mixedbench

A benchmark of posterior approximation and prediction for generalized linear mixed models (GLMMs) on real grouped data.

What and why

• Bayesian methods for GLMMs are hard to compare: each paper and released method tests them on its own few datasets. This benchmark aims to fix that.
• mixedbench lists the documented mixed-effects models of 641 public tabular datasets with grouping structure, each downloaded at a fixed version.
• A fixed set of rules turns each dataset into an inference problem ready to fit. Results of different methods are comparable.
• From release 1.1, suites add reference posteriors to score against.

Install

pip install mixedbench

No R needed: every dataset loads in Python.

Quickstart

from pathlib import Path
from mixedbench import suite

# fetched from CRAN at its pin and checked against suite 1.1's list; later calls are offline
problem = suite.load('lme4/sleepstudy/1', Path('cache'))

Check out the demo for a friendly introduction.

Contents

• The package mixedbench: suite (a problem by its id, in one call), registry (the registry files, summarized in SUMMARY.md), datasets (the loader) and contract (Problem, materialize, load).
• suite/1.1/candidates.csv: the candidate problems of suite 1.1 with their contract hashes; refused.csv: the rows left out, each with its reason.
• survey/: the pipeline that built the registry and its record; provenance, not needed to use the package.

Planned

• Release 1.1: suite 1.1 with reference posteriors, the metrics that score a method against them, and the scores of standard methods.
• Release 1.2: references for the oracle and predictive tracks, more families, and the retirement of sources that went offline.
• Later: an R loader, an "as published" prior track, and a mirror fallback for sources that go offline.

Progress is tracked in the issues.

Contributing

Interested in becoming part of mixedbench? Check out CONTRIBUTING.md.

Citing

Please cite the release you used: CITATION.cff, or click "Cite this repository" on GitHub. All versions share the DOI 10.5281/zenodo.23285683.

License

• Code: Apache-2.0. Registry and suite files: CC BY 4.0.
• The data keep their sources' terms: they are fetched at first use, not redistributed.