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[python] Geneformer CLS embeddings #1225

Merged
merged 6 commits into from
Jul 10, 2024
Merged

[python] Geneformer CLS embeddings #1225

merged 6 commits into from
Jul 10, 2024

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mlin
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@mlin mlin commented Jul 7, 2024

Minor updates to Geneformer scripts and WDL to use new emb_mode="cls" setting.

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codecov bot commented Jul 7, 2024

Codecov Report

Attention: Patch coverage is 25.00000% with 3 lines in your changes missing coverage. Please review.

Project coverage is 91.18%. Comparing base (55d0856) to head (d58e9ed).

Files Patch % Lines
...xperimental/ml/huggingface/geneformer_tokenizer.py 25.00% 3 Missing ⚠️
Additional details and impacted files
@@           Coverage Diff           @@
##             main    #1225   +/-   ##
=======================================
  Coverage   91.18%   91.18%           
=======================================
  Files          80       80           
  Lines        6327     6327           
=======================================
  Hits         5769     5769           
  Misses        558      558           
Flag Coverage Δ
unittests 91.18% <25.00%> (ø)

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@mlin mlin marked this pull request as ready for review July 9, 2024 17:27
@mlin mlin requested a review from pablo-gar July 9, 2024 17:27
@mlin mlin merged commit e9a786d into main Jul 10, 2024
17 checks passed
@mlin mlin deleted the mlin/geneformer-cls branch July 10, 2024 00:42
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2 participants