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Updating LOIO visualization #47

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merged 11 commits into from
Feb 6, 2024
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@gwaybio gwaybio commented Oct 30, 2023

I include the following adjustments:

  1. Refactoring LOIO_evaluation.ipynb to summarize the new LOIO analysis (updated since Updating LOIO analysis to include all features spaces #46 )
  2. Adding new feature space performance visualizations (adding to panel A, changing structure of panel B)
  3. Focusing only on CP features in panels C and D

Note, this figure will also likely update as we continue writing and compiling the story. I consider the LOIO analysis wrapped up at this point, however 🎉

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gwaybio commented Oct 30, 2023

I'm taking both Jenna and Cameron to review - please do so when you have an opportunity and the brain mood. There is no rush!!

(I should clarify that we only need one review, no need for both!)

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LGTM! I have a few minor comments about the figure to address but overall a very interesting visualization of the LOIO assessment 😄

3.evaluate_model/scripts/nbconverted/LOIO_evaluation.py Outdated Show resolved Hide resolved
7.figures/figures/main_figure_4_loio.png Outdated Show resolved Hide resolved
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gwaybio commented Feb 4, 2024

Thanks again for the review @jenna-tomkinson - Given the extensive updates to this PR, would you be able to give this another look? Please focus on the figure, and I hope that it will not take too much time :)

main_figure_4_loio

I consider the LOIO analysis wrapped up at this point, however 🎉

☝️ Haha, silly me 🙃


Edit: In the most recent commit, I removed panel A, to be moved to the supplement.

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Love the changes to this figure! I left one question on the figure for you to address, but overall this PR is great and ready to merge!

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This figure looks so much better and tells the story in a more clean and concise manner!

I only have one question:

Are these figures showing the result from the balanced or unbalanced model, with or without IC, and is this with all nuclei features (not a subset for AreaShape)?

This will probably be stated in the figure legend, but wanted to ask since I am curious what model I am looking at.

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Great questions! This is our standard model: Balanced, with IC, and all features. I add clarification in 8618141

Going to merge now, thanks again!

@gwaybio gwaybio merged commit d045101 into WayScience:main Feb 6, 2024
@gwaybio gwaybio deleted the update-loio-figure branch February 6, 2024 02:58
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