Skip to content

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

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Draft
wants to merge 47 commits into
base: beta
Choose a base branch
from
Draft

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

wants to merge 47 commits into from

Conversation

@AlexanderAivazidis
Copy link

@AlexanderAivazidis AlexanderAivazidis commented Aug 26, 2024

No description provided.

@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 <[email protected]>
@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 <[email protected]>
@AlexanderAivazidis
feat(_velocity_module): Added a MultiVelocityModule for multiome data.
b0ce0f9 
Signed-off-by: Alexander Aivazidis <[email protected]>
@AlexanderAivazidis
feat(_velocity_model): Added a MultiVelocityModelAuto class for multi…
2abf5ec 
…ome data

Signed-off-by: Alexander Aivazidis <[email protected]>
@AlexanderAivazidis
feat(_transcription_dynamics): Added function for multiome dynamics.
7b9c355 
Signed-off-by: Alexander Aivazidis <[email protected]>
@AlexanderAivazidis
feat(_test_transcription_dynamics): Unit tests for transcription dyna…
6955c46 
…mics functions.

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

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

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

Signed-off-by: Alexander Aivazidis <[email protected]>
@AlexanderAivazidis
feat(_velocity_model): Sampling latent discrete parameter for modelli…
113c3a4 
…ng stochastic gene activation.

Signed-off-by: Alexander Aivazidis <[email protected]>
@AlexanderAivazidis
feat(_test_transcription_dynamics): Adapted test to include latent di…
40581dc 
…screte parameter for gene state.

Signed-off-by: Alexander Aivazidis <[email protected]>
@AlexanderAivazidis
feat(_models): Initial commit for new knn_model.
c90af64 
Signed-off-by: Alexander Aivazidis <[email protected]>
@AlexanderAivazidis
feat(preprocess.py): Added function for computation of metacells.
211d9b5 
Signed-off-by: Alexander Aivazidis <[email protected]>
@AlexanderAivazidis
feat(tests): Added function to produce synthetic AnnData.
73b1b87 
Signed-off-by: Alexander Aivazidis <[email protected]>
@AlexanderAivazidis
feat(tests): Added test for compute_metacell function.
725a0bd 
Signed-off-by: Alexander Aivazidis <[email protected]>
@AlexanderAivazidis
feat(tests): Added test for synthetic_AnnData function.
a5f31df 
Signed-off-by: Alexander Aivazidis <[email protected]>
@AlexanderAivazidis
feat(models): Started knn model in a new folder.
58a48e9 
Signed-off-by: Alexander Aivazidis <[email protected]>
@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

This comment was marked as outdated.

Sign in to view

@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 <[email protected]>
@AlexanderAivazidis
feat(knn_model): Basic regulatory function, using 2 layer neural net,…
3c840cb 
… for knn model.

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

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

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

Signed-off-by: Alexander Aivazidis <[email protected]>
@AlexanderAivazidis
feat(knn_model): Added init file
a69fda0 
Signed-off-by: Alexander Aivazidis <[email protected]>
@AlexanderAivazidis
feat(knn_model): Completed first version of knn_model that trains wit…
39da15c 
…hout errors.

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

Signed-off-by: Alexander Aivazidis <[email protected]>
@AlexanderAivazidis
fix(compute_metacell): copying over var_names
9fec683 
Signed-off-by: Alexander Aivazidis <[email protected]>
@AlexanderAivazidis
feat(velocity_model): changed neural networks to be similar to cellda…
bba3a2f 
…ncer

Signed-off-by: Alexander Aivazidis <[email protected]>
@cameronraysmith cameronraysmith modified the milestones: 0.4.x, 0.5.x Mar 20, 2025
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@cameronraysmith cameronraysmith cameronraysmith requested changes

Assignees

@AlexanderAivazidis AlexanderAivazidis

Labels

enhancement New feature or request python Pull requests that update Python code

Projects

None yet

Milestone

0.5.x

Development

Successfully merging this pull request may close these issues.

3 participants

@AlexanderAivazidis @cameronraysmith