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Add Geneformer #6

Merged
merged 24 commits into from
Nov 8, 2024
Merged

Add Geneformer #6

merged 24 commits into from
Nov 8, 2024

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lazappi
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@lazappi lazappi commented Oct 23, 2024 •
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Describe your changes

Add the Geneformer 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!

Current progress

  • Add component files
  • Get required model files
  • Tokenize data
  • Embed data
  • Create output file
  • Add to pipeline
  • Clean up code, arguments etc.

lazappi and others added 23 commits October 2, 2024 11:31
@lazappi
Add cxg_immune_cell_atlas as a test resource
f47eff9
@lazappi
Add SCimilarity component
175a3f8
@lazappi
Add SCimiliarity to benchmark workflow
a9931e1
@lazappi
Update script to extract model
84394c3
@lazappi
Add SCimilarity model path to benchmark workflow
5e0038c
@lazappi
Add base_method API to disable tests for SCimilarity
c927cb1
@lazappi
Replace cxg_mouse_pancreas_atlas with cxg_immune_cell_atlas
5c74f37
@lazappi
Style SCimiliarity script
7b6fea3
@lazappi
Remove test resources from SCimiliarity config
cca5715
@lazappi
Fix file names in test resources state.yaml
30e8b14
@lazappi
Add scimilarity as dependency to benchmark workflow
b2188b5
@lazappi
Update compute environment
ca95e44
@lazappi
Update model file path
ce57335
@lazappi
Create geneformer files
c60a7da
@lazappi
Set SCimilarity name in Python script
99a7078
@lazappi
Adjust container settings
f4b98e1 
Depend on base method config because of input model file
@lazappi
Download dictionary files in script
fbaf8b1
@lazappi
Merge remote-tracking branch 'origin/main' into feature/no-ref/add-Ge…
1e7dfa0 
…neformer

* origin/main:
  Add arguments for filtering methods in benchmark workflow (#4)
  Add SCimilarity (#3)
@lazappi
Prepare and tokenize data, attempt to embed
b1d1520
@lazappi
Store and output embedding
e3abd30
@lazappi
Add Geneformer to benchmark workflow
1e00a52
@lazappi
Add argument to select model version to use
113a892
@lazappi
Style Geneformer script
f26eb24
@lazappi lazappi marked this pull request as ready for review October 29, 2024 10:16
@lazappi lazappi requested a review from rcannood October 29, 2024 10:19
@lazappi
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lazappi commented Oct 29, 2024

  • The CI tests are failing because there is no GPU. I'm not sure how we want to handle that.
  • I haven't updated the CHANGELOG because it doesn't have anything for this task yet. Maybe that needs a separate PR?

@lazappi
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lazappi commented Oct 30, 2024

Ok, checks are passing now 🎉!

KaiWaldrant
KaiWaldrant approved these changes Nov 8, 2024
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LGTM!

@rcannood rcannood merged commit 2158882 into main Nov 8, 2024
3 checks passed
lazappi added a commit that referenced this pull request Nov 22, 2024
@lazappi
Merge remote-tracking branch 'origin/main' into feature/no-ref/add-sc…
5ece7e2 
…PRINT

* origin/main:
  fix repository name
  Migrate from core to openproblems (#11)
  fix broken urls
  fix wf
  Pre-filter batches in hvg overlap metric (#9)
  Adjust resources (#10)
  Add scGPT (#8)
  Add UCE method (#7)
  Add Geneformer (#6)
  fix submodule
  Update common submodule
@lazappi lazappi deleted the feature/no-ref/add-Geneformer branch November 22, 2024 12:34
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@KaiWaldrant KaiWaldrant KaiWaldrant approved these changes

@rcannood rcannood Awaiting requested review from rcannood

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3 participants
@lazappi @KaiWaldrant @rcannood