Add JSON artifact reader for inference #87
Workflow file for this run
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| name: Check Models | |
| on: | |
| push: | |
| branches: | |
| - main | |
| paths: | |
| - 'flexynesis/**' | |
| - '.github/workflows/models.yml' | |
| - './pyproject.toml' | |
| - './manifest.scm' | |
| - './guix.scm' | |
| pull_request: | |
| branches: | |
| - main | |
| paths: | |
| - 'flexynesis/**' | |
| - '.github/workflows/models.yml' | |
| - 'pyproject.toml' | |
| - 'manifest.scm' | |
| - 'guix.scm' | |
| jobs: | |
| run_package: | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-latest] | |
| python-version: ["3.11", "3.12", "3.13"] # Exclude 3.14 due to qdldl build failure | |
| runs-on: ${{ matrix.os }} | |
| name: Python ${{ matrix.python-version }} on ${{ matrix.os }} | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v6 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v6 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install OpenMP (macOS only) | |
| if: runner.os == 'macOS' | |
| run: brew install libomp | |
| - name: Install my package from source | |
| run: python -m pip install -e . | |
| - name: Download dataset1 | |
| run: | | |
| curl -L -o dataset1.tgz https://bimsbstatic.mdc-berlin.de/akalin/buyar/flexynesis-benchmark-datasets/dataset1.tgz | |
| tar -xzvf dataset1.tgz | |
| - name: Download dataset2 | |
| run: | | |
| curl -L -o dataset2.tgz https://bimsbstatic.mdc-berlin.de/akalin/buyar/flexynesis-benchmark-datasets/dataset2.tgz | |
| tar -xzvf dataset2.tgz | |
| - name: Download LGG_GBM_dataset | |
| run: | | |
| curl -L -o lgggbm_tcga_pub_processed.tgz https://bimsbstatic.mdc-berlin.de/akalin/buyar/flexynesis-benchmark-datasets/lgggbm_tcga_pub_processed.tgz | |
| tar -xzvf lgggbm_tcga_pub_processed.tgz | |
| - name: Run DirectPred | |
| shell: bash -l {0} | |
| run: | | |
| flexynesis --data_path dataset1 --model_class DirectPred --target_variables Erlotinib --fusion_type early --hpo_iter 1 --features_min 50 --features_top_percentile 5 --log_transform False --data_types gex,cnv --outdir . --prefix erlotinib_direct --early_stop_patience 3 --use_loss_weighting False | |
| flexynesis --pretrained_model erlotinib_direct.final_model.pth --artifacts erlotinib_direct.artifacts.joblib --data_path_test dataset1/test --target_variables Erlotinib | |
| - name: Run DirectPred_TestSurvival | |
| shell: bash -l {0} | |
| run: | | |
| flexynesis --data_path lgggbm_tcga_pub_processed --model_class DirectPred --target_variables STUDY --fusion_type intermediate --hpo_iter 1 --features_min 50 --features_top_percentile 5 --log_transform False --data_types mut,cna --outdir . --prefix lgg_surv --early_stop_patience 3 --use_loss_weighting False --surv_event_var OS_STATUS --surv_time_var OS_MONTHS | |
| flexynesis --pretrained_model lgg_surv.final_model.pth --artifacts lgg_surv.artifacts.joblib --data_path_test lgggbm_tcga_pub_processed/test --target_variables STUDY,OS_STATUS | |
| - name: Run DirectPred_TestCovariates | |
| shell: bash -l {0} | |
| run: | | |
| flexynesis --data_path lgggbm_tcga_pub_processed --model_class DirectPred --target_variables STUDY --fusion_type intermediate --hpo_iter 1 --features_min 50 --features_top_percentile 5 --log_transform False --data_types mut --outdir . --prefix lgg_surv --early_stop_patience 3 --use_loss_weighting False --covariates BCR_STATUS | |
| flexynesis --pretrained_model lgg_surv.final_model.pth --artifacts lgg_surv.artifacts.joblib --data_path_test lgggbm_tcga_pub_processed/test --target_variables STUDY | |
| - name: Run DirectPred_Test_Explainers | |
| shell: bash -l {0} | |
| run: | | |
| flexynesis --data_path lgggbm_tcga_pub_processed --model_class DirectPred --target_variables STUDY --fusion_type intermediate --hpo_iter 1 --features_min 50 --features_top_percentile 5 --log_transform False --data_types mut --outdir . --prefix lgg_surv --early_stop_patience 3 --use_loss_weighting False --feature_importance_method Both | |
| flexynesis --pretrained_model lgg_surv.final_model.pth --artifacts lgg_surv.artifacts.joblib --data_path_test lgggbm_tcga_pub_processed/test --target_variables STUDY | |
| - name: Run supervised_vae | |
| shell: bash -l {0} | |
| run: | | |
| flexynesis --data_path dataset1 --model_class supervised_vae --target_variables Erlotinib,Crizotinib --fusion_type early --hpo_iter 1 --features_min 50 --features_top_percentile 5 --log_transform False --data_types gex,cnv --outdir . --prefix erlotinib_svae --early_stop_patience 3 --use_loss_weighting True | |
| flexynesis --pretrained_model erlotinib_svae.final_model.pth --artifacts erlotinib_svae.artifacts.joblib --data_path_test dataset1/test --target_variables Erlotinib,Crizotinib | |
| - name: Run CrossModalPred | |
| shell: bash -l {0} | |
| run: | | |
| flexynesis --data_path dataset1 --model_class CrossModalPred --target_variables Erlotinib --fusion_type intermediate --hpo_iter 1 --features_min 50 --features_top_percentile 5 --log_transform False --data_types gex,cnv --input_layers gex --output_layers cnv --outdir . --prefix erlotinib_crossmodal --early_stop_patience 3 --use_loss_weighting True | |
| flexynesis --pretrained_model erlotinib_crossmodal.final_model.pth --artifacts erlotinib_crossmodal.artifacts.joblib --data_path_test dataset1/test --target_variables Erlotinib | |
| - name: Run MultiTripletNetwork | |
| shell: bash -l {0} | |
| run: | | |
| flexynesis --data_path dataset2 --model_class MultiTripletNetwork --target_variables y --fusion_type early --hpo_iter 1 --features_min 50 --features_top_percentile 5 --log_transform False --data_types gex,meth --outdir . --prefix msi_triplet --early_stop_patience 3 | |
| flexynesis --pretrained_model msi_triplet.final_model.pth --artifacts msi_triplet.artifacts.joblib --data_path_test dataset2/test --target_variables y | |
| - name: Run GNN | |
| shell: bash -l {0} | |
| run: | | |
| export FLEXYNESIS_CACHE=./dataset1 | |
| flexynesis --data_path dataset1 --model_class GNN --target_variables Erlotinib --fusion_type intermediate --hpo_iter 1 --features_top_percentile 10 --log_transform False --data_types gex --outdir . --prefix erlotinib_gnn --early_stop_patience 3 --use_loss_weighting False --subsample 50 | |
| flexynesis --pretrained_model erlotinib_gnn.final_model.pth --artifacts erlotinib_gnn.artifacts.joblib --data_path_test dataset1/test --target_variables Erlotinib | |