Skip to content

Decrease peak memory usage of eregulon enrichment#616

Open
EmielGeeraerts wants to merge 5 commits intoaertslab:developmentfrom
EmielGeeraerts:parallelaucell
Open

Decrease peak memory usage of eregulon enrichment#616
EmielGeeraerts wants to merge 5 commits intoaertslab:developmentfrom
EmielGeeraerts:parallelaucell

Conversation

@EmielGeeraerts
Copy link
Copy Markdown

Goal: decrease maximum memory usage during eregulon enrichment

Method:

  • Load data as backed adata instead of (dense) pd.DataFrame
  • Chunk eregulon enrichment into sets of [chunk_size] cells to avoid unsparsing the feature matrix when ranking features. Processes chunks of the feature matrix in parallel

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.

2 participants