New metric: ksim #75
Open
New metric: ksim #75
+111
−0
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
rcannood
reviewed
Aug 20, 2025
Co-authored-by: Robrecht Cannoodt <[email protected]>
…h_integration into features/ksim
|
@mumichae it's good to go! Please check out whenever you have time :) |
mumichae
commented
Sep 24, 2025
src/metrics/ksim/config.vsh.yaml
Outdated
| label: kSIM | ||
| summary: "The kSIM acceptance rate measures whether cells of the same pre-annotated cell type are still close to each other in the local neighborhoods after batch correction." | ||
| description: | | ||
| The kSIM acceptance rate requires ground truth cell type information and measures whether the neighbors of a cell have the same cell type as it does. If a method overcorrects the batch effects, it will have a low kSIM acceptance rate. We use the HNSW algorithm to find k-NNs (including the cell itself) for each cell i and denote the number of neighbors that have the same cell type as i as . In addition, we require at least β fraction of neighbors of cell i to have the same cell type as i in order to say cell i has a consistent neighborhood. |
There was a problem hiding this comment.
Could you rephrase in your own words? Also, parameters don't make much sense when the formula isn't included. You could rephrase in such a way that the formula isn't needed to understand the metric
There was a problem hiding this comment.
Could you please rephrase the use of "we", since refers to the study authors, not the Openproblems team. Passive voice would be the best here.
mumichae
commented
Sep 25, 2025
|
|
||
| * Added `metrics/kbet_pg` and `metrics/kbet_pg_label` components (PR #52). | ||
|
|
||
| * Added `metircs/ksim` component (PR #75). |
There was a problem hiding this comment.
Suggested change
| * Added `metircs/ksim` component (PR #75). | |
| * Added `metrics/ksim` component (PR #75). |
src/metrics/ksim/config.vsh.yaml
Outdated
| label: kSIM | ||
| summary: "The kSIM acceptance rate measures whether cells of the same pre-annotated cell type are still close to each other in the local neighborhoods after batch correction." | ||
| description: | | ||
| The kSIM acceptance rate requires ground truth cell type information and measures whether the neighbors of a cell have the same cell type as it does. If a method overcorrects the batch effects, it will have a low kSIM acceptance rate. We use the HNSW algorithm to find k-NNs (including the cell itself) for each cell i and denote the number of neighbors that have the same cell type as i as . In addition, we require at least β fraction of neighbors of cell i to have the same cell type as i in order to say cell i has a consistent neighborhood. |
There was a problem hiding this comment.
Could you please rephrase the use of "we", since refers to the study authors, not the Openproblems team. Passive voice would be the best here.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Describe your changes
Checklist before requesting a review
I have performed a self-review of my code
Check the correct box. Does this PR contain:
Proposed changes are described in the CHANGELOG.md
CI Tests succeed and look good!