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Add fine-tuned scGPT #17

Merged
merged 14 commits into from
Jan 17, 2025
Merged

Add fine-tuned scGPT #17

merged 14 commits into from
Jan 17, 2025

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lazappi
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@lazappi lazappi commented Dec 10, 2024 •
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Describe your changes

Add a fine-tuned version of the scGPT foundation model as a method.

Checklist before requesting a review

  • I have performed a self-review of my code

  • Check the correct box. Does this PR contain:

    • Breaking changes
    • New functionality
    • Major changes
    • Minor changes
    • Bug fixes

  • Proposed changes are described in the CHANGELOG.md

  • CI Tests succeed and look good!

@lazappi lazappi requested a review from rcannood December 10, 2024 10:04
@lazappi
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lazappi commented Dec 10, 2024

This will probably have conflicts with #16 so that should probably be merged first

@lazappi
Merge remote-tracking branch 'origin/main' into feature/no-ref/add-sc…
381605d 
…GPT-finetuned

* origin/main:
  Add argument to give model path to scGPT (#16)
@lazappi
Add model arguments to scgpt_finetuned
7e845e7 
Fixed some things in scgpt_zeroshot...
rcannood
rcannood approved these changes Jan 13, 2025
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LGTM!

@lazappi
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lazappi commented Jan 13, 2025

Do you want to exclude it in the run_full_*.sh scripts? At the moment it's only excluded from the local runs.

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Do you want to exclude it in the run_full_*.sh scripts? At the moment it's only excluded from the local runs.

Oh i see -- yes please! At least for now

@lazappi
Exclude scgpt_finetuned from full benchmark runs
cd171cd 
Need to sort out GPU infrastructure
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lazappi commented Jan 14, 2025

Oh i see -- yes please! At least for now

Done

@lazappi
Merge remote-tracking branch 'origin/main' into feature/no-ref/add-sc…
ad07a22 
…GPT-finetuned

* origin/main:
  Pin scPRINT version (#25)
  Increase UCE memory tag (#24)
  Add exit codes helper file (#26)
  Include all features in solution (#28)
  Update common submodule (#29)
@rcannood rcannood merged commit 6191552 into main Jan 17, 2025
3 checks passed
@rcannood rcannood deleted the feature/no-ref/add-scGPT-finetuned branch January 17, 2025 07:38
lazappi added a commit that referenced this pull request Jan 17, 2025
@lazappi
Merge remote-tracking branch 'origin/main' into bugfix/no-ref/adjust-…
b3b584e 
…resources

* origin/main:
  Add batch_hvg var column to solution (#31)
  Add fine-tuned scGPT (#17)
lazappi added a commit to HelloWorldLTY/task_batch_integration that referenced this pull request Jan 27, 2025
@lazappi
Merge remote-tracking branch 'origin/main' into HelloWorldLTY/main
5c6b249 
* origin/main: (28 commits)
  Adjust pyliger dependencies (openproblems-bio#43)
  Minor run adjustments (openproblems-bio#44)
  Fix reference in task description (openproblems-bio#45)
  Remove grouping bottleneck (openproblems-bio#42)
  Retry with single core in geneformer (openproblems-bio#41)
  Adjustments based on benchmark run (openproblems-bio#39)
  Update compute environment (openproblems-bio#35)
  Replace "+" in batch names for liger (openproblems-bio#37)
  Update common submodule to commit 62268aa  (openproblems-bio#38)
  Adjust features filter in scPRINT (openproblems-bio#36)
  minor tweaks to the cell cycle component (openproblems-bio#34)
  Update common submodule to commit a2e845 (openproblems-bio#33)
  Increase time resources (openproblems-bio#27)
  GPU adjustments (openproblems-bio#32)
  Add batch_hvg var column to solution (openproblems-bio#31)
  Add fine-tuned scGPT (openproblems-bio#17)
  Bump scIB to v1.1.7 (openproblems-bio#30)
  Pin scPRINT version (openproblems-bio#25)
  Increase UCE memory tag (openproblems-bio#24)
  Add exit codes helper file (openproblems-bio#26)
  ...
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@lazappi @rcannood