Skip to content

feat: ROBUST #240

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.

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

Open
wants to merge 12 commits into
base: main
Choose a base branch
from
Open

feat: ROBUST #240

wants to merge 12 commits into from

Conversation

tristan-f-r
Copy link
Collaborator

@tristan-f-r tristan-f-r commented May 28, 2025

Closes #109. ROBUST has only one quirk and was a straightforward integration.

ROBUST does come with a way to automatically derive scores from preset databases, but we should probably let SPRAS handle that instead. (@ntalluri namely, I think leaving out namespace and the non-file study-bias-score params is okay, but I would love to know if this is okay to do.)

@tristan-f-r tristan-f-r marked this pull request as draft May 28, 2025 23:45
@tristan-f-r tristan-f-r marked this pull request as ready for review May 29, 2025 17:07
@tristan-f-r tristan-f-r added the algorithm Pathway reconstruction algorithm to add to SPRAS label May 29, 2025
@tristan-f-r tristan-f-r changed the title feat: robust feat: ROBUST May 29, 2025
@tristan-f-r tristan-f-r marked this pull request as draft May 30, 2025 06:05
# to nodes if they are overstudied. By taking the inverse of these, this deincentivizes ROBUST from exploring nodes
# with low prizes, which approximates the idea of incentivizing exploring nodes with positive prizes.
# See more at "Online bias-aware disease module mining with ROBUST-Web," as the original ROBUST paper
# did not incorporate study bias scores.
Copy link
Collaborator Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

The strangest part of this PR is this - to allow for users to incorporate prizes, this transforms them into ROBUST's penalizing study bias scores.

@tristan-f-r tristan-f-r marked this pull request as ready for review May 30, 2025 16:13
@tristan-f-r tristan-f-r mentioned this pull request May 30, 2025
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
algorithm Pathway reconstruction algorithm to add to SPRAS
Projects
None yet
Development

Successfully merging this pull request may close these issues.

Add ROBUST
1 participant