Code

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

Code

Draft

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

  committed
  b4c100f

  Copy full SHA for b4c100f

• fix(vscode): disable automatic python env activation

  AlexanderAivazidis

  committed
  c1ee5cb

  Copy full SHA for c1ee5cb

• corrected ATAC argument type from layer name to anndata object

  AlexanderAivazidis

  committed
  f8d04f3

  Copy full SHA for f8d04f3

• feat[PyroVelocity]: added atac_data to setup_anndata method

  AlexanderAivazidis

  committed
  c83e065

  Copy full SHA for c83e065

• fix[PyroVelocity]: missing colon in Args description

  Show description for 8661a36
  AlexanderAivazidis

  committed
  8661a36

  Copy full SHA for 8661a36

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

  Show description for c643465
  AlexanderAivazidis

  committed
  c643465

  Copy full SHA for c643465

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

  Show description for b0ce0f9
  AlexanderAivazidis

  committed
  b0ce0f9

  Copy full SHA for b0ce0f9

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

  Show description for 2abf5ec
  AlexanderAivazidis

  committed
  2abf5ec

  Copy full SHA for 2abf5ec

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

  Show description for 7b9c355
  AlexanderAivazidis

  committed
  7b9c355

  Copy full SHA for 7b9c355

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

  Show description for 6955c46
  AlexanderAivazidis

  committed
  6955c46

  Copy full SHA for 6955c46

• feat(_test_velocity_model): Unit tests for velocity model

  Show description for db8cbb1
  AlexanderAivazidis

  committed
  db8cbb1

  Copy full SHA for db8cbb1

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

  Show description for b708935
  AlexanderAivazidis

  committed
  b708935

  Copy full SHA for b708935

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

  Show description for 7c7c73b
  AlexanderAivazidis

  committed
  7c7c73b

  Copy full SHA for 7c7c73b

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

  Show description for e383388
  AlexanderAivazidis

  committed
  e383388

  Copy full SHA for e383388

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

  Show description for fc9be1a
  AlexanderAivazidis

  committed
  fc9be1a

  Copy full SHA for fc9be1a

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

  AlexanderAivazidis

  committed
  94569f8

  Copy full SHA for 94569f8

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

  Show description for 750be4a
  AlexanderAivazidis

  committed
  750be4a

  Copy full SHA for 750be4a

• fix(_velocity): Handling atac data.

  Show description for a2628d4
  AlexanderAivazidis

  committed
  a2628d4

  Copy full SHA for a2628d4

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

  Show description for ec34568
  AlexanderAivazidis

  committed
  ec34568

  Copy full SHA for ec34568

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

  Show description for 085d7ac
  AlexanderAivazidis

  committed
  085d7ac

  Copy full SHA for 085d7ac

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

  Show description for fbd06a8
  AlexanderAivazidis

  committed
  fbd06a8

  Copy full SHA for fbd06a8

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

  Show description for 113c3a4
  AlexanderAivazidis

  committed
  113c3a4

  Copy full SHA for 113c3a4

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

  Show description for 40581dc
  AlexanderAivazidis

  committed
  40581dc

  Copy full SHA for 40581dc

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

  Show description for c90af64
  AlexanderAivazidis

  committed
  c90af64

  Copy full SHA for c90af64

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

  Show description for 211d9b5
  AlexanderAivazidis

  committed
  211d9b5

  Copy full SHA for 211d9b5

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

  Show description for 73b1b87
  AlexanderAivazidis

  committed
  73b1b87

  Copy full SHA for 73b1b87

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

  Show description for 725a0bd
  AlexanderAivazidis

  committed
  725a0bd

  Copy full SHA for 725a0bd

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

  Show description for a5f31df
  AlexanderAivazidis

  committed
  a5f31df

  Copy full SHA for a5f31df

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

  Show description for 58a48e9
  AlexanderAivazidis

  committed
  58a48e9

  Copy full SHA for 58a48e9

Commits on Aug 29, 2024

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

  Show description for 75f8196
  AlexanderAivazidis

  committed
  75f8196

  Copy full SHA for 75f8196

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

  Show description for 3c840cb
  AlexanderAivazidis

  committed
  3c840cb

  Copy full SHA for 3c840cb

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

  Show description for fbca112
  AlexanderAivazidis

  committed
  fbca112

  Copy full SHA for fbca112

Commits on Sep 3, 2024

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

  Show description for 33aae38
  AlexanderAivazidis

  committed
  33aae38

  Copy full SHA for 33aae38

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

  Show description for ae19b05
  AlexanderAivazidis

  committed
  ae19b05

  Copy full SHA for ae19b05

• fix(regulatory_function_1): needs numpy import

  Show description for 567f700
  AlexanderAivazidis

  committed
  567f700

  Copy full SHA for 567f700

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

  Show description for 8586e15
  AlexanderAivazidis

  committed
  8586e15

  Copy full SHA for 8586e15

Commits on Sep 5, 2024

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

  Show description for 5628463
  AlexanderAivazidis

  committed
  5628463

  Copy full SHA for 5628463

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

  Show description for f34d7c5
  AlexanderAivazidis

  committed
  f34d7c5

  Copy full SHA for f34d7c5

• fix(_velocity_module): Fixed various imports.

  Show description for 3963a4d
  AlexanderAivazidis

  committed
  3963a4d

  Copy full SHA for 3963a4d

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

  Show description for a2e301e
  AlexanderAivazidis

  committed
  a2e301e

  Copy full SHA for a2e301e

• feat(knn_model): Added init file

  Show description for a69fda0
  AlexanderAivazidis

  committed
  a69fda0

  Copy full SHA for a69fda0

Commits on Sep 6, 2024

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

  Show description for 39da15c
  AlexanderAivazidis

  committed
  39da15c

  Copy full SHA for 39da15c

Commits on Sep 13, 2024

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

  Show description for e5a715b
  AlexanderAivazidis

  committed
  e5a715b

  Copy full SHA for e5a715b

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

  Show description for f51a3dd
  AlexanderAivazidis

  committed
  f51a3dd

  Copy full SHA for f51a3dd

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

  Show description for 46cb17d
  AlexanderAivazidis

  committed
  46cb17d

  Copy full SHA for 46cb17d

• fix(compute_metacell): copying over var_names

  Show description for 9fec683
  AlexanderAivazidis

  committed
  9fec683

  Copy full SHA for 9fec683

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

  Show description for bba3a2f
  AlexanderAivazidis

  committed
  bba3a2f

  Copy full SHA for bba3a2f