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.

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

Update metaclusterers.py #42

Open
wants to merge 7 commits into
base: master
Choose a base branch
from

Conversation

AvantiShri
Copy link
Collaborator

Attempt to patch the scalability of the metaclustering code

Attempt to patch the scalability of the metaclustering code
@AvantiShri
Copy link
Collaborator Author

@tchiruvolu I haven't tested out this code, but can you try out this fix for the metaclustering scalability? To install this branch of tf-modisco you need to do:

pip uninstall modisco #uninstall your current version
git clone https://github.com/kundajelab/tfmodisco.git
cd tfmodisco
git checkout AvantiShri-metaclusteringpatch
pip install --editable . #the --editable flag just means that if the soruce is edited later, the changes will get picked up

I basically changed two things as you can see in https://github.com/kundajelab/tfmodisco/pull/42/files; (1) all_possible_activity_patterns is now only populated according to activity patterns that appear in the set of seqlets, and (2) the set of all possible compatible activity patterns is generated in a runtime proportional to 2^number_of_tasks rather than 3^number_of_tasks.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

1 participant