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| outputs/predictions/task1/autoencoder_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/autoencoder_features_10_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/autoencoder_features_20_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/autoencoder_features_50_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/med3d_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/med3d_features_10_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/med3d_features_20_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/med3d_features_50_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/modelsgen_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/modelsgen_features_10_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/modelsgen_features_20_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/modelsgen_features_50_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/nnclr_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/nnclr_features_10_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/nnclr_features_20_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/nnclr_features_50_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/simclr_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/simclr_features_10_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/simclr_features_20_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/simclr_features_50_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/swav_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/swav_features_10_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/swav_features_20_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/swav_features_50_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task2/modelsgen_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task2/modelsgen_features_10_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task2/modelsgen_features_20_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task2/modelsgen_features_50_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task3/LUNG1/foundation_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task3/LUNG1/modelsgen_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task3/RADIO/foundation_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task3/RADIO/modelsgen_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| output/features/foundation_features/task1/test_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| output/features/foundation_features/task1/train_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| output/features/foundation_features/task1/val_features.csv filter=lfs diff=lfs merge=lfs -text | ||
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| output/features/foundation_features/task2/val_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| output/features/foundation_features/task3/lung1.csv filter=lfs diff=lfs merge=lfs -text | ||
| output/features/foundation_features/task3/radio.csv filter=lfs diff=lfs merge=lfs -text | ||
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| outputs/features/foundation_features/task1/train_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/features/foundation_features/task1/val_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/features/foundation_features/task2/test_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/features/foundation_features/task2/train_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/features/foundation_features/task2/val_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/features/foundation_features/task3/lung1.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/features/foundation_features/task3/radio.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/stability/foundation_features/lung1_feats.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/stability/supervised/lung1_feats.csv filter=lfs diff=lfs merge=lfs -text | ||
| models/pretrained/fmcib/model_weights.torch filter=lfs diff=lfs merge=lfs -text | ||
| outputs/features/baselines/med3d/task1/test_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/features/baselines/med3d/task1/train_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/features/baselines/med3d/task1/val_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/features/baselines/models_genesis/task1/test_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/features/baselines/models_genesis/task1/train_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/features/baselines/models_genesis/task1/val_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/features/baselines/models_genesis/task2/test_features.csv filter=lfs diff=lfs merge=lfs -text | ||
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| outputs/features/baselines/models_genesis/task2/val_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/features/baselines/models_genesis/task3/lung1_features.csv filter=lfs diff=lfs merge=lfs -text | ||
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| outputs/features/fmcib/task3/lung1.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/features/fmcib/task3/radio.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/features/pretraining_comparison/autoencoder/task1/test_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/features/pretraining_comparison/autoencoder/task1/train_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/features/pretraining_comparison/autoencoder/task1/val_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/features/pretraining_comparison/nnclr/task1/test_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/features/pretraining_comparison/nnclr/task1/train_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/features/pretraining_comparison/nnclr/task1/val_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/features/pretraining_comparison/simclr/task1/test_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/features/pretraining_comparison/simclr/task1/train_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/features/pretraining_comparison/simclr/task1/val_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/features/pretraining_comparison/swav/task1/test_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/features/pretraining_comparison/swav/task1/train_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/features/pretraining_comparison/swav/task1/val_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/baselines/med3d_features/med3d_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/baselines/med3d_features/med3d_features_10_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/baselines/med3d_features/med3d_features_20_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/baselines/med3d_features/med3d_features_50_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/baselines/models_genesis_features/modelsgen_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/baselines/models_genesis_features/modelsgen_features_10_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/baselines/models_genesis_features/modelsgen_features_20_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/baselines/models_genesis_features/modelsgen_features_50_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/pretraining_comparison/autoencoder/autoencoder_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/pretraining_comparison/autoencoder/autoencoder_features_10_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/pretraining_comparison/autoencoder/autoencoder_features_20_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/pretraining_comparison/autoencoder/autoencoder_features_50_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/pretraining_comparison/nnclr/nnclr_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/pretraining_comparison/nnclr/nnclr_features_10_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/pretraining_comparison/nnclr/nnclr_features_20_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/pretraining_comparison/nnclr/nnclr_features_50_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/pretraining_comparison/simclr/simclr_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/pretraining_comparison/simclr/simclr_features_10_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/pretraining_comparison/simclr/simclr_features_20_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/pretraining_comparison/simclr/simclr_features_50_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/pretraining_comparison/swav/swav_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/pretraining_comparison/swav/swav_features_10_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/pretraining_comparison/swav/swav_features_20_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task1/pretraining_comparison/swav/swav_features_50_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task2/baselines/models_genesis_features/modelsgen_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task2/baselines/models_genesis_features/modelsgen_features_10_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task2/baselines/models_genesis_features/modelsgen_features_20_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task2/baselines/models_genesis_features/modelsgen_features_50_percent.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task3/LUNG1/baselines/modelsgen_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| outputs/predictions/task3/RADIO/baselines/modelsgen_features.csv filter=lfs diff=lfs merge=lfs -text | ||
| models/baselines/task1/fmcib_finetuned.torch filter=lfs diff=lfs merge=lfs -text | ||
| models/baselines/task1/supervised.torch filter=lfs diff=lfs merge=lfs -text | ||
| models/baselines/task2/fmcib_finetuned.torch filter=lfs diff=lfs merge=lfs -text | ||
| models/baselines/task2/supervised.torch filter=lfs diff=lfs merge=lfs -text | ||
| models/baselines/task2/supervised_finetuned.torch filter=lfs diff=lfs merge=lfs -text | ||
| models/baselines/task3/fmcib_finetuned.torch filter=lfs diff=lfs merge=lfs -text | ||
| models/baselines/task3/supervised.torch filter=lfs diff=lfs merge=lfs -text | ||
| models/baselines/task3/supervised_finetuned.torch filter=lfs diff=lfs merge=lfs -text |
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| name: ci | ||
| on: | ||
| push: | ||
| branches: | ||
| - master | ||
|
|
||
| permissions: | ||
| contents: write | ||
| jobs: | ||
| deploy: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| - name: Configure Git Credentials | ||
| run: | | ||
| git config user.name github-actions[bot] | ||
| git config user.email 41898282+github-actions[bot]@users.noreply.github.com | ||
| - uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: 3.x | ||
| - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV | ||
| - uses: actions/cache@v4 | ||
| with: | ||
| key: mkdocs-material-${{ env.cache_id }} | ||
| path: .cache | ||
| restore-keys: | | ||
| mkdocs-material- | ||
| - run: pip install mkdocs-material | ||
| - run: mkdocs gh-deploy --force |
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| name: Auto Publish | ||
| on: | ||
| push: | ||
| branches: | ||
| - master | ||
|
|
||
| jobs: | ||
| build: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
| - name: Set up Python | ||
| uses: actions/[email protected] | ||
| with: | ||
| python-version: 3.8 | ||
|
|
||
| - name: Install poetry | ||
| run: make setup | ||
|
|
||
| - name: Bump version | ||
| run: | | ||
| poetry version prerelease | ||
|
|
||
| - name: Commit & push changes | ||
| run: | | ||
| git config --local user.email "[email protected]" | ||
| git config --local user.name "GitHub Action" | ||
| git add . | ||
| git commit -m "Bump version" || echo "No changes to commit" | ||
| git push | ||
| - name: Build and publish to pypi | ||
| uses: JRubics/[email protected] | ||
| with: | ||
| python_version: 3.8 | ||
| pypi_token: ${{ secrets.PYPI_TOKEN }} | ||
| allow_poetry_pre_release: "yes" | ||
| ignore_dev_requirements: "yes" |
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