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add preconditioning matrix to barker proposal #730

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ismael-mendoza
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@ismael-mendoza ismael-mendoza commented Aug 29, 2024

Overview

This PR attempts to add a preconditioning matrix to the barker proposal implementation, as in appendix G of https://arxiv.org/abs/1908.11812

Discussion / Questions

  • Not sure if this is the best way to take the sqrt of the inverse mass matrix? I redo the computation of the inverse twice (tried to follow HMC but didn't seem appropriate to create a metric)
  • Do I need to update the PDF? (not used anywhere in the codebase)
  • I added step_size and the inverse_mass_matrix to the BarkerState (didnt' have any of these before), OK?
  • It's not very clear in the Barker paper but the step_size (sigma) is a 'global scale' and the inverse mass matrix is separate. Are these redundant? See implementation from authors here (in R) - https://github.com/gzanella/barker/blob/master/functions.R

Thank you for opening a PR!

A few important guidelines and requirements before we can merge your PR:

  • If I add a new sampler, there is an issue discussing it already;
  • We should be able to understand what the PR does from its title only;
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  • There are links to all the relevant issues, discussions and PRs;
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Consider opening a Draft PR if your work is still in progress but you would like some feedback from other contributors.

@ismael-mendoza ismael-mendoza changed the title barker proposal with preconditioning matrix add preconditioning matrix to barker proposal Aug 29, 2024
@ismael-mendoza
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ismael-mendoza commented Sep 1, 2024

Closing because I jsut read the guidelines and noticed the commit and pre-commit requirements (will create a new PR)

@AdrienCorenflos
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Nw -> the commit pre-commit stuff is only last stage. In the meantime you can just try to get the logic right and then ask for a review when you think you have the Lego pieces fitting together.

@AdrienCorenflos
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Feel free to open a new pr or reopen this one, at the end of the day it doesn't matter much.

@ismael-mendoza
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Thanks @AdrienCorenflos that makes sense, I'll open a new one but remember that for next time. For reference opened #731

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2 participants