Merge branch 'main' into add_lightning_DLI

Author: nvkevlu

examples/tutorials/self-paced-training/part-1_federated_learning_introduction/chapter-2_develop_federated_learning_applications/02.3_convert_machine_learning_to_federated_learning/02.3.3_convert_survival_analysis_to_federated_learning/code/figs/km_curve_baseline.png

@@ -0,0 +1,115 @@
+# Copyright (c) 2025, 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 os
+
+from src.kaplan_meier_wf import KM
+from src.kaplan_meier_wf_he import KM_HE
+
+from nvflare import FedJob
+from nvflare.job_config.script_runner import ScriptRunner
+
+
+def main():
+    args = define_parser()
+    # Default paths
+    data_root = "/tmp/nvflare/dataset/km_data"
+    he_context_path = "/tmp/nvflare/he_context/he_context_client.txt"
+
+    # Set the script and config
+    if args.encryption:
+        job_name = "KM_HE"
+        train_script = "src/kaplan_meier_train_he.py"
+        script_args = f"--data_root {data_root} --he_context_path {he_context_path}"
+    else:
+        job_name = "KM"
+        train_script = "src/kaplan_meier_train.py"
+        script_args = f"--data_root {data_root}"
+
+    # Set the number of clients and threads
+    num_clients = args.num_clients
+    if args.num_threads:
+        num_threads = args.num_threads
+    else:
+        num_threads = num_clients
+
+    # Set the output workspace and job directories
+    workspace_dir = os.path.join(args.workspace_dir, job_name)
+    job_dir = args.job_dir
+
+    # Create the FedJob
+    job = FedJob(name=job_name, min_clients=num_clients)
+
+    # Define the KM controller workflow and send to server
+    if args.encryption:
+        controller = KM_HE(min_clients=num_clients, he_context_path=he_context_path)
+    else:
+        controller = KM(min_clients=num_clients)
+    job.to_server(controller)
+
+    # Define the ScriptRunner and send to all clients
+    runner = ScriptRunner(
+        script=train_script,
+        script_args=script_args,
+        params_exchange_format="raw",
+        launch_external_process=False,
+    )
+    job.to_clients(runner, tasks=["train"])
+
+    # Export the job
+    print("job_dir=", job_dir)
+    job.export_job(job_dir)
+
+    # Run the job
+    print("workspace_dir=", workspace_dir)
+    print("num_threads=", num_threads)
+    job.simulator_run(workspace_dir, n_clients=num_clients, threads=num_threads)
+
+
+def define_parser():
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        "--workspace_dir",
+        type=str,
+        default="/tmp/nvflare/jobs/km/workdir",
+        help="work directory, default to '/tmp/nvflare/jobs/km/workdir'",
+    )
+    parser.add_argument(
+        "--job_dir",
+        type=str,
+        default="/tmp/nvflare/jobs/km/jobdir",
+        help="directory for job export, default to '/tmp/nvflare/jobs/km/jobdir'",
+    )
+    parser.add_argument(
+        "--encryption",
+        action=argparse.BooleanOptionalAction,
+        help="whether to enable encryption, default to False",
+    )
+    parser.add_argument(
+        "--num_clients",
+        type=int,
+        default=5,
+        help="number of clients to simulate, default to 5",
+    )
+    parser.add_argument(
+        "--num_threads",
+        type=int,
+        help="number of threads to use for FL simulation, default to the number of clients if not specified",
+    )
+    return parser.parse_args()
+
+
+if __name__ == "__main__":
+    main()

examples/tutorials/self-paced-training/part-1_federated_learning_introduction/chapter-2_develop_federated_learning_applications/02.3_convert_machine_learning_to_federated_learning/02.3.3_convert_survival_analysis_to_federated_learning/code/figs/km_curve_fl.png

@@ -0,0 +1,3 @@
+lifelines
+tenseal
+scikit-survival

examples/tutorials/self-paced-training/part-1_federated_learning_introduction/chapter-2_develop_federated_learning_applications/02.3_convert_machine_learning_to_federated_learning/02.3.3_convert_survival_analysis_to_federated_learning/code/figs/km_curve_fl_he.png

@@ -0,0 +1,152 @@
+# Copyright (c) 2024, 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 json
+import os
+
+import matplotlib.pyplot as plt
+import numpy as np
+import pandas as pd
+from lifelines import KaplanMeierFitter
+from lifelines.utils import survival_table_from_events
+
+# (1) import nvflare client API
+import nvflare.client as flare
+from nvflare.app_common.abstract.fl_model import FLModel, ParamsType
+
+
+# Client code
+def details_save(kmf):
+    # Get the survival function at all observed time points
+    survival_function_at_all_times = kmf.survival_function_
+    # Get the timeline (time points)
+    timeline = survival_function_at_all_times.index.values
+    # Get the KM estimate
+    km_estimate = survival_function_at_all_times["KM_estimate"].values
+    # Get the event count at each time point
+    event_count = kmf.event_table.iloc[:, 0].values  # Assuming the first column is the observed events
+    # Get the survival rate at each time point (using the 1st column of the survival function)
+    survival_rate = 1 - survival_function_at_all_times.iloc[:, 0].values
+    # Return the results
+    results = {
+        "timeline": timeline.tolist(),
+        "km_estimate": km_estimate.tolist(),
+        "event_count": event_count.tolist(),
+        "survival_rate": survival_rate.tolist(),
+    }
+    file_path = os.path.join(os.getcwd(), "km_global.json")
+    print(f"save the details of KM analysis result to {file_path} \n")
+    with open(file_path, "w") as json_file:
+        json.dump(results, json_file, indent=4)
+
+
+def plot_and_save(kmf):
+    # Plot and save the Kaplan-Meier survival curve
+    plt.figure()
+    plt.title("Federated")
+    kmf.plot_survival_function()
+    plt.ylim(0, 1)
+    plt.ylabel("prob")
+    plt.xlabel("time")
+    plt.legend("", frameon=False)
+    plt.tight_layout()
+    file_path = os.path.join(os.getcwd(), "km_curve_fl.png")
+    print(f"save the curve plot to {file_path} \n")
+    plt.savefig(file_path)
+
+
+def main():
+    parser = argparse.ArgumentParser(description="KM analysis")
+    parser.add_argument("--data_root", type=str, help="Root path for data files")
+    args = parser.parse_args()
+
+    flare.init()
+
+    site_name = flare.get_site_name()
+    print(f"Kaplan-meier analysis for {site_name}")
+
+    # get local data
+    data_path = os.path.join(args.data_root, site_name + ".csv")
+    data = pd.read_csv(data_path)
+    event_local = data["event"]
+    time_local = data["time"]
+
+    while flare.is_running():
+        # receives global message from NVFlare
+        global_msg = flare.receive()
+        curr_round = global_msg.current_round
+        print(f"current_round={curr_round}")
+
+        if curr_round == 1:
+            # First round:
+            # Empty payload from server, send local histogram
+            # Convert local data to histogram
+            event_table = survival_table_from_events(time_local, event_local)
+            hist_idx = event_table.index.values.astype(int)
+            hist_obs = {}
+            hist_cen = {}
+            for idx in range(max(hist_idx)):
+                hist_obs[idx] = 0
+                hist_cen[idx] = 0
+            # Assign values
+            idx = event_table.index.values.astype(int)
+            observed = event_table["observed"].to_numpy()
+            censored = event_table["censored"].to_numpy()
+            for i in range(len(idx)):
+                hist_obs[idx[i]] = observed[i]
+                hist_cen[idx[i]] = censored[i]
+            # Send histograms to server
+            response = FLModel(params={"hist_obs": hist_obs, "hist_cen": hist_cen}, params_type=ParamsType.FULL)
+            flare.send(response)
+
+        elif curr_round == 2:
+            # Get global histograms
+            hist_obs_global = global_msg.params["hist_obs_global"]
+            hist_cen_global = global_msg.params["hist_cen_global"]
+            # Unfold histogram to event list
+            time_unfold = []
+            event_unfold = []
+            for i in hist_obs_global.keys():
+                for j in range(hist_obs_global[i]):
+                    time_unfold.append(i)
+                    event_unfold.append(True)
+                for k in range(hist_cen_global[i]):
+                    time_unfold.append(i)
+                    event_unfold.append(False)
+            time_unfold = np.array(time_unfold)
+            event_unfold = np.array(event_unfold)
+
+            # Perform Kaplan-Meier analysis on global aggregated information
+            # Create a Kaplan-Meier estimator
+            kmf = KaplanMeierFitter()
+
+            # Fit the model
+            kmf.fit(durations=time_unfold, event_observed=event_unfold)
+
+            # Plot and save the KM curve
+            plot_and_save(kmf)
+
+            # Save details of the KM result to a json file
+            details_save(kmf)
+
+            # Send a simple response to server
+            response = FLModel(params={}, params_type=ParamsType.FULL)
+            flare.send(response)
+
+    print(f"finish send for {site_name}, complete")
+
+
+if __name__ == "__main__":
+    main()