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add xgdp#446

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tereshchuk1 wants to merge 18 commits into
daisybio:developmentfrom
tereshchuk1:add-xgdp
Open

add xgdp#446
tereshchuk1 wants to merge 18 commits into
daisybio:developmentfrom
tereshchuk1:add-xgdp

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@tereshchuk1

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Adds XGDP. The model combines a GNN branch for drug molecular graphs with a 1D-CNN branch for cell line gene expression, with optional cross-attention.

Adapted from the original repository with the following changes for drevalpy integration:

  • Merged upstream/development and resolved conflicts
  • Edge features aligned to 7-dim to match the existing create_drug_graphs.py featurizer
  • CNN input size computed dynamically instead of hardcoded
  • Fixed MSE loss shape mismatch
  • Added ensure_drug_graphs fixture to tests/conftest.py
  • Suppressed S614 for torch.load(..., weights_only=False) (required for torch_geometric.data.Data)

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⚠️ Please install the 'codecov app svg image' to ensure uploads and comments are reliably processed by Codecov.

Codecov Report

❌ Patch coverage is 21.29472% with 924 lines in your changes missing coverage. Please review.
✅ Project coverage is 74.79%. Comparing base (7d24cd6) to head (6162099).
⚠️ Report is 39 commits behind head on development.

Files with missing lines Patch % Lines
drevalpy/models/XGDP/_models.py 11.45% 881 Missing ⚠️
drevalpy/models/XGDP/xgdp.py 84.93% 22 Missing ⚠️
tests/conftest.py 22.22% 21 Missing ⚠️
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Additional details and impacted files
@@               Coverage Diff               @@
##           development     #446      +/-   ##
===============================================
- Coverage        80.34%   74.79%   -5.56%     
===============================================
  Files              101      118      +17     
  Lines             8171    10124    +1953     
===============================================
+ Hits              6565     7572    +1007     
- Misses            1606     2552     +946     

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6 participants