/pull/129
  • remove ns by @NoemiAM in https://github.com/undark-lab/swyft/pull/131
  • Release/v0.4.4 by @cweniger in https://github.com/undark-lab/swyft/pull/134

Full Changelog: https://github.com/undark-lab/swyft/compare/v0.4.3...v0.4.4

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cweniger almost 3 years ago

swyft - v0.4.3

What's Changed

  • Added and updated tutorials @cweniger in https://github.com/undark-lab/swyft/pull/122
  • Improving documentation @cweniger in https://github.com/undark-lab/swyft/pull/123
  • Solving problems with pytorch lightning 2.0.x @cweniger in https://github.com/undark-lab/swyft/pull/124

Full Changelog: https://github.com/undark-lab/swyft/compare/v0.4.2...v0.4.3

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cweniger about 3 years ago

swyft - Release v0.4.2

What's Changed

  • Fix plotzz and plotpp to deal with N-dim posteriors by @cweniger in https://github.com/undark-lab/swyft/pull/109
  • Update README.rst by @bkmi in https://github.com/undark-lab/swyft/pull/114
  • Merge current dev branch by @cweniger in https://github.com/undark-lab/swyft/pull/115
  • Update setup.cfg by @cweniger in https://github.com/undark-lab/swyft/pull/118
  • Bug fix for ZarrStore dataloaders split by @NoemiAM in https://github.com/undark-lab/swyft/pull/120
  • Update README.rst by @cweniger in https://github.com/undark-lab/swyft/pull/121

New Contributors

  • @NoemiAM made their first contribution in https://github.com/undark-lab/swyft/pull/120

Full Changelog: https://github.com/undark-lab/swyft/compare/v0.4.1...v0.4.2

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cweniger about 3 years ago

swyft - Pre-release v0.4.2

Overview

Fixes: - Math in docstrings - Functionality of LogRatioEstimator1dimGaussian, added minstd argument for stability - Fix tqdm progress bars in notebooks

Enhancements: - Automatic plot axes assignment - LogRatioEstimators can take different summaries for different ratios - Coverage estimation uses noisy logratios in order to make coverage plots useful for classification problems

What's Changed

  • Fix plotzz and plotpp to deal with N-dim posteriors by @cweniger in https://github.com/undark-lab/swyft/pull/109
  • Update README.rst by @bkmi in https://github.com/undark-lab/swyft/pull/114
  • Merge current dev branch by @cweniger in https://github.com/undark-lab/swyft/pull/115

Full Changelog: https://github.com/undark-lab/swyft/compare/v0.4.1.post1...v0.4.2-pre1

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cweniger over 3 years ago

swyft - Post-release v0.4.1

Fix image link in readme.rst.

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cweniger over 3 years ago

swyft - Bugfix release v0.4.1

Fixing installation and documentation bugs

Full Changelog: https://github.com/undark-lab/swyft/compare/v0.4.0...v0.4.1

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cweniger over 3 years ago

swyft - Release v0.4.0 (with new pytorch-lightning based API)

Release of Swyft with pytorch-lightning based API.

What's changed

  • Training is handled by pytorch-lightning
  • More flexible inference network architectures (enabling training of conditional ratios, ratios of different variables, etc)
  • New simulation model based on definition of the full graphical model
  • New ZarrStore for parallel simulations
  • More efficient handling of coverage tests

See tutorial notebooks for example use-cases.

What's next

  • Incorporation of all Swyft v0.3.x functionality (violin plots, etc)

Full Changelog: https://github.com/undark-lab/swyft/compare/v0.3.2...v0.4.0

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cweniger over 3 years ago

swyft - Pre-release v0.4.0 (aka swift-lightning)

First prerelease version of swyft v0.4.0 (aka swyft-lightning) with complete interface overhaul.

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cweniger almost 4 years ago

swyft - swyft: Truncated Marginal Neural Ratio Estimation in Python

  • Introduced a version using import swyft; swyft.__version__
  • Added labels for violin marginals.
  • Followed the requested changes from the JOSS review thread.

Full Changelog: https://github.com/undark-lab/swyft/compare/v0.3.1...v0.3.2

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by bkmi about 4 years ago

swyft - Naming / documentation consistency, changed core inference objects, reduced abstraction

Big Changes

  • Documentation and tests have been significantly improved with nearly all user facing functions having a useful docstring and test. There are also new example notebooks explaining all of the core functionality of swyft.
  • The main inferences classes are now MarginalRatioEstimator, the trainable estimator, and MarginalPosterior, the marginal sampling tool. Older classes have been simply deleted. Truncated estimation must be done by the user, there is an example notebook if you want to see how.
  • Priors have been updated and can be specified using pytorch distributions. Although the interpolated grid technique is still available, consider it deprecated and inaccurate.
  • There is a WeightedMarginalSamples dataclass now which handles functionality internally. Marginals themselves are still dictionaries.
  • This version has been submitted to JOSS.

What's Changed

  • Fix simulator test warnings by @fnattino in https://github.com/undark-lab/swyft/pull/77
  • remove unstable simulator tests by @fnattino in https://github.com/undark-lab/swyft/pull/85
  • Refactor directory/memory stores as single objects by @fnattino in https://github.com/undark-lab/swyft/pull/84
  • update store/simulator notebooks following refactoring by @fnattino in https://github.com/undark-lab/swyft/pull/92
  • Rst vs md by @bkmi in https://github.com/undark-lab/swyft/pull/94
  • The future of swyft by @bkmi in https://github.com/undark-lab/swyft/pull/82
  • Fix Dask simulator performance issue by @fnattino in https://github.com/undark-lab/swyft/pull/99

Full Changelog: https://github.com/undark-lab/swyft/compare/v0.2.1...v0.3.0

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by bkmi over 4 years ago

swyft - Improved Dask

This release incorporates the changes made by the eScience center to the dask simulator as well as a small amount of complex number support.

What's Changed

  • add pnames argument and attribute to DaskSimulator by @fnattino in https://github.com/undark-lab/swyft/pull/55
  • Issue/30 by @rogerkuou in https://github.com/undark-lab/swyft/pull/56
  • Fix unit test by @rogerkuou in https://github.com/undark-lab/swyft/pull/75
  • Simulator and store clean up by @fnattino in https://github.com/undark-lab/swyft/pull/74
  • added eScience examples Ext. Sim, Dir. Store, Dask Sim by @meiertgrootes in https://github.com/undark-lab/swyft/pull/81
  • fix stochastic behavior in simulator test by @rogerkuou in https://github.com/undark-lab/swyft/pull/88
  • Added notebooks demonstrating use of external simulators, directory store, and Dask simulator

New Contributors

  • @meiertgrootes made their first contribution in https://github.com/undark-lab/swyft/pull/81

Full Changelog: https://github.com/undark-lab/swyft/compare/v0.2.0...v0.2.1

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by bkmi over 4 years ago

swyft - Better API (v0.2.0)

  • Type hints
  • Estimates for empirical vs nominal mass
  • Clean up API: more transparent (and more verbose)
  • Safer use of datastore through add functions
  • Removal of confusing Microscope and Task classes
  • Pickel default revision 4 for backwards compatibility
  • Lots of code refactoring and clean up
  • Training diagnostics and posterior diagnostics
  • New example notebooks
  • Clean up of documentation on readthedocs.io

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cweniger almost 5 years ago

swyft - Preparation of next point relase.

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cweniger almost 5 years ago

swyft - Task, Posteriors and Bounds

This release is overdue and tags the current version of the API, which is used in various ongoing projects. There will be a few breaking changes in the next release, which will be described w.r.t. this one.

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cweniger almost 5 years ago

swyft - NeurIPS Notebook Update

Fix RatioEstimator.train settings to support NeurIPS notebooks.

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by bkmi over 5 years ago

swyft - Initial release with NeurIPS paper.

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cweniger over 5 years ago

swyft -

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cweniger over 5 years ago

swyft - Pre-release Workflow Test

  • API finished for this release
  • example notebooks created

This is primarily for testing the workflow deployment.

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by bkmi over 5 years ago