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

Add OpenPhenom benchmarking notebook #84

Merged
merged 5 commits into from
Nov 11, 2024
Merged

Add OpenPhenom benchmarking notebook #84

merged 5 commits into from
Nov 11, 2024

Conversation

kian-kd
Copy link
Contributor

@kian-kd kian-kd commented Nov 11, 2024

What?

  • update the benchmarking notebook to use pca-centerscale instead of TVN
  • show example run for OpenPhenom model

Copy link

Check out this pull request on  ReviewNB

See visual diffs & provide feedback on Jupyter Notebooks.


Powered by ReviewNB

@@ -0,0 +1,2858 @@
{
Copy link
Contributor

@fedecomitani fedecomitani Nov 11, 2024

Choose a reason for hiding this comment

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

Line #3.    openphenom_embeddings = pd.read_parquet("data/OpenPhenom_rxrx3-core_embeddings.parquet")  # download from huggingface

Do we want to add an example of how to download the data from hugging face? Or a link to the hf repo?


Reply via ReviewNB

@fedecomitani
Copy link
Contributor

We might want a separate folder, notebooks/rxrx3-core, specifically for this notebook.
See this conversation.

Copy link
Contributor

@fedecomitani fedecomitani left a comment

Choose a reason for hiding this comment

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

Minor comments, I'm ok to approve once resolved.

@kian-kd
Copy link
Contributor Author

kian-kd commented Nov 11, 2024

I don't really think we need a separate folder for the notebook since it's self-contained. Instead I added a description of the benchmark to the readme @fedecomitani

README.md Outdated Show resolved Hide resolved
fedecomitani
fedecomitani previously approved these changes Nov 11, 2024
Copy link
Contributor

@fedecomitani fedecomitani left a comment

Choose a reason for hiding this comment

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

lgtm

@kian-kd kian-kd merged commit 8a4d512 into trunk Nov 11, 2024
4 checks passed
@kian-kd kian-kd deleted the openphenom branch November 11, 2024 20:12
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