Novelty Score Calculation Update #30
Merged
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
Updated novelty score calcualtions including integrations of: 1. Clinical Trials/ Clinical Approvals - MVP1 2. TDLs - MVP2 3. Gene Distinctiveness - MVP2
maximusunc
requested changes
Sep 27, 2024
Removed local imports from files and transferred functions from the files to compute_novelty.py
Due to code import in compute_novelty.py, removed files: known.py, molecular_similarity.py, extr_smile_molpro_by_id.py
Removed commented code from compute_novelty.py
Switched error cases to include 0s instead of "NAN" ion the Dataframe.
Redis is implemented in the function get_publication_info to compute recency score at a much faster rate.
Used updated links to produce SMILEs for Molecular similarity computation in lesser time.
This was referenced Nov 20, 2024
Closed
maximusunc
requested changes
Nov 20, 2024
Collaborator
maximusunc
left a comment
maximusunc
left a comment
There was a problem hiding this comment.
- Please remove the
.ideafolder from this PR, and add it to the.gitignore. - This repo also uses black, which is why one of the CI/CD checks is failing. This auto-formats all the code and makes sure that it is formatted to a certain standard. I would get all your other commits in order and then run this, which will make many many updates and then you can commit all these black changes together.
Removed commented lines of code Removed system path lines Updated code to remove depreciation issues Removed chk_gene_nmf.py Updated code to look for publications in all applicable locations for all ARAs
maximusunc
requested changes
Nov 20, 2024
Collaborator
maximusunc
left a comment
maximusunc
left a comment
There was a problem hiding this comment.
The code no longer works "as is". All of the existing imports that have to do with gene_nmf and dcc need to be changed to relative imports.
maximusunc
reviewed
Nov 20, 2024
maximusunc
approved these changes
Nov 22, 2024
Collaborator
maximusunc
left a comment
maximusunc
left a comment
There was a problem hiding this comment.
Looks good! Thanks for all your work @pg427 !!
This was referenced Nov 22, 2024
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
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.
Updated novelty score calcualtions including integrations of: