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[python] Geneformer updates for July 2024 LTS #961

Merged
merged 52 commits into from
Jul 5, 2024
Merged

[python] Geneformer updates for July 2024 LTS #961

merged 52 commits into from
Jul 5, 2024

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mlin
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@mlin mlin commented Jan 31, 2024 •
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Sorry for the heavyweight PR -- numerous changes to our Geneformer API and workflows accumulated for the new LTS:

  • Run tokenization/fine-tuning/forward-pass WDLs on AWS HealthOmics instead of Batch
  • Update the upstream Geneformer version
    • Add new special_token flag
    • Use a gene ID consolidation mapping, with modifications to the sparse math to implement
    • Add WDL inputs for slight variations on embeddings we want to try
  • Update ontologies for cell subclasses

Noting loose ends for potential future cleanup:

  • Use published version of new Geneformer model, once available
  • Replace legacy cell subclass mapper with cellxgene-ontology-guide

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codecov bot commented Jan 31, 2024 •
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Codecov Report

Attention: Patch coverage is 72.54902% with 14 lines in your changes missing coverage. Please review.

Project coverage is 91.12%. Comparing base (f775282) to head (e12a102).
Report is 2 commits behind head on main.

Files Patch % Lines
...xperimental/ml/huggingface/geneformer_tokenizer.py 72.34% 13 Missing ⚠️
...sts/experimental/ml/huggingface/test_geneformer.py 66.66% 1 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##             main     #961      +/-   ##
==========================================
- Coverage   91.19%   91.12%   -0.07%     
==========================================
  Files          77       79       +2     
  Lines        5971     6173     +202     
==========================================
+ Hits         5445     5625     +180     
- Misses        526      548      +22
Flag Coverage Δ
unittests 91.12% <72.54%> (-0.07%) ⬇️

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@mlin mlin changed the title [python] run Geneformer WDLs on HealthOmics managed service instead of AWS Batch [python] Geneformer updates for July 2024 LTS Jul 3, 2024
@mlin mlin marked this pull request as ready for review July 3, 2024 08:06
@mlin mlin merged commit 1b24d78 into main Jul 5, 2024
17 checks passed
@mlin mlin deleted the mlin/geneformer-healthomics branch July 5, 2024 22:24
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@pablo-gar pablo-gar pablo-gar approved these changes

@ebezzi ebezzi Awaiting requested review from ebezzi

@ivirshup ivirshup Awaiting requested review from ivirshup

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@mlin @pablo-gar