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Adding model with cycle consistency and VampPrior #2421

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Adding model with cycle consistency and VampPrior #2421

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Commits on Jan 14, 2024

  1. add model and tests

    @Hrovatin
    Hrovatin committed Jan 14, 2024
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  2. update documentation

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  3. move embedding to device

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Commits on Jan 19, 2024

  1. Merge branch 'main' into main

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Commits on Jan 21, 2024

  1. pr comments

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  2. Merge branch 'main' of https://github.com/Hrovatin/scvi-tools

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Commits on Jan 22, 2024

  1. Merge branch 'main' into main

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Commits on Feb 5, 2024

  1. Merge branch 'main' into main

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Commits on Feb 7, 2024

  1. updates

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  2. Merge branch 'main' of https://github.com/Hrovatin/scvi-tools

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Commits on Feb 20, 2024

  1. Merge branch 'main' into main

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Commits on Mar 11, 2024

  1. Merge branch 'main' into main

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Commits on Mar 15, 2024

  1. Update scvi/external/sysvi/_base_components.py

    @martinkim0
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  2. Update scvi/external/sysvi/_base_components.py

    @martinkim0
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  3. Update scvi/external/sysvi/_base_components.py

    @martinkim0
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  4. Update scvi/external/sysvi/_model.py

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  5. Update scvi/external/sysvi/_model.py

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  6. Update scvi/external/sysvi/_model.py

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  7. Update scvi/external/sysvi/_model.py

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  8. Update scvi/external/sysvi/_model.py

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  9. Update scvi/external/sysvi/_model.py

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  10. Update scvi/external/sysvi/_model.py

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Commits on Sep 14, 2024

  1. merge

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  3. merge

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  4. Merge branch 'main' of https://github.com/Hrovatin/scvi-tools

    @Hrovatin
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  5. merge

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  6. extend var documentation and remove unused "linear" mode

    @Hrovatin
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  7. update var documentation

    @Hrovatin
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  9. var activation to softplus

    @Hrovatin
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  10. clarify pseudoinputs_data_indices description and assert it matches s… 

    …pecified n_prior_components number
    @Hrovatin
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  11. also check ndim for pseudoinputs_data_indices

    @Hrovatin
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  12. remove obtainng cycle latent representations in user interface

    @Hrovatin
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  13. latent always returns np and add option to return_dist

    @Hrovatin
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  14. bugfix

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  15. rm unused cycle latent retrieval

    @Hrovatin
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  16. bugfix

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  17. rm adata validation parts repeated in super

    @Hrovatin
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  18. bugfix

    @Hrovatin
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  19. put back original _validate_anndata

    @Hrovatin
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  20. remove too many custom checks from adata validation

    @Hrovatin
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  21. covariate type explanation

    @Hrovatin
    Hrovatin committed Sep 14, 2024
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  22. revert var exp

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  23. bugfix

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  24. rm reconstr loss f that not reused

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  25. explain why cycle loss computed on standardized values

    @Hrovatin
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  26. add return statement

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  27. Merge branch 'main' of https://github.com/Hrovatin/scvi-tools

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Commits on Oct 19, 2024

  1. Merge branch 'main' of https://github.com/scverse/scvi-tools

    @Hrovatin
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Commits on Oct 20, 2024

  1. unify SysVI with scvi-tools code

    @Hrovatin
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Commits on Oct 26, 2024

  1. use adatamanager to access filed statistics

    @Hrovatin
    Hrovatin committed Oct 26, 2024
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  2. documentation

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    Hrovatin committed Oct 26, 2024
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  3. Merge branch 'main' of https://github.com/Hrovatin/scvi-tools

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Commits on Oct 27, 2024

  1. optionally change var activation function

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  3. documentation improvements

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  4. Use real instead of mock covariates in cycle 

    For code simplicity the use of mock covariates was replaced with real covariates in cycle. Needs testing on real data.
    @Hrovatin
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  5. improve documentation

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  6. Merge branch 'main' of https://github.com/Hrovatin/scvi-tools

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  8. improve documentation

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  9. fix bug introduced when renaming parameters in generative function

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  10. Merge branch 'main' of https://github.com/Hrovatin/scvi-tools

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  12. rename tests to prevent automatic test failure

    @Hrovatin
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  13. Merge branch 'main' of https://github.com/Hrovatin/scvi-tools

    @Hrovatin
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  14. fix typo in docstring and formatting

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    Hrovatin committed Oct 27, 2024
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  15. ruff fixes

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Commits on Nov 1, 2024

  1. bugfix in embedding of covariates

    @Hrovatin
    Hrovatin committed Nov 1, 2024
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  2. bugfix in test for checking cov embeding

    @Hrovatin
    Hrovatin committed Nov 1, 2024
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Commits on Nov 19, 2024

  1. Change var activation to softplus

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