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LDA implementation #1132

Merged
merged 56 commits into from
Sep 23, 2021
Merged

LDA implementation #1132

merged 56 commits into from
Sep 23, 2021

Commits on Sep 17, 2021

  1. first draft lda model and module

    @justjhong
    justjhong committed Sep 17, 2021
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  2. working sanity test

    @justjhong
    justjhong committed Sep 17, 2021
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  3. nits

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    justjhong committed Sep 17, 2021
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  4. make model and guide PyroModules

    @justjhong
    justjhong committed Sep 17, 2021
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  5. renaming, remove alpha posterior, add optional prior params, use FCLa… 

    …yers in encoder
    @justjhong
    justjhong committed Sep 17, 2021
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  6. auto move data

    @justjhong
    justjhong committed Sep 17, 2021
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  7. fix device logic

    @justjhong
    justjhong committed Sep 17, 2021
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  8. automove for encoder

    @justjhong
    justjhong committed Sep 17, 2021
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  9. add components, transform, and perplexity to mirror sklearn

    @justjhong
    justjhong committed Sep 17, 2021
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  10. scale encoder output

    @justjhong
    justjhong committed Sep 17, 2021
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  11. debug statement

    @justjhong
    justjhong committed Sep 17, 2021
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  12. softplus in encoder

    @justjhong
    justjhong committed Sep 17, 2021
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  13. log(1+x) before passing x into encoder

    @justjhong
    justjhong committed Sep 17, 2021
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  14. remove debug

    @justjhong
    justjhong committed Sep 17, 2021
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  15. fix for non np array X

    @justjhong
    justjhong committed Sep 17, 2021
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  16. get componenets returns dataframe

    @justjhong
    justjhong committed Sep 17, 2021
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  17. fix bugs in perplexity computation

    @justjhong
    justjhong committed Sep 17, 2021
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  18. add docstrings to lda

    @justjhong
    justjhong committed Sep 17, 2021
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  19. remove use of dataset

    @justjhong
    justjhong committed Sep 17, 2021
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  20. codacy

    @justjhong
    justjhong committed Sep 17, 2021
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  21. codacy fix

    @justjhong
    justjhong committed Sep 17, 2021
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  22. add plate subsampling for proper elbo computation

    @justjhong
    justjhong committed Sep 17, 2021
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  23. debug stuff

    @justjhong
    justjhong committed Sep 17, 2021
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  24. change to PyroParam

    @justjhong
    justjhong committed Sep 17, 2021
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  25. add get_elbo function

    @justjhong
    justjhong committed Sep 17, 2021
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  26. change to torch Parameter

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    justjhong committed Sep 17, 2021
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  27. try aggregating elbos

    @justjhong
    justjhong committed Sep 17, 2021
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  28. fix prior assignment

    @justjhong
    justjhong committed Sep 17, 2021
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  29. categorical bow and scale based on input size

    @justjhong
    justjhong committed Sep 17, 2021
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  30. remove sklearn implementations

    @justjhong
    justjhong committed Sep 17, 2021
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  31. add docstrings

    @justjhong
    justjhong committed Sep 17, 2021
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  32. fix test

    @justjhong
    justjhong committed Sep 17, 2021
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  33. address comments

    @justjhong
    justjhong committed Sep 17, 2021
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  34. save load test

    @justjhong
    justjhong committed Sep 17, 2021
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  35. add layer to encoder

    @justjhong
    justjhong committed Sep 17, 2021
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  36. clamp dirichlet parameters

    @justjhong
    justjhong committed Sep 17, 2021
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  37. add kl annealing

    @justjhong
    justjhong committed Sep 17, 2021
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  38. minor fixes

    @justjhong
    justjhong committed Sep 17, 2021
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  39. fix tests

    @justjhong
    justjhong committed Sep 17, 2021
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  40. change topic gene dist to use MAP inference

    @justjhong
    justjhong committed Sep 17, 2021
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  41. fix event dim

    @justjhong
    justjhong committed Sep 17, 2021
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  42. fix softmax dim

    @justjhong
    justjhong committed Sep 17, 2021
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  43. fix dtypes

    @justjhong
    justjhong committed Sep 17, 2021
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  44. switch to logistic normal

    @justjhong
    justjhong committed Sep 17, 2021
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  45. softplus variances

    @justjhong
    justjhong committed Sep 17, 2021
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  46. remove unnecessary softplus

    @justjhong
    justjhong committed Sep 17, 2021
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Commits on Sep 20, 2021

  1. add note about progress bar elbo

    @justjhong
    justjhong committed Sep 20, 2021
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  2. factor out kl weight logic

    @justjhong
    justjhong committed Sep 20, 2021
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  3. do not anneal emprical sample statement

    @justjhong
    justjhong committed Sep 20, 2021
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  4. add lda to api docs

    @justjhong
    justjhong committed Sep 20, 2021
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  5. add blei reference

    @justjhong
    justjhong committed Sep 20, 2021
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  6. improve api docs

    @justjhong
    justjhong committed Sep 20, 2021
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  7. rename to amortized lda

    @justjhong
    justjhong committed Sep 20, 2021
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Commits on Sep 21, 2021

  1. move check if trained to base

    @justjhong
    justjhong committed Sep 21, 2021
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Commits on Sep 22, 2021

  1. missing param doc

    @justjhong
    justjhong committed Sep 22, 2021
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Commits on Sep 23, 2021

  1. add docstring

    @justjhong
    justjhong committed Sep 23, 2021
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