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

Explore parallelization of ancestry_analysis #83

Open

smlmbrt opened this issue Mar 1, 2024 · 1 comment

Labels

Member

smlmbrt commented Mar 1, 2024

Some places where additional cores may get a speed increase:

n_jobs in random forest classifier

pgscatalog_utils/pgscatalog_utils/ancestry/tools.py

Line 160 in cf5d0d5

clf_rf = RandomForestClassifier(random_state=32)
In pgs_adjust writing the adjustments as a loop (this will likely depend on how costly the repeated subsetting is):
1. Subsetting data
2. fitting adjustments
3. return adjustment

smlmbrt added the enhancement label

Member Author

smlmbrt commented Mar 2, 2024

I think the speed problems are actually solved by this: a713443

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment