Running time

[AnGorge]

Hey Bora
i tried many time to run the script but it's very computational extensive and my machine broke down many times I use this script #!/bin/bash

Define different model architectures

models=("DirectPred" "SupervisedVAE" "GNN")

Define different data type combinations

data_types=("mutation" "mutation,rna" "mutation,cnv")

Define different fusion methods (only for models that support it)

fusion_methods=("early" "intermediate")

Dataset path

DATA_PATH="ccle_vs_gdsc"

Iterate over all model and data type combinations

for model in "${models[@]}"; do
for data in "${data_types[@]}"; do

# If model is GNN, do not include --fusion_type
if [[ "$model" == "GNN" ]]; then
  echo "Running Flexynesis with Model: $model | Data: $data (NO FUSION) | HPO Iterations: 15"
  flexynesis --data_path "$DATA_PATH" \
    --model_class "$model" \
    --target_variables Erlotinib \
    --hpo_iter 15 \  # This controls training rounds instead of --epochs
    --features_top_percentile 5 \
    --variance_threshold 0.1 \
    --correlation_threshold 0.8 \
    --data_types "$data"
else
  for fusion in "${fusion_methods[@]}"; do
    echo "Running Flexynesis with Model: $model | Data: $data | Fusion: $fusion | HPO Iterations: 15"
    flexynesis --data_path "$DATA_PATH" \
      --model_class "$model" \
      --target_variables Erlotinib \
      --hpo_iter 15 \  
      --features_top_percentile 5 \
      --variance_threshold 0.1 \
      --correlation_threshold 0.8 \
      --data_types "$data" \
      --fusion_type "$fusion"
  done
fi

done
done

echo "All experiments completed!"

I see that it has 500 epoch which I think it's too much how can I reduce n. of epochs ?
and how can I edit it to run easily in my machine and if not can I only add the collected results before the machine shut down and not completing the all tasks ?
Thanks

[borauyar]

You can decrease run times by setting a higher variance threshold (thus decrease number of considered features).
You can set --early_stop_patience to a lower value.
You can pass a custom configuration file using --config_path argument. See example config file here: https://github.com/BIMSBbioinfo/flexynesis/blob/main/examples/configs/hpo_configuration.yaml