alea-inference 0.2.5

A tool to perform toyMC-based inference constructions

alea

alea is a flexible statistical inference framework. The Python package is designed for constructing, handling, and fitting statistical models, computing confidence intervals and conducting sensitivity studies. It is primarily developed for the XENONnT dark matter experiment, but can be used for any statistical inference problem.

Alea aims to model the statistical behaviour of an experiment, which again depends on your knowledge of the underlying physics-- this can range from the very simple, such as measuring a gaussian-distributed random variable, to complex likelihoods where each model component is created by physics simulations (GEANT4), fast detector simulations (for example appletree for XENONnT) or a data-driven method.

If you use alea in your research, please consider citing the software published on zenodo.

Installation

You can install alea from PyPI using pip but beware that it is listed there as alea-inference! Thus, you need to run

pip install alea-inference

For the latest version, you can install directly from the GitHub repository by cloning the repository and running

cd alea
pip install .

You are now ready to use alea!

Getting started

The best way to get started is to check out the documentation and have a look at our tutorial notebooks. To explore the notebooks interactively, you can use Binder.

Acknowledgements

alea is a public package inherited the spirits of previously private XENON likelihood definition and inference construction code binference that based on the blueice repo https://github.com/JelleAalbers/blueice.

Binference was developed for XENON1T WIMP searches by Knut Dundas Morå, and for the first XENONnT results by Robert Hammann, Knut Dundas Morå and Tim Wolf.

What's Changed

• Consistent sorting for BlueiceExtendedModel by @hammannr in https://github.com/XENONnT/alea/pull/149
• Fixed data storing by @hammannr in https://github.com/XENONnT/alea/pull/152
• Add lxml_html_clean to fix readthedocs building error by @zihaoxu98 in https://github.com/XENONnT/alea/pull/157
• Fitting index variables by @zihaoxu98 in https://github.com/XENONnT/alea/pull/156
• Print Argument combinations to be submitted by @hammannr in https://github.com/XENONnT/alea/pull/151
• Minor changes to fitting index variables (PR #156) by @hammannr in https://github.com/XENONnT/alea/pull/159
• Set i_batch for SubmitterLocal when submitting by @dachengx in https://github.com/XENONnT/alea/pull/164
• Debug for interpolator deduction of NeymanConstructor by @dachengx in https://github.com/XENONnT/alea/pull/165
• The first i batch should be 0 by @dachengx in https://github.com/XENONnT/alea/pull/166
• Try prefix every file path in likelihood configuration with template folder by @dachengx in https://github.com/XENONnT/alea/pull/169
• Forbid prexing every key when adapt_likelihood_config_for_blueice by @FaroutYLq in https://github.com/XENONnT/alea/pull/170
• Refactored Pegasus-based OSG submitter by @FaroutYLq in https://github.com/XENONnT/alea/pull/163
• Try fixing https://github.com/XENONnT/alea/issues/173 by @dachengx in https://github.com/XENONnT/alea/pull/176
• Allow assigning kwargs in debug mode by @dachengx in https://github.com/XENONnT/alea/pull/174
• Allow confidence_level in filename by @dachengx in https://github.com/XENONnT/alea/pull/179
• Add 68% coverage as one of the defaults of confidence_levels by @dachengx in https://github.com/XENONnT/alea/pull/180
• Document to increase CPUs by @FaroutYLq in https://github.com/XENONnT/alea/pull/178

New Contributors

• @FaroutYLq made their first contribution in https://github.com/XENONnT/alea/pull/170

Full Changelog: https://github.com/XENONnT/alea/compare/v0.2.4...v0.2.5

0.2.4 / 2024-03-18

• Point away from alea for physics models by @kdund in https://github.com/XENONnT/alea/pull/143
• Make "piecewise" the default pdf interpolation by @hammannr in https://github.com/XENONnT/alea/pull/142
• Enforce bins in config and template to match by @hammannr in https://github.com/XENONnT/alea/pull/144
• Make model histograms accessible by @hammannr in https://github.com/XENONnT/alea/pull/140
• Make local submitter verbose by @hammannr in https://github.com/XENONnT/alea/pull/146
• Estimator of signal multiplier based on perturbation theory by @zihaoxu98 in https://github.com/XENONnT/alea/pull/147

Full Changelog: https://github.com/XENONnT/alea/compare/v0.2.3...v0.2.4

0.2.3 / 2024-02-22

• Improve check of already made toydata and output by @dachengx in https://github.com/XENONnT/alea/pull/128
• Combine several jobs into one to save computation resources by @dachengx in https://github.com/XENONnT/alea/pull/131
• Check locate loaded package by @dachengx in https://github.com/XENONnT/alea/pull/134
• Update hypotheses and common_hypothesis by pre_process_poi by @dachengx in https://github.com/XENONnT/alea/pull/135
• Print total number of submitted jobs by @dachengx in https://github.com/XENONnT/alea/pull/137

Full Changelog: https://github.com/XENONnT/alea/compare/v0.2.2...v0.2.3

0.2.2 / 2024-01-13

• Save dtype of valid_fit as bool by @dachengx in https://github.com/XENONnT/alea/pull/123
• Optional setting of random seed for debugging by @dachengx in https://github.com/XENONnT/alea/pull/122
• Tiny minor change on docstring by @dachengx in https://github.com/XENONnT/alea/pull/126
• Change example filename extension by @kdund in https://github.com/XENONnT/alea/pull/93
• Add axis_names to example templates by @hammannr in https://github.com/XENONnT/alea/pull/127
• Evaluate blueice_anchors expression by @dachengx in https://github.com/XENONnT/alea/pull/124
• Update pypi to use trusted publisher by @dachengx in https://github.com/XENONnT/alea/pull/130
• Update versions of blueice and inference-interface by @dachengx in https://github.com/XENONnT/alea/pull/132

Full Changelog: https://github.com/XENONnT/alea/compare/v0.2.1...v0.2.2

0.2.1 / 2023-12-08

• Add optional argument degree_of_freedom for asymptotic_critical_value by @dachengx in https://github.com/XENONnT/alea/pull/86
• Update readthedocs configurations by @dachengx in https://github.com/XENONnT/alea/pull/88
• Update tutorials by @hammannr in https://github.com/XENONnT/alea/pull/89
• Add column to toyMC results with minuit convergence flag by @kdund in https://github.com/XENONnT/alea/pull/91
• Debug a typo at docstring of fittable parameter by @dachengx in https://github.com/XENONnT/alea/pull/95
• Improve documentation by @hammannr in https://github.com/XENONnT/alea/pull/101
• Update Neyman threshold when changing runner_args by @hammannr in https://github.com/XENONnT/alea/pull/100
• Allow submitter to skip the already succeeded files by @dachengx in https://github.com/XENONnT/alea/pull/94
• Print time usage of Runner.run by @dachengx in https://github.com/XENONnT/alea/pull/104
• Get expectation values per likelihood term by @hammannr in https://github.com/XENONnT/alea/pull/106
• Prevent arguments to submission variations being changed by deepcopy-ing them. by @dachengx in https://github.com/XENONnT/alea/pull/107
• Make error message more explicit that an excecutable is not found and… by @kdund in https://github.com/XENONnT/alea/pull/109
• Read poi and expectation directly from output_filename to accelerate NeymanConstructor by @dachengx in https://github.com/XENONnT/alea/pull/108
• Direct call of used parameters of model by @dachengx in https://github.com/XENONnT/alea/pull/112
• Add function to get all sources names from all likelihoods by @dachengx in https://github.com/XENONnT/alea/pull/111
• Make sure values of parameters that need re-initialization are not changed by @hammannr in https://github.com/XENONnT/alea/pull/110
• Allow all computation names by @kdund in https://github.com/XENONnT/alea/pull/116
• Debug for the missing argument in _read_poi by @dachengx in https://github.com/XENONnT/alea/pull/118
• Remove unnecessary warning given new ptype constraints by @dachengx in https://github.com/XENONnT/alea/pull/119

Full Changelog: https://github.com/XENONnT/alea/compare/v0.2.0...v0.2.1

0.2.0 / 2023-09-01

• Proposal to use pre-commit for continuous integration by @dachengx in https://github.com/XENONnT/alea/pull/78
• Example notebooks by @hammannr in https://github.com/XENONnT/alea/pull/75
• Simplify TemplateSource, CombinedSource and SpectrumTemplateSource by @dachengx in https://github.com/XENONnT/alea/pull/69
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/XENONnT/alea/pull/80
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/XENONnT/alea/pull/82
• Add Submitter and NeymanConstructor by @dachengx in https://github.com/XENONnT/alea/pull/79

New Contributors

• @pre-commit-ci made their first contribution in https://github.com/XENONnT/alea/pull/80

Full Changelog: https://github.com/XENONnT/alea/compare/v0.1.0...v0.2.0

0.1.0 / 2023-08-11

• Unify and clean code style and docstring by @dachengx in https://github.com/XENONnT/alea/pull/68
• First runner manipulating statistical model by @dachengx in https://github.com/XENONnT/alea/pull/50
• Set best_fit_args to confidence_interval_args if None by @kdund in https://github.com/XENONnT/alea/pull/76
• Livetime scaling by @kdund in https://github.com/XENONnT/alea/pull/73

Full Changelog: https://github.com/XENONnT/alea/compare/v0.0.0...v0.1.0

0.0.0 / 2023-07-28

• readme update with pointer to previous work in lieu of commit history by @kdund in https://github.com/XENONnT/alea/pull/8
• Adds a statistical model base class (under construction by @kdund in https://github.com/XENONnT/alea/pull/7
• change folder/module name by @kdund in https://github.com/XENONnT/alea/pull/9
• Move submission_script.py also from binference to here by @dachengx in https://github.com/XENONnT/alea/pull/10
• Add simple gaussian model by @hammannr in https://github.com/XENONnT/alea/pull/12
• Parameter class by @hammannr in https://github.com/XENONnT/alea/pull/19
• Confidence intervals by @kdund in https://github.com/XENONnT/alea/pull/27
• Update README.md by @kdund in https://github.com/XENONnT/alea/pull/29
• Init code style checking, pytest, and coverage by @dachengx in https://github.com/XENONnT/alea/pull/31
• Add templates for wimp example by @hoetzsch in https://github.com/XENONnT/alea/pull/30
• Removes all hash for parameters not used for each source, and for all… by @kdund in https://github.com/XENONnT/alea/pull/37
• First implementation of an nT-like likelihood by @hammannr in https://github.com/XENONnT/alea/pull/32
• Check if some parameter is not set as guess when fitting by @kdund in https://github.com/XENONnT/alea/pull/44
• Fix likelihood_names check in statistical_model.store_data to handle unnamed likelihoods by @kdund in https://github.com/XENONnT/alea/pull/45
• Create pull_request_template.md by @dachengx in https://github.com/XENONnT/alea/pull/46
• Codes style cleaning by @dachengx in https://github.com/XENONnT/alea/pull/49
• First runner manipulating statistical model by @dachengx in https://github.com/XENONnT/alea/pull/47
• Run test on main not master by @dachengx in https://github.com/XENONnT/alea/pull/55
• Simplify file structure by @dachengx in https://github.com/XENONnT/alea/pull/51
• Move blueice_extended_model to models by @dachengx in https://github.com/XENONnT/alea/pull/56
• Change data format to only use structured arrays by @kdund in https://github.com/XENONnT/alea/pull/42
• Another fitting test by @kdund in https://github.com/XENONnT/alea/pull/59
• Add first tests module and file indexing system by @dachengx in https://github.com/XENONnT/alea/pull/54
• Shape parameters by @hammannr in https://github.com/XENONnT/alea/pull/58
• Recover examples folder, update file indexing, add notebooks folder, remove legacies by @dachengx in https://github.com/XENONnT/alea/pull/61
• Remove pdf_cache folder before pytest by @dachengx in https://github.com/XENONnT/alea/pull/65
• Make 0.0.0, initialize documentation structure based on readthedocs, add badges to README by @dachengx in https://github.com/XENONnT/alea/pull/66

New Contributors

• @kdund made their first contribution in https://github.com/XENONnT/alea/pull/8
• @dachengx made their first contribution in https://github.com/XENONnT/alea/pull/10
• @hammannr made their first contribution in https://github.com/XENONnT/alea/pull/12
• @hoetzsch made their first contribution in https://github.com/XENONnT/alea/pull/30