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feat(models): add k-NN model #649

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feat(models): add k-NN model #649

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@AlexanderAivazidis
added atac_layer argument to train_model tasks and made tests for it
b4c100f
@AlexanderAivazidis
fix(vscode): disable automatic python env activation
c1ee5cb
@AlexanderAivazidis
corrected ATAC argument type from layer name to anndata object
f8d04f3
@AlexanderAivazidis
feat[PyroVelocity]: added atac_data to setup_anndata method
c83e065
@AlexanderAivazidis
fix[PyroVelocity]: missing colon in Args description
8661a36 
Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
feat(VelocityTrainingMixin): Added atac data to train_faster method
c643465 
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>
@AlexanderAivazidis
feat(_velocity_module): Added a MultiVelocityModule for multiome data.
b0ce0f9 
Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
feat(_velocity_model): Added a MultiVelocityModelAuto class for multi…
2abf5ec 
…ome data

Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
feat(_transcription_dynamics): Added function for multiome dynamics.
7b9c355 
Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
feat(_test_transcription_dynamics): Unit tests for transcription dyna…
6955c46 
…mics functions.

Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
feat(_test_velocity_model): Unit tests for velocity model
db8cbb1 
Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
feat(.gitignore): Added example_notebooks directory to .gitignore file.
b708935 
Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
fix[_trainer_]: checking for existence of atac data
7c7c73b 
Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
fix(_velocity): Save existence of atac data in adata
e383388 
Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
fix(_velocity_model): LogNormal instead of Normal likelihood for atac…
fc9be1a 
… data

Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
fix(_trainer.py): Properly processing atac data
94569f8
@AlexanderAivazidis
fix(_transcription_dynamics): Ensuring no inplace tensor operations i…
750be4a 
…n functions.

Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
fix(_velocity): Handling atac data.
a2628d4 
Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
fix(_velocity_module): Removed rates from multivariateNormalGuide, be…
ec34568 
…cause they caused dimension errors during posterior sampling.

Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
fix(train): Ensure atac data is handled properly.
085d7ac 
Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
feat(_transcription_dynamics): Added latent discrete parameter for mo…
fbd06a8 
…delling stochastic gene activation.

Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
feat(_velocity_model): Sampling latent discrete parameter for modelli…
113c3a4 
…ng stochastic gene activation.

Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
feat(_test_transcription_dynamics): Adapted test to include latent di…
40581dc 
…screte parameter for gene state.

Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
feat(_models): Initial commit for new knn_model.
c90af64 
Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
feat(preprocess.py): Added function for computation of metacells.
211d9b5 
Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
feat(tests): Added function to produce synthetic AnnData.
73b1b87 
Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
feat(tests): Added test for compute_metacell function.
725a0bd 
Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
feat(tests): Added test for synthetic_AnnData function.
a5f31df 
Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
feat(models): Started knn model in a new folder.
58a48e9 
Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis AlexanderAivazidis added the enhancement New feature or request label Aug 26, 2024
@AlexanderAivazidis AlexanderAivazidis added the python Pull requests that update Python code label Aug 26, 2024
@AlexanderAivazidis AlexanderAivazidis self-assigned this Aug 26, 2024
@AlexanderAivazidis AlexanderAivazidis requested a review from a team as a code owner August 26, 2024 21:35
@AlexanderAivazidis AlexanderAivazidis changed the base branch from main to beta August 26, 2024 22:29
@cameronraysmith cameronraysmith added this to the 0.4.x milestone Aug 27, 2024
@cameronraysmith cameronraysmith changed the title Knn model feat(models): add k-NN model Aug 27, 2024
cameronraysmith

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@cameronraysmith cameronraysmith marked this pull request as draft August 27, 2024 20:23
@AlexanderAivazidis
feat(knn_model): Basic vector field for knn_model.
75f8196 
Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
feat(knn_model): Basic regulatory function, using 2 layer neural net,…
3c840cb 
… for knn model.

Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
feat(knn_model): Initial commit for pyro model for knn model.
fbca112 
Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
feat(train.py): resolved merge conflict by keeping change proposed in…
33aae38 
… beta branch.

Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
fix(preprocess): Added spliced/unspliced count aggregation to metacells.
ae19b05 
Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
fix(regulatory_function_1): needs numpy import
567f700 
Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
fix(preprocess): need to return sparse matrix in layers after metacel…
8586e15 
…l construction

Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
fix(knn_model._velocity): Fixed various bugs in imports.
5628463 
Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
feat(knn_model._velocity_model): Completed first draft of the model.
f34d7c5 
Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
fix(_velocity_module): Fixed various imports.
3963a4d 
Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
feat(regulatory_function_1): Adapted function to deal with more than …
a2e301e 
…one cell at a time.

Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
feat(knn_model): Added init file
a69fda0 
Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
feat(knn_model): Completed first version of knn_model that trains wit…
39da15c 
…hout errors.

Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
fix(_velocity): Provide number of cells in each metacell to model.
e5a715b 
Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
fix(_velocity_model): Various fixes to model architecture.
f51a3dd 
Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
feat(_velocity_module): Provide number of cells in each metacell to m…
46cb17d 
…odel.

Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
fix(compute_metacell): copying over var_names
9fec683 
Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
@AlexanderAivazidis
feat(velocity_model): changed neural networks to be similar to cellda…
bba3a2f 
…ncer

Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>
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@cameronraysmith cameronraysmith cameronraysmith requested changes

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