MLDynamicMetabolicControl/dvc.yaml at main · Toepfer-Lab/MLDynamicMetabolicControl · GitHub

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stages:

  generate_data:
    cmd: >
      python scripts/generate_fba_data.py
      --model-path ${data.model_path}
      --vman ${data.vman}
      --condition ${data.condition}
      --n-samples ${data.n_samples}
    deps:
      - scripts/generate_fba_data.py
      - src/
    params:
      - data.vman
      - data.condition
      - data.n_samples
    outs:
      - data/fba_data_${data.vman}_${data.condition}.npz

  train_surrogate:
    cmd: >
      python scripts/train_surrogate.py
      --vman ${data.vman}
      --condition ${data.condition}
      --hidden-dim ${training.hidden_dim}
      --epochs ${training.epochs}
      --patience ${training.patience}
      --lr ${training.lr}
      --model-name ${data.vman}_trained_model_input-1_output-4_hidden-${training.hidden_dim}
    deps:
      - data/fba_data_${data.vman}_${data.condition}.npz
      - scripts/train_surrogate.py
      - src/
    params:
      - training.hidden_dim
      - training.epochs
      - training.patience
      - training.lr
    outs:
      - trained_models/${data.vman}_trained_model_input-1_output-4_hidden-${training.hidden_dim}.pt

  optimize:
    cmd: >
      python scripts/optimize_vman.py
      --checkpoint trained_models/${data.vman}_trained_model_input-1_output-4_hidden-${training.hidden_dim}.pt
      --t-start ${optimize.t_start}
      --t-end ${optimize.t_end}
      --num-intervals ${optimize.num_intervals}
      --n-eval ${optimize.n_eval}
      --bounds-lower ${optimize.bounds_lower}
      --bounds-upper ${optimize.bounds_upper}
      --initial-state ${optimize.initial_state}
      --output-path results/optimize_vman_${data.vman}_hidden-${training.hidden_dim}_tend-${optimize.t_end}_N-${optimize.num_intervals}.npz
      --logs-path results/optimize_vman_${data.vman}_hidden-${training.hidden_dim}_tend-${optimize.t_end}_N-${optimize.num_intervals}_logs.npz
    deps:
      - trained_models/${data.vman}_trained_model_input-1_output-4_hidden-${training.hidden_dim}.pt
      - scripts/optimize_vman.py
      - src/
    params:
      - optimize
    outs:
      - results/optimize_vman_${data.vman}_hidden-${training.hidden_dim}_tend-${optimize.t_end}_N-${optimize.num_intervals}.npz
      - results/optimize_vman_${data.vman}_hidden-${training.hidden_dim}_tend-${optimize.t_end}_N-${optimize.num_intervals}_logs.npz

  plot:
    cmd: >
      python scripts/plot_optimize_vman.py
      --results results/optimize_vman_${data.vman}_hidden-${training.hidden_dim}_tend-${optimize.t_end}_N-${optimize.num_intervals}.npz
      --logs results/optimize_vman_${data.vman}_hidden-${training.hidden_dim}_tend-${optimize.t_end}_N-${optimize.num_intervals}_logs.npz
      --outdir plots/tend-${optimize.t_end}_N-${optimize.num_intervals}
    deps:
      - results/optimize_vman_${data.vman}_hidden-${training.hidden_dim}_tend-${optimize.t_end}_N-${optimize.num_intervals}.npz
      - results/optimize_vman_${data.vman}_hidden-${training.hidden_dim}_tend-${optimize.t_end}_N-${optimize.num_intervals}_logs.npz
      - scripts/plot_optimize_vman.py
    outs:
      - plots/tend-${optimize.t_end}_N-${optimize.num_intervals}/