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Expose scGPT fine-tuning epochs and batch size - #118
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Daesun-Ryu wants to merge 1 commit into
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rcannood
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Oct 19, 2026
rcannood
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@Daesun-Ryu Thanks for the PR; exposing the epochs and batch size makes sense.
Could you review my comments and apply the changes?
Could you also add yourself as a contributor to _viash.yaml?
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| scgpt_training_parameters: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| - uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: "3.12" | ||
| - run: python -m pip install PyYAML==6.0.3 | ||
| - run: >- | ||
| python -B -m unittest discover | ||
| -s src/methods/scgpt_finetuned -p test_training_params.py -v |
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Undo these changes to our CI
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| scgpt_training_parameters: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| - run: python -m pip install PyYAML==6.0.3 | |
| - run: >- | |
| python -B -m unittest discover | |
| -s src/methods/scgpt_finetuned -p test_training_params.py -v |
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| * Expose `methods/scgpt_finetuned`'s epochs and batch size as arguments, preserving defaults of 15 and 64. | ||
| Batch size also applies to validation and embedding (issue #111). |
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This isn't a bug fix but a minor change.
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Summary
--epochsand--batch_size, preserving production defaults of 15 and 64 (minimum 1).info.test_default(epochs 2, batch size 4) without changing normal benchmark settings.Validation
Limits
Refs #111