# Stein Thinning
### About
Stein Thinning is a tool for post-processing the output of a sampling procedure,
such as Markov chain Monte Carlo (MCMC). It aims to minimise a Stein discrepancy,
selecting a subsequence of samples that best represent the distributional target.
The user provides two arrays: one containing the samples and another containing
the corresponding gradients of the log-target. Stein Thinning returns a vector
of indices, indicating which samples were selected.
In favourable circumstances, Stein Thinning is able to:
* automatically identify and remove the burn-in period from MCMC,
* perform bias-removal for biased sampling procedures,
* provide improved approximations of the distributional target,
* offer a compressed representation of sample-based output.
### API Documentation
```{eval-rst}
.. autosummary::
:toctree: _autosummary
:template: custom-module-template.rst
:caption: Modules:
:recursive:
stein_thinning.kernel
stein_thinning.stein
stein_thinning.thinning
```
### Installation
Implementations of Stein Thinning are available for Python, R, and MATLAB:
* [Install for Python](https://github.com/wilson-ye-chen/stein_thinning#installing-via-git)
* [Install for R](https://github.com/wilson-ye-chen/stein.thinning#installing-via-github)
* [Install for MATLAB](https://github.com/wilson-ye-chen/stein_thinning_matlab#installation)
### Get Started
First, it is important to parametrise the distributional target so that it
has a positive and differentiable density {math}`p(x)` on {math}`\mathbb{R}^d`.
In [Python](https://github.com/wilson-ye-chen/stein_thinning#getting-started),
[R](https://github.com/wilson-ye-chen/stein.thinning#getting-started),
or [MATLAB](https://github.com/wilson-ye-chen/stein_thinning_matlab#getting-started),
it takes a single function call to start Stein Thinning:
```python
indices = thin(samples, gradients, m)
```
Here
* ```samples``` is an array with {math}`n` rows and {math}`d` columns, whose rows are the samples produced by a sampling method, such as MCMC,
* ```gradients``` is an array with {math}`n` rows and {math}`d` columns, whose rows contain the gradients {math}`\nabla\log p(x)` where {math}`x` is the corresponding row of ```samples```,
* ```m``` is an integer, specifying the number of representative samples required,
* ```indices``` is a vector of length {math}`m`, whose elements are integers in {math}`\{1,\dots,n\}`, indicating which samples were selected.
### Stan Examples
Stein Thinning can be used to post-process the output directly from the Stan family of probabilistic programming languages:
* [PyStan](https://github.com/wilson-ye-chen/stein_thinning#pystan-example)
* [RStan](https://github.com/wilson-ye-chen/stein.thinning#rstan-example)
### Citing Stein Thinning
Riabiz M, Chen WY, Cockayne J, Swietach P, Niederer SA, Mackey L, Oates CJ (2022) Optimal Thinning of MCMC Output. Journal of the Royal Statistical Society, Series B, 84(4), 1059-1081. [arXiv](https://arxiv.org/abs/2005.03952)
### Papers Inspired By Stein Thinning
Benard C, Staber B, Da Veiga S (2023) Kernel Stein Discrepancy thinning: a theoretical perspective of pathologies and a practical fix with regularization. [arXiv](https://arxiv.org/abs/2301.13528)
Fisher MA, Oates CJ (2022) Gradient-Free Kernel Stein Discrepancy [arXiv](https://arxiv.org/abs/2207.02636)
Anastasiou A, Barp A, Briol F-X, Ebner B, Gaunt RE, Ghaderinezhad F, Gorham J, Gretton A, Ley C, Liu Q, Mackey L, Oates CJ, Reinert G, Swan Y (2023) Stein’s Method Meets Computational Statistics: A Review of Some Recent Developments. Statistical Science, 38(1), 120–139. [arXiv](https://arxiv.org/abs/2105.03481)
Hawkins C, Koppel A, Zhang Z (2022) Online, Informative MCMC Thinning with Kernelized Stein Discrepancy. [arXiv](https://arxiv.org/abs/2201.07130)
Teymur O, Gorham J, Riabiz M, Oates CJ (2021) Optimal Quantisation of Probability Measures Using Maximum Mean Discrepancy. International Conference on Artificial Intelligence and Statistics (AISTATS 2021). [Conference](http://proceedings.mlr.press/v130/teymur21a.html) [arXiv](https://arxiv.org/abs/2010.07064)
Chopin N, Ducrocq G (2021) Fast compression of MCMC output. Entropy, 23(8), 1017. [Journal](https://www.mdpi.com/1099-4300/23/8/1017) [arXiv](https://arxiv.org/abs/2107.04552)
South LF, Riabiz M, Teymur O, Oates C (2021) Post-Processing of MCMC. Annual Reviews of Statistics and its Application, 9, 529-555. [arXiv](https://arxiv.org/abs/2103.16048)
### Acknowledgements
This work was supported by the Lloyd’s Register Foundation Programme on Data-Centric Engineering and the Programme on Health and Medical Sciences at The Alan Turing Institute (UK), the British Heart Foundation (SP/18/6/33805, RG/15/9/31534, PG/15/91/31812, FS/18/27/33543), the UK Research and Innovation Strategic Priorities Fund (EP/T001569/1), the UK Engineering and Physical Sciences Research Council (EP/P01268X/1, NS/A000049/1, EP/M012492/1), the UK National Institute for Health Research (II-LB-1116-20001) and the Wellcome Trust (WT 203148/Z/16/Z).