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feat(train_model): add atac layer argument #542

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feat(train_model): add atac layer argument #542

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Commits on Jul 15, 2024

  1. added atac_layer argument to train_model tasks and made tests for it

    @AlexanderAivazidis
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  2. fix(vscode): disable automatic python env activation

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    AlexanderAivazidis committed Jul 15, 2024
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  3. corrected ATAC argument type from layer name to anndata object

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    AlexanderAivazidis committed Jul 15, 2024
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  4. feat[PyroVelocity]: added atac_data to setup_anndata method

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    AlexanderAivazidis committed Jul 15, 2024
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  5. fix[PyroVelocity]: missing colon in Args description 

    Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
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  6. feat(VelocityTrainingMixin): Added atac data to train_faster method 

    In the long run  we should refactor code, so that training uses
scvi-tools modules.

Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
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    AlexanderAivazidis committed Jul 15, 2024
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Commits on Jul 22, 2024

  1. feat(_velocity_module): Added a MultiVelocityModule for multiome data. 

    Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
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    AlexanderAivazidis committed Jul 22, 2024
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  2. feat(_velocity_model): Added a MultiVelocityModelAuto class for multi… 

    …ome data

Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
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    AlexanderAivazidis committed Jul 22, 2024
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  3. feat(_transcription_dynamics): Added function for multiome dynamics. 

    Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
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    AlexanderAivazidis committed Jul 22, 2024
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  4. feat(_test_transcription_dynamics): Unit tests for transcription dyna… 

    …mics functions.

Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
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    AlexanderAivazidis committed Jul 22, 2024
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  5. feat(_test_velocity_model): Unit tests for velocity model 

    Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
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    AlexanderAivazidis committed Jul 22, 2024
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  6. feat(.gitignore): Added example_notebooks directory to .gitignore file. 

    Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
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    AlexanderAivazidis committed Jul 22, 2024
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  7. fix[_trainer_]: checking for existence of atac data 

    Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
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    AlexanderAivazidis committed Jul 22, 2024
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  8. fix(_velocity): Save existence of atac data in adata 

    Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
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    AlexanderAivazidis committed Jul 22, 2024
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  9. fix(_velocity_model): LogNormal instead of Normal likelihood for atac… 

    … data

Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
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    AlexanderAivazidis committed Jul 22, 2024
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Commits on Jul 26, 2024

  1. fix(_trainer.py): Properly processing atac data

    @AlexanderAivazidis
    AlexanderAivazidis committed Jul 26, 2024
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  2. fix(_transcription_dynamics): Ensuring no inplace tensor operations i… 

    …n functions.

Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
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    AlexanderAivazidis committed Jul 26, 2024
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  3. fix(_velocity): Handling atac data. 

    Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
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    AlexanderAivazidis committed Jul 26, 2024
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  4. fix(_velocity_module): Removed rates from multivariateNormalGuide, be… 

    …cause they caused dimension errors during posterior sampling.

Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
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  5. fix(train): Ensure atac data is handled properly. 

    Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
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    AlexanderAivazidis committed Jul 26, 2024
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  6. feat(_transcription_dynamics): Added latent discrete parameter for mo… 

    …delling stochastic gene activation.

Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
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  7. feat(_velocity_model): Sampling latent discrete parameter for modelli… 

    …ng stochastic gene activation.

Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
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  8. feat(_test_transcription_dynamics): Adapted test to include latent di… 

    …screte parameter for gene state.

Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
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    AlexanderAivazidis committed Jul 26, 2024
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