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New Gibbs sampler using condition #2099

Merged
merged 71 commits into from
Apr 21, 2024
Merged

New Gibbs sampler using condition #2099

merged 71 commits into from
Apr 21, 2024

Commits on Oct 4, 2023

  1. initial work on the new gibbs sampler

    @torfjelde
    torfjelde committed Oct 4, 2023
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  2. added tests for the new Gibbs sampler

    @torfjelde
    torfjelde committed Oct 4, 2023
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  3. added tests for new Gibbs

    @torfjelde
    torfjelde committed Oct 4, 2023
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  4. new Gibbs is now sampling (correctly) sequentially

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Commits on Oct 6, 2023

  1. let's not overload merge just yet

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    torfjelde committed Oct 6, 2023
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  2. export GibbsV2 + added more samplers to the tests

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    torfjelde committed Oct 6, 2023
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Commits on Oct 8, 2023

  1. added TODO comment

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    torfjelde committed Oct 8, 2023
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  2. Merge branch 'master' into torfjelde/new-gibbs

    @yebai
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Commits on Oct 20, 2023

  1. Merge remote-tracking branch 'origin/torfjelde/new-gibbs' into torfje… 

    …lde/new-gibbs
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  2. Merge branch 'master' into torfjelde/new-gibbs

    @torfjelde
    torfjelde committed Oct 20, 2023
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Commits on Nov 15, 2023

  1. Merge branch 'master' into torfjelde/new-gibbs

    @torfjelde
    torfjelde committed Nov 15, 2023
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Commits on Nov 16, 2023

  1. removed lots of varinfo related merging functionality that is now 

    available in DynamicPPL
    @torfjelde
    torfjelde committed Nov 16, 2023
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  2. shifting some code around

    @torfjelde
    torfjelde committed Nov 16, 2023
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  3. removed redundant constructor for GibbsV2

    @torfjelde
    torfjelde committed Nov 16, 2023
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Commits on Nov 18, 2023

  1. added GibbsContext which is similar to FixContext but also computes 

    the log-prob of the fixed variables
    @torfjelde
    torfjelde committed Nov 18, 2023
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Commits on Nov 19, 2023

  1. adopted the rerun mechanism in Gibbs for GibbsV2, thus fixing the 

    issues with some of the tests for GibbsV2
    @torfjelde
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  2. broken tests are no longer broken

    @torfjelde
    torfjelde committed Nov 19, 2023
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  3. fix issues with dot_tilde_* impls for GibbsContext

    @torfjelde
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  4. fix for dot_tilde_assume when using GibbsContext

    @torfjelde
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  5. fixed re-running of models for Gibbs sampling properly this time

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  6. Merge branch 'master' into torfjelde/new-gibbs

    @torfjelde
    torfjelde authored Nov 19, 2023
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  7. added new gibbs to tests

    @torfjelde
    torfjelde committed Nov 19, 2023
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  8. added some further comments on why we need GibbsContext

    @torfjelde
    torfjelde committed Nov 19, 2023
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  9. went back to using DynamicPPL.condition rather than using custom 

    `GibbsContext` while we wait for
TuringLang/DynamicPPL.jl#563 to be merged
    @torfjelde
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  10. add concrete comment about reverting changes for gibbs_condition

    @torfjelde
    torfjelde committed Nov 19, 2023
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Commits on Nov 20, 2023

  1. Update test/mcmc/gibbs_new.jl 

    Co-authored-by: Hong Ge <3279477+yebai@users.noreply.github.com>
    @torfjelde @yebai
    torfjelde and yebai authored Nov 20, 2023
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  2. fixed recursive definition of condition varinfos

    @torfjelde
    torfjelde committed Nov 20, 2023
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  3. Merge remote-tracking branch 'origin/torfjelde/new-gibbs' into torfje… 

    …lde/new-gibbs
    @torfjelde
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  4. use fix instead of condition

    @torfjelde
    torfjelde committed Nov 20, 2023
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Commits on Nov 21, 2023

  1. Revert "use fix instead of condition" 

    This reverts commit f87e2d1.
    @torfjelde
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  2. rmeoved unnused symbol

    @torfjelde
    torfjelde committed Nov 21, 2023
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  3. Revert "went back to using DynamicPPL.condition rather than using c… 

    …ustom"

This reverts commit 53bd707.
    @torfjelde
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  4. bump compat entry of DynamicPPL so we can overload acclogp!

    @torfjelde
    torfjelde committed Nov 21, 2023
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  5. update assume for SMC samplers to make use of new acclogp!

    @torfjelde
    torfjelde committed Nov 21, 2023
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  6. added proper impl of acclogp!! for SMC samplers + made accessing 

    task local varinfo and rng a bit nicer
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    torfjelde committed Nov 21, 2023
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Commits on Nov 24, 2023

  1. added experimental module and moved gibbs to it

    @torfjelde
    torfjelde committed Nov 24, 2023
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  2. fixed now-inccorect references in new gibbs file

    @torfjelde
    torfjelde committed Nov 24, 2023
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  3. updated gibbs tests

    @torfjelde
    torfjelde committed Nov 24, 2023
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  4. moved experimental gibbs tests

    @torfjelde
    torfjelde committed Nov 24, 2023
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  5. updated tests to include experiemntal tests

    @torfjelde
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  6. removed refrences to previews tests of experimental Gibbs sampler

    @torfjelde
    torfjelde committed Nov 24, 2023
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Commits on Jan 28, 2024

  1. Merge branch 'master' into torfjelde/new-gibbs

    @torfjelde
    torfjelde committed Jan 28, 2024
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Commits on Jan 29, 2024

  1. removed solved TODO

    @torfjelde
    torfjelde committed Jan 29, 2024
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  2. added a comment on reconstruct_getvalue usage

    @torfjelde
    torfjelde committed Jan 29, 2024
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  3. bump patch version

    @torfjelde
    torfjelde committed Jan 29, 2024
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  4. added comments on future work

    @torfjelde
    torfjelde committed Jan 29, 2024
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  5. Update test/experimental/gibbs.jl

    @torfjelde
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  6. fixed bug where particle samplers didn't properly account for 

    weightings of logpdf, etc.
    @torfjelde
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  7. Merge remote-tracking branch 'origin/torfjelde/new-gibbs' into torfje… 

    …lde/new-gibbs
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Commits on Jan 30, 2024

  1. relax atol for a numerical test with Gibbs a bit

    @torfjelde
    torfjelde committed Jan 30, 2024
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Commits on Feb 27, 2024

  1. Merge branch 'master' into torfjelde/new-gibbs

    @yebai
    yebai authored Feb 27, 2024
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Commits on Mar 10, 2024

  1. Merge branch 'master' into torfjelde/new-gibbs

    @torfjelde
    torfjelde committed Mar 10, 2024
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  2. fixed bug with AbstractDict constructor for experimental Gibbs

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    torfjelde committed Mar 10, 2024
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Commits on Mar 20, 2024

  1. Merge branch 'master' into torfjelde/new-gibbs

    @torfjelde
    torfjelde committed Mar 20, 2024
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Commits on Apr 15, 2024

  1. aaaalways link the varinfo in the new Gibbs sampler, just to be sure

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Commits on Apr 17, 2024

  1. add test to cover recent improvement to DynamicPPL.subset 

    ref: TuringLang/DynamicPPL.jl#587
    @torfjelde
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  2. bump compat entry for DynamicPPL

    @torfjelde
    torfjelde committed Apr 17, 2024
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  3. added some docstrings

    @torfjelde
    torfjelde committed Apr 17, 2024
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  4. fixed test

    @torfjelde
    torfjelde committed Apr 17, 2024
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  5. fixed import

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    torfjelde committed Apr 17, 2024
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  6. another attempt at fixing tests

    @torfjelde
    torfjelde committed Apr 17, 2024
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  7. another attempt at fixing tests

    @torfjelde
    torfjelde committed Apr 17, 2024
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  8. attempt at fix tests

    @torfjelde
    torfjelde committed Apr 17, 2024
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  9. forgot something in previos commit

    @torfjelde
    torfjelde committed Apr 17, 2024
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  10. cleaned up the experimental Gibbs sampler a bit

    @torfjelde
    torfjelde committed Apr 17, 2024
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  11. removed accidentaly psuedocode inclusion

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Commits on Apr 19, 2024

  1. Apply suggestions from code review

    @torfjelde
    torfjelde authored Apr 19, 2024
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Commits on Apr 20, 2024

  1. relaxed olerance in one MH test a bit

    @torfjelde
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  2. Merge remote-tracking branch 'origin/torfjelde/new-gibbs' into torfje… 

    …lde/new-gibbs
    @torfjelde
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  3. Merge branch 'master' into torfjelde/new-gibbs

    @torfjelde
    torfjelde committed Apr 20, 2024
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  4. bump patch version

    @torfjelde
    torfjelde committed Apr 20, 2024
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