update baseline script, remove complex settings and keep basic only

examples/advanced/kaplan-meier-he/baseline_kaplan_meier.py

@@ -0,0 +1,72 @@
+# Copyright (c) 2023, NVIDIA CORPORATION.  All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import argparse
+
+import matplotlib.pyplot as plt
+import numpy as np
+from lifelines import KaplanMeierFitter
+from sksurv.datasets import load_veterans_lung_cancer
+
+
+def args_parser():
+    parser = argparse.ArgumentParser(description="Kaplan Meier Survival Analysis Baseline")
+    parser.add_argument(
+        "--output_curve_path",
+        type=str,
+        default="./km_curve_baseline.png",
+        help="save path for the output curve",
+    )
+    return parser
+
+
+def prepare_data(bin_days: int = 7):
+    data_x, data_y = load_veterans_lung_cancer()
+    total_data_num = data_x.shape[0]
+    print(f"Total data count: {total_data_num}")
+    event = data_y["Status"]
+    time = data_y["Survival_in_days"]
+    # Categorize data to a bin, default is a week (7 days)
+    time = np.ceil(time / bin_days).astype(int)
+    return event, time
+
+
+def main():
+    parser = args_parser()
+    args = parser.parse_args()
+
+    # Set parameters
+    output_curve_path = args.output_curve_path
+
+    # Generate data
+    event, time = prepare_data()
+
+    # Fit and plot Kaplan Meier curve with lifelines
+    kmf = KaplanMeierFitter()
+    # Fit the survival data
+    kmf.fit(time, event)
+    # Plot and save the Kaplan-Meier survival curve
+    plt.figure()
+    plt.title("Baseline")
+    kmf.plot_survival_function()
+    plt.ylim(0, 1)
+    plt.ylabel("prob")
+    plt.xlabel("time")
+    plt.legend("", frameon=False)
+    plt.tight_layout()
+    plt.savefig(output_curve_path)
+
+
+if __name__ == "__main__":
+    main()

examples/advanced/kaplan-meier-he/jobs/km_he/app/custom/km_train.py

@@ -164,7 +164,7 @@ def main():
             # Fit the model
             kmf.fit(durations=time_unfold, event_observed=event_unfold)
 
-            # Plot and save KM curve
+            # Plot and save the Kaplan-Meier survival curve
             plt.figure()
             plt.title("Federated HE")
             kmf.plot_survival_function()