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os\nimport pandas as pd\nimport numpy as np\nfrom tqdm.auto import tqdm\nimport xgboost as xgb\nfrom sklearn.model_selection import GridSearchCV\nfrom sklearn.model_selection import StratifiedKFold\nfrom sklearn.metrics import log_loss\nfrom sklearn.metrics import roc_auc_score\n\n\n# Define function to parse a dataset folder of TSV files\ndef parse_tsv_files(folder_path, feature_columns=('v_call', 'j_call')):\n    folder_name = os.path.basename(folder_path)\n    files = os.listdir(folder_path)\n    tsv_files = [f for f in files if f.endswith('.tsv')]\n    other_files = [f.name for f in os.scandir(folder_path) if not f.name.endswith('.tsv')]\n\n    print(f'Loading {len(tsv_files)} .tsv files from {folder_name} (remaining: {other_files}).')\n\n    metadata = None\n    if \"metadata.csv\" in files:\n        metadata = pd.read_csv(os.path.join(folder_path, \"metadata.csv\"))\n        metadata.set_index(\"filename\", inplace=True)\n\n    dataset_rows = []\n\n    for tsv_file in tqdm(tsv_files, desc=f\"Loading {folder_name}\"):\n        file_path = os.path.join(folder_path, tsv_file)\n        file_name, _ = os.path.splitext(tsv_file)\n\n        try:\n            df = pd.read_csv(file_path, sep=\"\\t\")\n        except Exception as e:\n            print(f\"Error loading {tsv_file}: {e}\")\n            continue\n\n        row = {\n            \"ID\": file_name,\n            \"dataset\": folder_name\n        }\n\n        if metadata is not None:\n            row[\"label_positive\"] = int(metadata.at[tsv_file, \"label_positive\"])\n\n        for col in feature_columns:\n            counts = df[col].value_counts() / len(df)\n            row.update(counts.to_dict())\n\n        dataset_rows.append(row)\n\n    return dataset_rows\n\n\n# Define function to load all train and test folders\ndef load_all_datasets(train_folders, test_folders, train_base_path, test_base_path):\n    train_rows = []\n    test_rows = []\n\n    for folder in tqdm(train_folders, desc=\"Train folders\"):\n        path = os.path.join(train_base_path, folder)\n        train_rows += parse_tsv_files(path)\n\n    for folder in tqdm(test_folders, desc=\"Test folders\"):\n        path = os.path.join(test_base_path, folder)\n        test_rows += parse_tsv_files(path)\n\n    return pd.DataFrame(train_rows), pd.DataFrame(test_rows)\n\n\n# Define function to run XGB Grid Search\ndef run_grid_search_xgb(X_train, y_train, base_params, param_grid, n_splits):\n    cv_splitter = StratifiedKFold(\n        n_splits=n_splits,\n        shuffle=True,\n        random_state=42\n    )\n\n    model = xgb.XGBClassifier(\n        **base_params,\n        use_label_encoder=False\n    )\n\n    grid_search = GridSearchCV(\n        estimator=model,\n        param_grid=param_grid,\n        scoring='neg_log_loss',\n        cv=cv_splitter,\n        n_jobs=-1,\n        verbose=2,\n        refit=True\n    )\n\n    print(\"\\nRunning Grid Search...\")\n    grid_search.fit(X_train, y_train)\n\n    print(\"Best Params:\", grid_search.best_params_)\n    print(\"Best Neg LogLoss:\", grid_search.best_score_)\n\n    return grid_search.best_estimator_\n\n\n# Define function to train the best model on full data\ndef train_final_model(model, X_train, y_train):\n    print(\"\\nTraining final model...\")\n    model.fit(X_train, y_train)\n    return model\n\n\n# Define function to generate predictions\ndef generate_predictions(model, X_test, dataset_test):\n    print(\"\\nGenerating predictions...\")\n    probabilities = model.predict_proba(X_test)[:, 1]\n\n    predictions_df = pd.DataFrame({\n        \"ID\": dataset_test[\"ID\"],\n        \"dataset\": dataset_test[\"dataset\"],\n        \"label_positive_probability\": probabilities\n    })\n\n    return predictions_df\n\n\n# Define function to create submission.csv\ndef prepare_submission(predictions_df, sample_path, output_path):\n    sample_df = pd.read_csv(sample_path)\n    sample_df = sample_df.drop(columns=['label_positive_probability'])\n\n    merged = pd.merge(\n        sample_df,\n        predictions_df,\n        on=['ID', 'dataset'],\n        how='left'\n    )\n\n    merged = merged.fillna(0.5)\n    merged = merged.drop_duplicates(subset=['ID', 'dataset'], keep='first')\n\n    merged.to_csv(output_path, index=False)\n    print(f\"Saved submission to: {output_path}\")\n\n\n# Define main workflow\ndef main():\n    PATH_DATASET = \"/kaggle/input/adaptive-immune-profiling-challenge-2025\"\n    PATH_TRAIN_DATASETS = os.path.join(PATH_DATASET, 'train_datasets', 'train_datasets')\n    PATH_TEST_DATASETS = os.path.join(PATH_DATASET, 'test_datasets', 'test_datasets')\n\n    train_folders = sorted(os.listdir(PATH_TRAIN_DATASETS))\n    test_folders = sorted(os.listdir(PATH_TEST_DATASETS))\n\n    print(\"Loading Train/Test datasets...\")\n    dataset_train, dataset_test = load_all_datasets(\n        train_folders,\n        test_folders,\n        PATH_TRAIN_DATASETS,\n        PATH_TEST_DATASETS\n    )\n\n    X_train = dataset_train.drop(['label_positive', 'ID', 'dataset'], axis=1).fillna(0)\n    y_train = dataset_train['label_positive']\n    X_test = dataset_test.drop(['ID', 'dataset'], axis=1).fillna(0)\n\n    excluded_features = ['TCRBV6-01', 'TCRBVA']\n    X_train = X_train.drop(excluded_features, axis=1, errors='ignore')\n\n    for col in set(X_train.columns) - set(X_test.columns):\n        X_test[col] = 0\n\n    X_test = X_test[X_train.columns]\n\n    base_params = {\n        'eval_metric': 'logloss',\n        'objective': 'binary:logistic',\n        'random_state': 42,\n        'importance_type': 'gain'\n    }\n\n    param_grid = {\n        'colsample_bytree': [0.58, 0.63842335244, 0.70],\n        'learning_rate': [0.02, 0.03256233, 0.05],\n        'max_depth': [18, 20, 22],\n        'reg_alpha': [0.05, 0.087314708, 0.15],\n        'reg_lambda': [0.003, 0.0072173962, 0.02],\n        'subsample': [0.7, 0.8, 0.9]\n    }\n\n    best_model = run_grid_search_xgb(\n        X_train,\n        y_train,\n        base_params,\n        param_grid,\n        n_splits=8\n    )\n\n    final_model = train_final_model(\n        best_model,\n        X_train,\n        y_train\n    )\n\n    predictions = generate_predictions(\n        final_model,\n        X_test,\n        dataset_test\n    )\n\n    sample_path = os.path.join(PATH_DATASET, \"sample_submissions.csv\")\n    prepare_submission(\n        predictions,\n        sample_path,\n        \"submission.csv\"\n    )\n\n\n# Run main workflow\nif __name__ == \"__main__\":\n    main()","metadata":{"_uuid":"97e93980-1a13-45ed-acb2-0e2598bd19f3","_cell_guid":"3640f7c8-2ac9-4dae-b515-645da8ebed4e","trusted":true,"collapsed":false,"jupyter":{"outputs_hidden":false}},"outputs":[],"execution_count":null}]}