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

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AlexanderAivazidis wants to merge 47 commits intobetapinellolab/pyrovelocity:betafrom knn_modelpinellolab/pyrovelocity:knn_modelCopy head branch name to clipboard

+3,477-94

Commits

Commits on Aug 26, 2024

• added atac_layer argument to train_model tasks and made tests for it

  AlexanderAivazidis

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  b4c100f

• fix(vscode): disable automatic python env activation

  AlexanderAivazidis

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• corrected ATAC argument type from layer name to anndata object

  AlexanderAivazidis

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• feat[PyroVelocity]: added atac_data to setup_anndata method

  AlexanderAivazidis

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• fix[PyroVelocity]: missing colon in Args description

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  AlexanderAivazidis

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  8661a36

• feat(VelocityTrainingMixin): Added atac data to train_faster method

  Show description for c643465
  AlexanderAivazidis

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  c643465

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

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  AlexanderAivazidis

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  b0ce0f9

• feat(_velocity_model): Added a MultiVelocityModelAuto class for multiome data

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  AlexanderAivazidis

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• feat(_transcription_dynamics): Added function for multiome dynamics.

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  AlexanderAivazidis

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• feat(_test_transcription_dynamics): Unit tests for transcription dynamics functions.

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  AlexanderAivazidis

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• feat(_test_velocity_model): Unit tests for velocity model

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  AlexanderAivazidis

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• feat(.gitignore): Added example_notebooks directory to .gitignore file.

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  AlexanderAivazidis

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• fix[_trainer_]: checking for existence of atac data

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  AlexanderAivazidis

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• fix(_velocity): Save existence of atac data in adata

  Show description for e383388
  AlexanderAivazidis

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• fix(_velocity_model): LogNormal instead of Normal likelihood for atac data

  Show description for fc9be1a
  AlexanderAivazidis

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  fc9be1a

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

  AlexanderAivazidis

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• fix(_transcription_dynamics): Ensuring no inplace tensor operations in functions.

  Show description for 750be4a
  AlexanderAivazidis

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  750be4a

• fix(_velocity): Handling atac data.

  Show description for a2628d4
  AlexanderAivazidis

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• fix(_velocity_module): Removed rates from multivariateNormalGuide, because they caused dimension errors during posterior sampling.

  Show description for ec34568
  AlexanderAivazidis

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  ec34568

• fix(train): Ensure atac data is handled properly.

  Show description for 085d7ac
  AlexanderAivazidis

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• feat(_transcription_dynamics): Added latent discrete parameter for modelling stochastic gene activation.

  Show description for fbd06a8
  AlexanderAivazidis

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  fbd06a8

• feat(_velocity_model): Sampling latent discrete parameter for modelling stochastic gene activation.

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  AlexanderAivazidis

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• feat(_test_transcription_dynamics): Adapted test to include latent discrete parameter for gene state.

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  AlexanderAivazidis

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  40581dc

• feat(_models): Initial commit for new knn_model.

  Show description for c90af64
  AlexanderAivazidis

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• feat(preprocess.py): Added function for computation of metacells.

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  AlexanderAivazidis

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• feat(tests): Added function to produce synthetic AnnData.

  Show description for 73b1b87
  AlexanderAivazidis

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• feat(tests): Added test for compute_metacell function.

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  AlexanderAivazidis

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• feat(tests): Added test for synthetic_AnnData function.

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  AlexanderAivazidis

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• feat(models): Started knn model in a new folder.

  Show description for 58a48e9
  AlexanderAivazidis

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  58a48e9

Commits on Aug 29, 2024

• feat(knn_model): Basic vector field for knn_model.

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  AlexanderAivazidis

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• feat(knn_model): Basic regulatory function, using 2 layer neural net, for knn model.

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  AlexanderAivazidis

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• feat(knn_model): Initial commit for pyro model for knn model.

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  AlexanderAivazidis

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Commits on Sep 3, 2024

• feat(train.py): resolved merge conflict by keeping change proposed in beta branch.

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  AlexanderAivazidis

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• fix(preprocess): Added spliced/unspliced count aggregation to metacells.

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  AlexanderAivazidis

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• fix(regulatory_function_1): needs numpy import

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  AlexanderAivazidis

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  567f700

• fix(preprocess): need to return sparse matrix in layers after metacell construction

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  AlexanderAivazidis

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  8586e15

Commits on Sep 5, 2024

• fix(knn_model._velocity): Fixed various bugs in imports.

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  AlexanderAivazidis

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  5628463

• feat(knn_model._velocity_model): Completed first draft of the model.

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  AlexanderAivazidis

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• fix(_velocity_module): Fixed various imports.

  Show description for 3963a4d
  AlexanderAivazidis

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• feat(regulatory_function_1): Adapted function to deal with more than one cell at a time.

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  AlexanderAivazidis

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• feat(knn_model): Added init file

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  AlexanderAivazidis

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Commits on Sep 6, 2024

• feat(knn_model): Completed first version of knn_model that trains without errors.

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  AlexanderAivazidis

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  39da15c

Commits on Sep 13, 2024

• fix(_velocity): Provide number of cells in each metacell to model.

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  AlexanderAivazidis

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  e5a715b

• fix(_velocity_model): Various fixes to model architecture.

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  AlexanderAivazidis

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• feat(_velocity_module): Provide number of cells in each metacell to model.

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  AlexanderAivazidis

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• fix(compute_metacell): copying over var_names

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  AlexanderAivazidis

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• feat(velocity_model): changed neural networks to be similar to celldancer

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  AlexanderAivazidis

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