Skip to content
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

Census cell similarity search: experimental Python API for metadata prediction #1115

Open
mlin opened this issue Apr 25, 2024 · 0 comments
Open

Census cell similarity search: experimental Python API for metadata prediction #1115

mlin opened this issue Apr 25, 2024 · 0 comments
Assignees
@mlin
Labels
P0 Priority 0 - Critical, fix ASAP!

Comments

@mlin
Copy link
Contributor

mlin commented Apr 25, 2024

Building on #1114, add another API method that predicts metadata attributes of the query cells based on the similar cells. The first pass can simply be a plurality vote of similar cells, with the vote share as the confidence score. In the future we can weight by distance or do other fancier modelling.
@mlin mlin self-assigned this Apr 25, 2024
@mlin mlin mentioned this issue Apr 25, 2024
Open
@metakuni metakuni transferred this issue from chanzuckerberg/single-cell Apr 28, 2024
@metakuni metakuni added the P0 Priority 0 - Critical, fix ASAP! label Apr 28, 2024
@mlin mlin mentioned this issue Jun 10, 2024
Merged
mlin added a commit that referenced this issue Aug 8, 2024
@mlin
Embeddings search experimental API (#1164)
6cf1f8a 
Adds two new functions to `cellxgene_census.experimental`:

1. `find_nearest_obs` uses TileDB-Vector-Search indexes of Census embeddings to find nearest neighbors of given embedding vectors (in an AnnData obsm layer). #1114
2. `predict_obs_metadata` uses the nearest neighbors to predict metadata attributes like cell_type and tissue_general for the query cells. Naive implementation is just a starting point to start experimenting with. #1115
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@mlin mlin

Labels
P0 Priority 0 - Critical, fix ASAP!
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@mlin @metakuni