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summaries

Comparison of summary statistic selection methods with a unifying perspective.

https://github.com/tillahoffmann/summaries

Science Score: 54.0%

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    CITATION.cff file
    Found CITATION.cff file
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    codemeta.json file
    Found codemeta.json file
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    Links to: arxiv.org
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    Low similarity (12.2%) to scientific vocabulary

Keywords

approximate-bayesian-computation conditional-density-estimation data-compression information-theory likelihood-free-inference simulation-based-inference summary-statistics
Last synced: 6 months ago · JSON representation ·

Repository

Comparison of summary statistic selection methods with a unifying perspective.

Basic Info
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Topics
approximate-bayesian-computation conditional-density-estimation data-compression information-theory likelihood-free-inference simulation-based-inference summary-statistics
Created about 4 years ago · Last pushed over 2 years ago
Metadata Files
Readme License Citation

README.rst 

summaries
=========

.. image:: https://github.com/tillahoffmann/summaries/actions/workflows/main.yml/badge.svg
  :target: https://github.com/tillahoffmann/summaries/actions/workflows/main.yml

This repository accompanies the preprint `"Minimizing the expected posterior entropy yields optimal summary statistics" `_ and can be used to reproduce all figures and reported results.

You can reproduce the results in three steps:

1. Set up a new, clean python virtual environment (you can also skip this step to use your host python environment, but your mileage may vary).
2. Install all the requirements by running :code:`pip install -r requirements.txt`.
3. Generate all result files by running the following code from the command line.

.. code-block:: bash

  # Ignore the figures until we have generated all data files.
  doit ignore figures
  # Generate the data files (use -n to parallelize if desired).
  doit -n [number of cores]
  # Generate the figures and a summary file `workspace/figures/figures.html`.
  doit forget figures
  doit figures

You will find all figures in the folder :code:`workspace/figures` together with a HTML report :code:`workspace/figures/figures.html` that contains additional information. This process takes about 40 minutes on an M1 MacBook Pro when parallelizing across six cores.

The code has been tested with python 3.9 on macOS 12.4 (Monterey) running on Apple silicon and on Ubuntu 20.04. The :code:`summaries` package has complete test coverage, and you can run :code:`pytest` from the repository root to verify that your installation is working.

Owner

  • Name: Till Hoffmann
  • Login: tillahoffmann
  • Kind: user
  • Location: Boston, MA
  • Company: Harvard T.H. Chan School of Public Health

Building network models at @HarvardChanSchool with a focus on open and reproducible science. Formerly @imperial, @spotify.

Citation (CITATION.cff) 

# yaml-language-server: $schema=https://citation-file-format.github.io/1.2.0/schema.json
cff-version: 1.2.0
message: If you use this software, please cite it as below.
title: Minimizing the Expected Posterior Entropy Yields Optimal Summary Statistics
url: "https://github.com/tillahoffmann/summaries"
authors:
- family-names: Hoffmann
  given-names: Till
  orcid: https://orcid.org/0000-0003-4403-0722
- family-names: Onnela
  given-names: Jukka-Pekka
  orcid: https://orcid.org/0000-0001-6613-8668
preferred-citation:
  type: article
  authors:
  - family-names: Hoffmann
    given-names: Till
    orcid: https://orcid.org/0000-0003-4403-0722
  - family-names: Onnela
    given-names: Jukka-Pekka
    orcid: https://orcid.org/0000-0001-6613-8668
  doi: 10.48550/arXiv.2206.02340
  journal: arXiv
  start: "2206.02340"
  title: Minimizing the Expected Posterior Entropy Yields Optimal Summary Statistics
  year: 2022

GitHub Events

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Last synced: 12 months ago

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  • Total issues: 5
  • Total pull requests: 29
  • Average time to close issues: 5 months
  • Average time to close pull requests: 20 days
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 0.4
  • Average comments per pull request: 0.07
  • Merged pull requests: 25
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
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Top Authors
Issue Authors
  • tillahoffmann (5)
Pull Request Authors
  • tillahoffmann (23)
Top Labels
Issue Labels
enhancement (2) maintenance (1) bug (1)
Pull Request Labels
maintenance (3) enhancement (2) bug (1)

Dependencies

requirements.in pypi
  • jupyter *
  • snakeviz *
  • tqdm *
requirements.txt pypi
  • 116 dependencies
setup.py pypi
  • cmdstanpy *
  • doit *
  • matplotlib *
  • numpy *
  • pandas *
  • scikit-learn *
  • scipy *
  • torch *
  • tqdm *
test_requirements.txt pypi
  • alabaster ==0.7.12 test
  • attrs ==21.4.0 test
  • babel ==2.10.3 test
  • certifi ==2022.6.15 test
  • charset-normalizer ==2.1.0 test
  • cloudpickle ==2.1.0 test
  • cmdstanpy ==1.0.2 test
  • coverage ==6.4.1 test
  • cycler ==0.11.0 test
  • docutils ==0.18.1 test
  • doit ==0.36.0 test
  • flake8 ==4.0.1 test
  • fonttools ==4.33.3 test
  • idna ==3.3 test
  • imagesize ==1.3.0 test
  • importlib-metadata ==4.12.0 test
  • iniconfig ==1.1.1 test
  • jinja2 ==3.1.2 test
  • joblib ==1.1.0 test
  • kiwisolver ==1.4.3 test
  • markupsafe ==2.1.1 test
  • matplotlib ==3.5.2 test
  • mccabe ==0.6.1 test
  • numpy ==1.23.0 test
  • packaging ==21.3 test
  • pandas ==1.4.3 test
  • pillow ==9.1.1 test
  • pluggy ==1.0.0 test
  • py ==1.11.0 test
  • pycodestyle ==2.8.0 test
  • pyflakes ==2.4.0 test
  • pygments ==2.12.0 test
  • pyparsing ==3.0.9 test
  • pytest ==7.1.2 test
  • pytest-bootstrap ==0.2.3 test
  • pytest-cov ==3.0.0 test
  • python-dateutil ==2.8.2 test
  • pytz ==2022.1 test
  • requests ==2.28.1 test
  • scikit-learn ==1.1.1 test
  • scipy ==1.8.1 test
  • six ==1.16.0 test
  • snowballstemmer ==2.2.0 test
  • sphinx ==5.0.2 test
  • sphinxcontrib-applehelp ==1.0.2 test
  • sphinxcontrib-devhelp ==1.0.2 test
  • sphinxcontrib-htmlhelp ==2.0.0 test
  • sphinxcontrib-jsmath ==1.0.1 test
  • sphinxcontrib-qthelp ==1.0.3 test
  • sphinxcontrib-serializinghtml ==1.1.5 test
  • threadpoolctl ==3.1.0 test
  • tomli ==2.0.1 test
  • torch ==1.12.0 test
  • tqdm ==4.64.0 test
  • typing-extensions ==4.2.0 test
  • ujson ==5.3.0 test
  • urllib3 ==1.26.9 test
  • zipp ==3.8.0 test
.github/workflows/main.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
test_requirements.in pypi