Add Length of Stay Dataset and Prediction Task

pyhealth/fake_los_data.csv

@@ -0,0 +1,6 @@
+patient_id,admission_date,discharge_date
+1,2023-01-01,2023-01-05
+2,2023-02-10,2023-02-15
+3,2023-03-20,2023-03-22
+4,2023-04-01,2023-04-10
+5,2023-05-05,2023-05-07

pyhealth/pyhealth/contrib/tasks/length_of_stay/fake_los_data.csv

@@ -0,0 +1,6 @@
+patient_id,admission_date,discharge_date
+1,2023-01-01,2023-01-05
+2,2023-02-10,2023-02-15
+3,2023-03-20,2023-03-22
+4,2023-04-01,2023-04-10
+5,2023-05-05,2023-05-07

pyhealth/pyhealth/contrib/tasks/length_of_stay/fakedata.py

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+import csv
+from datetime import datetime, timedelta
+
+def create_fake_los_data(filename="fake_los_data.csv"):
+    # Define headers expected by the LOS task
+    headers = ['admission_id', 'patient_id', 'admission_time', 'discharge_time']
+
+    # Prepare some example rows
+    base_date = datetime(2024, 1, 1, 10, 0)
+    rows = [
+        ['1', '1001', base_date.strftime("%Y-%m-%d %H:%M:%S"), (base_date + timedelta(days=4, hours=2)).strftime("%Y-%m-%d %H:%M:%S")],
+        ['2', '1002', (base_date + timedelta(days=1)).strftime("%Y-%m-%d %H:%M:%S"), (base_date + timedelta(days=3, hours=5)).strftime("%Y-%m-%d %H:%M:%S")],
+        ['3', '1003', (base_date + timedelta(days=2)).strftime("%Y-%m-%d %H:%M:%S"), (base_date + timedelta(days=5)).strftime("%Y-%m-%d %H:%M:%S")],
+    ]
+
+    # Write to CSV
+    with open(filename, mode='w', newline='') as csvfile:
+        writer = csv.writer(csvfile)
+        writer.writerow(headers)
+        writer.writerows(rows)
+
+    print(f"Created fake LOS data CSV file: {filename}")
+
+if __name__ == "__main__":
+    create_fake_los_data()

pyhealth/pyhealth/contrib/tasks/length_of_stay/lengthofstay.yaml

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+version: "1.4"
+
+tables:
+  admissions:
+    file_path: "fake_los_data.csv"
+    patient_id: "patient_id"
+    timestamp: "admission_date"
+    attributes:
+      - "patient_id"
+      - "admission_date"
+      - "discharge_date"

pyhealth/pyhealth/contrib/tasks/length_of_stay/lengthofstay.yaml.save

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+root: ./  # base path for your CSV files
+
+tables:
+  - fakedata.csv
+
+columns:
+  patient_id: patient_id
+  admission_time: admission_time
+  discharge_time: discharge_time
+  features:
+    - lab_results
+    - diagnoses
+  target:
+    length_of_stay: length_of_stay_days
+
+
+

pyhealth/pyhealth/contrib/tasks/length_of_stay/lengthofstay1.yaml

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+root: ./  # base path for your CSV files
+
+tables:
+  - fakedata.csv
+
+columns:
+  patient_id: patient_id
+  admission_time: admission_time
+  discharge_time: discharge_time
+  features:
+    - lab_results
+    - diagnoses
+  target:
+    length_of_stay: length_of_stay_days
+
+
+