Lokahi_data / app.py
eaglelandsonce's picture
Update app.py
da1d261 verified
raw
history blame
11.4 kB
import streamlit as st
import pandas as pd
import numpy as np
import random
from datetime import datetime, timedelta
# Seed for reproducibility
np.random.seed(42)
# Function to generate synthetic BreastCancer data
def generate_breast_cancer_data(num_patients):
primary_keys = [f"PPK_{i+1:05d}" for i in range(num_patients)]
ages = []
menopausal_status = []
tumor_sizes = []
lymph_nodes = []
grades = []
stages = []
er_status = []
pr_status = []
her2_status = []
ki67_level = []
tnbc_status = []
brca_mutation = []
overall_health = []
genomic_score = []
treatment = []
for i in range(num_patients):
age = int(np.random.normal(60, 10))
age = max(30, min(age, 80))
ages.append(age)
menopausal = "Post-menopausal" if age >= 50 else "Pre-menopausal"
menopausal_status.append(menopausal)
tumor_size = round(np.random.lognormal(mean=0.7, sigma=0.5), 2)
tumor_sizes.append(tumor_size)
lymph_node = (
"Positive"
if (tumor_size > 2.0 and np.random.rand() < 0.6)
or (tumor_size <= 2.0 and np.random.rand() < 0.3)
else "Negative"
)
lymph_nodes.append(lymph_node)
grade = np.random.choice([1, 2, 3], p=[0.1, 0.4, 0.5] if tumor_size > 2.0 else [0.3, 0.5, 0.2])
grades.append(grade)
if tumor_size <= 2.0 and lymph_node == "Negative":
stage = "I"
elif (tumor_size > 2.0 and tumor_size <= 5.0) and lymph_node == "Negative":
stage = "II"
elif lymph_node == "Positive" or tumor_size > 5.0:
stage = "III"
else:
stage = "II"
if np.random.rand() < 0.05:
stage = "IV"
stages.append(stage)
er = np.random.choice(["Positive", "Negative"], p=[0.75, 0.25])
pr = "Positive" if er == "Positive" and np.random.rand() > 0.1 else "Negative"
er_status.append(er)
pr_status.append(pr)
her2 = np.random.choice(["Positive", "Negative"], p=[0.3, 0.7] if grade == 3 else [0.15, 0.85])
her2_status.append(her2)
ki67 = "High" if grade == 3 and np.random.rand() < 0.8 else "Low"
ki67_level.append(ki67)
tnbc = "Positive" if er == "Negative" and pr == "Negative" and her2 == "Negative" else "Negative"
tnbc_status.append(tnbc)
brca = "Positive" if (tnbc == "Positive" or age < 40) and np.random.rand() < 0.2 else "Negative"
brca_mutation.append(brca)
health = "Good" if age < 65 and np.random.rand() < 0.9 else "Poor"
overall_health.append(health)
recurrence_score = (
np.random.choice(["Low", "Intermediate", "High"], p=[0.6, 0.3, 0.1])
if er == "Positive" and her2 == "Negative"
else "N/A"
)
genomic_score.append(recurrence_score)
if stage in ["I", "II"]:
if tnbc == "Positive":
treat = "Surgery, Chemotherapy, and Radiation Therapy"
elif er == "Positive" and recurrence_score != "N/A":
if recurrence_score == "High":
treat = "Surgery, Chemotherapy, Hormone Therapy, and Radiation Therapy"
elif recurrence_score == "Intermediate":
treat = "Surgery, Consider Chemotherapy, Hormone Therapy, and Radiation Therapy"
else:
treat = "Surgery, Hormone Therapy, and Radiation Therapy"
elif her2 == "Positive":
treat = "Surgery, HER2-Targeted Therapy, Chemotherapy, and Radiation Therapy"
else:
treat = "Surgery, Chemotherapy, and Radiation Therapy"
elif stage == "III":
treat = (
"Neoadjuvant Chemotherapy, Surgery, Radiation Therapy"
+ (", HER2-Targeted Therapy" if her2 == "Positive" else "")
+ (", Hormone Therapy" if er == "Positive" else "")
)
else:
treat = "Systemic Therapy (Palliative Care)"
treatment.append(treat)
breast_cancer_data = {
"PRIMARY_PERSON_KEY": primary_keys,
"Age": ages,
"Menopausal Status": menopausal_status,
"Tumor Size (cm)": tumor_sizes,
"Lymph Node Involvement": lymph_nodes,
"Tumor Grade": grades,
"Tumor Stage": stages,
"ER Status": er_status,
"PR Status": pr_status,
"HER2 Status": her2_status,
"Ki-67 Level": ki67_level,
"TNBC Status": tnbc_status,
"BRCA Mutation": brca_mutation,
"Overall Health": overall_health,
"Genomic Recurrence Score": genomic_score,
"Treatment": treatment,
}
return pd.DataFrame(breast_cancer_data)
# Function to generate Members
def generate_members_from_breast_cancer(breast_cancer_df):
return pd.DataFrame({
"MEMBER_ID": breast_cancer_df["PRIMARY_PERSON_KEY"],
"PRIMARY_PERSON_KEY": breast_cancer_df["PRIMARY_PERSON_KEY"],
"MEM_GENDER": ["F"] * len(breast_cancer_df),
"MEM_ETHNICITY": np.random.choice(["Hispanic", "Non-Hispanic", None], len(breast_cancer_df)),
"MEM_RACE": np.random.choice(["White", "Black", "Asian", None], len(breast_cancer_df)),
"MEM_STATE": np.random.choice(["MI", "HI", "CA"], len(breast_cancer_df)),
"MEM_ZIP3": np.random.randint(100, 999, len(breast_cancer_df)),
})
# Function to generate Enrollments
def generate_enrollments_from_breast_cancer(breast_cancer_df):
return pd.DataFrame({
"PRIMARY_PERSON_KEY": breast_cancer_df["PRIMARY_PERSON_KEY"],
"MEM_STAT": np.random.choice(["ACTIVE", "INACTIVE"], len(breast_cancer_df)),
"PAYER_LOB": np.random.choice(["MEDICAID", "COMMERCIAL", "MEDICARE"], len(breast_cancer_df)),
"PAYER_TYPE": np.random.choice(["PPO", "HMO"], len(breast_cancer_df)),
"RELATION": np.random.choice(["SUBSCRIBER", "DEPENDENT"], len(breast_cancer_df)),
})
# Function to generate Services
def generate_services(num_services, primary_keys):
return pd.DataFrame({
"PRIMARY_PERSON_KEY": np.random.choice(primary_keys, num_services),
"SERVICE_SETTING": np.random.choice(["OUTPATIENT", "INPATIENT"], num_services),
"PROC_CODE": np.random.randint(1000, 9999, num_services),
"SERVICE_DATE": pd.date_range(start="2023-01-01", periods=num_services).to_numpy(),
"AMOUNT_BILLED": np.random.uniform(500, 15000, num_services),
"AMOUNT_PAID": np.random.uniform(500, 15000, num_services),
"CLAIM_STATUS": np.random.choice(["PAID", "DENIED", "PENDING"], num_services),
"RELATION": np.random.choice(["SUBSCRIBER", "DEPENDENT"], num_services),
})
# Function to generate Providers
def generate_providers(num_providers):
return pd.DataFrame({
"PROVIDER_ID": [f"PROV_{i+1:05d}" for i in range(num_providers)],
"PROV_NAME": np.random.choice(["Clinic A", "Clinic B", "Clinic C"], num_providers),
"PROV_STATE": np.random.choice(["MI", "HI", "CA"], num_providers),
"PROV_ZIP": np.random.randint(10000, 99999, num_providers),
"PROV_SPECIALTY": np.random.choice(["Oncology", "Radiology", "Surgery"], num_providers),
"PROV_TAXONOMY": np.random.choice(["208100000X", "207RE0101X"], num_providers),
})
# Function to generate Wearable Data
def generate_wearable_data(num_patients, num_measurements, start_datetime, time_interval, cancer_rate, chemo_brain_effect, primary_keys):
num_cancer_patients = int((cancer_rate / 100) * num_patients)
cancer_patients = set(random.sample(primary_keys, num_cancer_patients))
baseline_activity = 2000
baseline_heart_rate = 80
baseline_o2 = 98.2
activity_reduction_factor = (100 - chemo_brain_effect) / 100.0
chemo_heart_rate_increase = 5
data_rows = []
timestamps = [start_datetime + i * time_interval for i in range(num_measurements)]
for pkey in primary_keys:
is_cancer = pkey in cancer_patients
for ts in timestamps:
activity_var = random.randint(-300, 300)
hr_var = random.randint(-3, 3)
o2_var = random.uniform(-0.3, 0.3)
if is_cancer:
activity = int((baseline_activity + activity_var) * activity_reduction_factor)
heart_rate = baseline_heart_rate + hr_var + chemo_heart_rate_increase
else:
activity = baseline_activity + activity_var
heart_rate = baseline_heart_rate + hr_var
o2_sat = baseline_o2 + o2_var
activity = max(activity, 0)
heart_rate = max(heart_rate, 50)
o2_sat = max(o2_sat, 90.0)
data_rows.append([
pkey,
ts.strftime("%Y-%m-%d %H:%M:%S"),
activity,
heart_rate,
round(o2_sat, 1)
])
return pd.DataFrame(data_rows, columns=["PRIMARY_PERSON_KEY", "Measurement_Timestamp", "Activity_Level", "Heart_Rate", "O2_Saturation"])
# Main Streamlit App
st.title("Synthetic Medical Data Generator with Wearable Data")
# Sliders
num_patients = st.slider("Number of Breast Cancer Patients to Generate", 10, 1000, 100)
num_measurements = st.slider("Measurements per Patient (Wearable Data)", 1, 100, 10)
num_services = st.slider("Number of Services to Generate", 10, 2000, 500)
num_providers = st.slider("Number of Providers to Generate", 10, 500, 100)
start_date = st.date_input("Wearable Data Start Date", value=datetime(2024, 12, 1))
start_time = st.time_input("Wearable Data Start Time", value=datetime(2024, 12, 1, 8, 0).time())
cancer_rate = st.slider("Percentage of Patients with Cancer (Wearable Data)", 0, 100, 30)
chemo_brain_effect = st.slider("Chemo Brain Impact on Activity Level (in % reduction)", 0, 50, 20)
if st.button("Generate Data"):
primary_keys = [f"PPK_{i+1:05d}" for i in range(num_patients)]
wearable_start_datetime = datetime.combine(start_date, start_time)
breast_cancer_df = generate_breast_cancer_data(num_patients)
members_df = generate_members_from_breast_cancer(breast_cancer_df)
enrollments_df = generate_enrollments_from_breast_cancer(breast_cancer_df)
services_df = generate_services(num_services, primary_keys)
providers_df = generate_providers(num_providers)
wearable_data = generate_wearable_data(
num_patients, num_measurements, wearable_start_datetime, timedelta(hours=1), cancer_rate, chemo_brain_effect, primary_keys
)
st.subheader("Breast Cancer Data")
st.dataframe(breast_cancer_df.head())
st.download_button("Download Breast Cancer Data", breast_cancer_df.to_csv(index=False), "breast_cancer.csv")
st.subheader("Members Data")
st.dataframe(members_df.head())
st.download_button("Download Members Data", members_df.to_csv(index=False), "members.csv")
st.subheader("Enrollments Data")
st.dataframe(enrollments_df.head())
st.download_button("Download Enrollments Data", enrollments_df.to_csv(index=False), "enrollments.csv")
st.subheader("Services Data")
st.dataframe(services_df.head())
st.download_button("Download Services Data", services_df.to_csv(index=False), "services.csv")
st.subheader("Providers Data")
st.dataframe(providers_df.head())
st.download_button("Download Providers Data", providers_df.to_csv(index=False