DeepTraCDR/Scenario1/Regression/train_random.py

import argparse
import numpy as np
import torch
from sklearn.model_selection import KFold
from DeepTraCDR_model import DeepTraCDR, Optimizer
from data_sampler import RegressionSampler
from data_loader import load_data

def parse_arguments() -> argparse.Namespace:
    """
    Parses command-line arguments for the DeepTraCDR regression task.

    Returns:
        Parsed arguments as a Namespace object.
    """
    parser = argparse.ArgumentParser(description="DeepTraCDR Regression Task")
    parser.add_argument('-device', type=str, default="cuda:0" if torch.cuda.is_available() else "cpu",
                        help="Device to run the model on (e.g., 'cuda:0' or 'cpu')")
    parser.add_argument('-data', type=str, default='gdsc', help="Dataset to use (default: gdsc)")
    parser.add_argument('--wd', type=float, default=1e-5, help="Weight decay for optimizer")
    parser.add_argument('--layer_size', nargs='+', type=int, default=[512], help="Layer sizes for the model")
    parser.add_argument('--gamma', type=float, default=15, help="Gamma parameter for decoder")
    parser.add_argument('--epochs', type=int, default=1000, help="Number of training epochs")
    parser.add_argument('--test_freq', type=int, default=50, help="Frequency of evaluation during training")
    parser.add_argument('--lr', type=float, default=0.0001, help="Learning rate for optimizer")
    parser.add_argument('--patience', type=int, default=20, help="Patience for early stopping")
    return parser.parse_args()

def normalize_adj_matrix(adj_matrix: np.ndarray) -> torch.Tensor:
    """
    Normalizes the adjacency matrix using min-shift normalization and converts it to a torch tensor.

    Args:
        adj_matrix: Input adjacency matrix as a NumPy array.

    Returns:
        Normalized adjacency matrix as a torch tensor.
    """
    adj_matrix = adj_matrix - np.min(adj_matrix)
    if isinstance(adj_matrix, np.ndarray):
        adj_matrix = torch.from_numpy(adj_matrix).float()
    return adj_matrix

def main():
    """
    Main function to run the DeepTraCDR regression task with k-fold cross-validation.
    """
    # Set precision for matrix multiplication
    torch.set_float32_matmul_precision('high')

    # Parse command-line arguments
    args = parse_arguments()

    # Load dataset
    full_adj, drug_fingerprints, exprs, null_mask, pos_num, args = load_data(args)
    print(f"Original full_adj shape: {full_adj.shape}")
    print(f"Normalized full_adj shape: {full_adj.shape}")
    print("\n--- Data Shapes ---")
    print(f"Expression data shape: {exprs.shape}")
    print(f"Null mask shape: {null_mask.shape}")

    # Normalize adjacency matrix
    full_adj = normalize_adj_matrix(full_adj)

    # Initialize k-fold cross-validation parameters
    k = 5
    n_kfolds = 5
    all_metrics = {'rmse': [], 'pcc': [], 'scc': []}

    # Perform k-fold cross-validation
    for n_kfold in range(n_kfolds):
        kfold = KFold(n_splits=k, shuffle=True, random_state=n_kfold)
        for fold, (train_idx, test_idx) in enumerate(kfold.split(np.arange(pos_num))):
            # Initialize data sampler
            sampler = RegressionSampler(full_adj, train_idx, test_idx, null_mask)

            # Initialize model
            model = DeepTraCDR(
                adj_mat=full_adj,
                cell_exprs=exprs,
                drug_finger=drug_fingerprints,
                layer_size=args.layer_size,
                gamma=args.gamma,
                device=args.device
            )

            # Initialize optimizer
            opt = Optimizer(
                model=model,
                train_data=sampler.train_data,
                test_data=sampler.test_data,
                test_mask=sampler.test_mask,
                train_mask=sampler.train_mask,
                adj_matrix=full_adj,
                lr=args.lr,
                wd=args.wd,
                epochs=args.epochs,
                test_freq=args.test_freq,
                device=args.device,
                patience=args.patience
            )

            # Train model and collect metrics
            true, pred, best_rmse, best_pcc, best_scc = opt.train()
            all_metrics['rmse'].append(best_rmse)
            all_metrics['pcc'].append(best_pcc)
            all_metrics['scc'].append(best_scc)

            print(f"Fold {n_kfold * k + fold + 1}: RMSE={best_rmse:.4f}, PCC={best_pcc:.4f}, SCC={best_scc:.4f}")

    # Compute and display final average metrics
    print("\nFinal Average Metrics:")
    for metric, values in all_metrics.items():
        mean = np.mean(values)
        std = np.std(values)
        print(f"{metric.upper()}: {mean:.4f} ± {std:.4f}")

if __name__ == "__main__":
    main()