summaries2

https://github.com/tillahoffmann/summaries2

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Keywords

approximate-bayesian-computation likelihood-free-inference simulation-based-inference summary-statistics

Last synced: 6 months ago · JSON representation ·

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Host: GitHub
Owner: tillahoffmann
License: bsd-3-clause
Language: Python
Default Branch: main
Homepage:
Size: 171 KB

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approximate-bayesian-computation likelihood-free-inference simulation-based-inference summary-statistics

Created over 2 years ago · Last pushed 10 months ago

Metadata Files

Readme License Citation

Minimizing the Expected Posterior Entropy Yields Optimal Summaries

This repository contains code and data to reproduce the results presented in the manuscript Minimizing the Expected Posterior Entropy Yields Optimal Summaries.

Figures and tables can be regenerated by executing the following steps:

Ensure a recent Python version is installed; this code has been tested with Python 3.10 on Ubuntu and macOS.
Optionally, create a new virtual environment.
Install the Python requirements by executing pip install -r requirements.txt from the root directory of the repository.
Install CmdStan by executing python -m cmdstanpy.install_cmdstan --version 2.31.0. Other recent versions of CmdStan may also work but have not been tested.
Optionally, verify the installation by executing pytest -v.
Execute cook exec "*:evaluation" which will run all experiments and generate evaluation metrics which are saved at workspace/[experiment name]/evaluation.csv.
Execute each of the Jupyter notebooks (saved as markdown files) in the notebooks folder to generate the figures.

Results Structure

After running the experiments (see above), the workspace folder contains all results. It is structured as follows, and the folder structure is repeated for each experiment.

python benchmark-large # One folder for each experiment. data # Train, validation, and test split as pickle files; other temp files may also be present. test.pkl train.pkl validation.pkl ... samples # (Approximate) posterior samples as pickle files. [sampler configuration name].pkl ... transformers # Trained transformers, e.g., posterior mean estimators, as pickle files. [transformer configuration name]-[digits].pkl # One of three replications with diff. seeds. [transformer configuration name].pkl # Best transformer amongst the three replications. evaluation.csv # Evaluation of different summary statistic extraction methods. benchmark-small ... coalescent ... tree-large ... tree-large ... figures # Contains PDF figures after executing notebooks.

Each evaluation.csv file has seven columns: - path which refers to one of the methods used to extract summaries. - three columns {nlp,rmise,mise} which are best estimates of negative log probability loss, root mean integrated squared error, and mean integrated squared error, respectively. The estimates are obtained by averaging over all samples in the corresponding test set. - three columns {nlp,rmise,mise}_err which are standard errors obtained as sqrt(var / (n - 1)), where var is the variance of the metric in the test set, and n is the size of the test set.

Owner

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

Website: http://tillahoffmann.github.io/
Twitter: tillahoffmann
Repositories: 89
Profile: https://github.com/tillahoffmann

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/onnela-lab/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

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