remove evaluate_baseline_performance flag; it is now a boolean flag, …

…only run if it is set
BIMSBbioinfo · Jul 12, 2024 · 39d8cc0 · 39d8cc0
1 parent 5f0983f
commit 39d8cc0
Showing 1 changed file with 6 additions and 6 deletions.
diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
@@ -75,34 +75,34 @@ jobs:
       shell: bash -l {0}
       run: |
         conda activate my_env
-        flexynesis --data_path dataset1 --model_class DirectPred --target_variables Erlotinib --batch_variables Crizotinib --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 --evaluate_baseline_performance False
+        flexynesis --data_path dataset1 --model_class DirectPred --target_variables Erlotinib --batch_variables Crizotinib --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
 
     - name: Run DirectPred_TestSurvival
       shell: bash -l {0}
       run: |
         conda activate my_env
-        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 --evaluate_baseline_performance False --surv_event_var OS_STATUS --surv_time_var OS_MONTHS
+        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
 
     - name: Run supervised_vae
       shell: bash -l {0}
       run: |
         conda activate my_env
-        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 --evaluate_baseline_performance False
+        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
 
     - name: Run CrossModalPred 
       shell: bash -l {0}
       run: |
         conda activate my_env
-        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 --evaluate_baseline_performance False
+        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 
 
     - name: Run MultiTripletNetwork
       shell: bash -l {0}
       run: |
         conda activate my_env
-        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 --evaluate_baseline_performance False
+        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 
 
     - name: Run GNN
       shell: bash -l {0}
       run: |
         conda activate my_env
-        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_direct --early_stop_patience 3 --use_loss_weighting False --evaluate_baseline_performance False --subsample 50
+        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_direct --early_stop_patience 3 --use_loss_weighting False --subsample 50