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patient_MIMICIII_exp.py
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patient_MIMICIII_exp.py
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import pandas as pd
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
import random
from sklearn.model_selection import train_test_split
import nlpaug.augmenter.word as naw
import torch.optim as optim
from torch.utils.data import DataLoader, TensorDataset, Dataset, Subset
from transformers import BertTokenizer, BertModel, RobertaTokenizer, RobertaModel
from scipy.stats import wasserstein_distance
df = pd.read_csv("structured_MIMICIII.csv")
df_notes = pd.read_csv("unstructured_MIMICIII.csv")
df_demographics = df[['subject_id', 'gender', 'ethnic_group', 'race', 'age', 'insurance', 'readmission_30_days_label']]
df_demographics = df_demographics.drop_duplicates()
df_longitudinal = df[['subject_id', 'heartrate', 'sysbp', 'diasbp', 'meanbp', 'resprate', 'tempc', 'spo2',
'Anion gap', 'Arterial Base Excess', 'Arterial CO2 Pressure',
'Arterial O2 pressure', 'BUN', 'Calcium non-ionized',
'Chloride (serum)', 'Creatinine', 'Glucose (serum)',
'Glucose finger stick', 'HCO3 (serum)', 'Hematocrit (serum)',
'Hemoglobin', 'Magnesium', 'PH (Arterial)', 'Phosphorous',
'Platelet Count', 'Potassium (serum)', 'Sodium (serum)', 'WBC']]
def generate_different_category(original, categories):
"""Select a different category than the original."""
synthetic = np.random.choice(categories)
while synthetic == original:
synthetic = np.random.choice(categories)
return synthetic
synthetic_sex = df_demographics['gender'].apply(lambda x: generate_different_category(x, [0, 1]))
synthetic_ethnic_group = df_demographics['ethnic_group'].apply(lambda x: generate_different_category(x, [0, 1, 2]))
synthetic_race = df_demographics['race'].apply(lambda x: generate_different_category(x, [0, 1, 2, 3, 4]))
synthetic_coverage = df_demographics['insurance'].apply(lambda x: generate_different_category(x, [0, 1, 2]))
# Create synthetic data for age ensuring it stays within the range of 50-100
# We will randomly select an age within the range that is different from the original age
age_groups = {
'50-60': range(50, 61),
'60-70': range(60, 71),
'70-80': range(70, 81),
'80-90': range(80, 91),
'90-100': range(90, 101)
}
def get_age_group(age):
for group, ages in age_groups.items():
if age in ages:
return group
return None
def get_synthetic_age(real_age_group):
other_groups = [group for group in age_groups if group != real_age_group]
selected_group = random.choice(other_groups)
return random.choice(list(age_groups[selected_group]))
synthetic_age = df_demographics['age'].apply(lambda x: get_synthetic_age(get_age_group(x)))
#age_range = list(range(50, 101))
#synthetic_age = df_demographics['age'].apply(lambda x: generate_different_category(x, age_range))
# Compile the synthetic demographic DataFrame
df_synthetic_demographics = pd.DataFrame({
'gender': synthetic_sex,
'ethnic_group': synthetic_ethnic_group,
'race': synthetic_race,
'age': synthetic_age,
'insurance': synthetic_coverage,
})
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
longitudinal_features = df.loc[:, 'heartrate':'WBC']
longitudinal_features_array = longitudinal_features.to_numpy()
data_min = longitudinal_features_array.min(axis=(0, 1), keepdims=True)
data_max = longitudinal_features_array.max(axis=(0, 1), keepdims=True)
# Normalize data to [-1, 1]
normalized_data = (longitudinal_features_array - data_min) / (data_max - data_min) * 2 - 1
num_patients = 4302
num_timepoints = 12
num_features = 27
data_reshaped = normalized_data.reshape((num_patients, num_timepoints, num_features))
# Convert the NumPy array to a PyTorch tensor and send to device
data_tensor = torch.tensor(data_reshaped, dtype=torch.float32).to(device)
# Flatten the tensor to fit the GAN input shape: [num_patients * num_timepoints, num_features]
data_tensor_flat = data_tensor.view(num_patients * num_timepoints, num_features)
# Define the GAN's Generator and Discriminator architectures
class Generator(nn.Module):
def __init__(self, input_size, output_size):
super(Generator, self).__init__()
self.model = nn.Sequential(
nn.Linear(input_size, 128),
nn.BatchNorm1d(128),
nn.ReLU(),
nn.Linear(128, 256),
nn.BatchNorm1d(256),
nn.ReLU(),
nn.Linear(256, output_size),
nn.Tanh()
)
def forward(self, z):
return self.model(z)
class Discriminator(nn.Module):
def __init__(self):
super(Discriminator, self).__init__()
self.model = nn.Sequential(
nn.Linear(num_features, 128),
nn.LeakyReLU(0.2),
nn.Dropout(0.3),
nn.Linear(128, 256),
nn.LeakyReLU(0.2),
nn.Dropout(0.3),
nn.Linear(256, 1),
nn.Sigmoid()
)
def forward(self, patient_data):
return self.model(patient_data)
# Initialize the Generator and Discriminator
z_dim = 100
generator = Generator(input_size=z_dim, output_size=num_features).to(device)
generator = torch.nn.DataParallel(generator)
discriminator = Discriminator().to(device)
discriminator = torch.nn.DataParallel(discriminator)
# Set up optimizers for both G and D
# Optimizers
optimizer_G = optim.Adam(generator.parameters(), lr=0.0002, betas=(0.5, 0.999))
optimizer_D = optim.Adam(discriminator.parameters(), lr=0.0002, betas=(0.5, 0.999))
# Learning rate schedulers
scheduler_G = torch.optim.lr_scheduler.StepLR(optimizer_G, step_size=10, gamma=0.9)
scheduler_D = torch.optim.lr_scheduler.StepLR(optimizer_D, step_size=10, gamma=0.9)
# Binary cross entropy loss and DataLoader
criterion = nn.BCELoss()
dataloader = DataLoader(TensorDataset(data_tensor_flat), batch_size=64, shuffle=True)
# Training loop for the GAN
epochs = 10
for epoch in range(epochs):
for i, (patients_data,) in enumerate(dataloader):
real_data = patients_data
real_labels = torch.full((patients_data.size(0), 1), 0.9, device=device)
# Generate fake data and labels
z = torch.randn(patients_data.size(0), z_dim, device=device)
fake_data = generator(z)
fake_labels = torch.full((patients_data.size(0), 1), 0.1, device=device)
# Train the discriminator on real data
optimizer_D.zero_grad()
real_loss = criterion(discriminator(real_data), real_labels)
real_loss.backward()
# Train the discriminator on fake data
fake_loss = criterion(discriminator(fake_data.detach()), fake_labels)
fake_loss.backward()
optimizer_D.step()
scheduler_D.step()
# Train the generator
optimizer_G.zero_grad()
generator_loss = criterion(discriminator(fake_data), real_labels)
generator_loss.backward()
optimizer_G.step()
scheduler_G.step()
if epoch % 10 == 0:
print(f"Epoch {epoch}/{epochs} | D Loss: {real_loss + fake_loss} | G Loss: {generator_loss}")
# Generate synthetic data for the entire dataset
z = torch.randn(num_patients * num_timepoints, z_dim, device=device)
synthetic_data_flat = generator(z)
# Optionally reshape it to the original data format
synthetic_longitudinal_normalized = synthetic_data_flat.view(num_patients, num_timepoints, num_features).detach().cpu().numpy()
# Denormalize the synthetic data back to the original feature ranges
synthetic_longitudinal = synthetic_longitudinal_normalized * (data_max - data_min) / 2 + (data_max + data_min) / 2
synthetic_longitudinal = torch.tensor(synthetic_longitudinal).float()
df_real_demographics = df_demographics[['gender', 'ethnic_group', 'race', 'age', 'insurance']]
real_demographics = torch.tensor(df_real_demographics.values).float()
synthetic_demographics = torch.tensor(df_synthetic_demographics.values).float()
real_longitudinal = torch.tensor(longitudinal_features_array.reshape((num_patients, num_timepoints, num_features))).float()
# synthetic note obtained from Llama2 generation using notes_for_llama2.py
#tokenizer = BertTokenizer.from_pretrained('bert-base-uncased')
#model = BertModel.from_pretrained('bert-base-uncased')
tokenizer = RobertaTokenizer.from_pretrained('roberta-base')
model = RobertaModel.from_pretrained('roberta-base')
model.to(device)
model = torch.nn.DataParallel(model)
# Function to create embeddings for a batch of texts
def create_embeddings(texts):
# Tokenize and prepare the texts as BERT input format
inputs = tokenizer(texts, padding=True, truncation=True, max_length=512, return_tensors="pt")
# Get embeddings
with torch.no_grad():
outputs = model(**inputs)
# Use the output of the first token ([CLS] token) for sentence embedding
return outputs.last_hidden_state[:, 0, :]
# Process the 'notes' column in batches and collect embeddings
batch_size = 32 # You can adjust the batch size depending on your memory availability
embeddings = []
for start_idx in range(0, len(df_notes['note']), batch_size):
batch_texts = df_notes['note'][start_idx:start_idx + batch_size].tolist()
batch_embeddings = create_embeddings(batch_texts)
embeddings.append(batch_embeddings)
# Concatenate all batch embeddings into a single tensor
real_notes = torch.cat(embeddings, dim=0)
embeddings = []
for start_idx in range(0, len(df_notes['synthetic_note']), batch_size):
batch_texts = df_notes['synthetic_note'][start_idx:start_idx + batch_size].tolist()
batch_embeddings = create_embeddings(batch_texts)
embeddings.append(batch_embeddings)
# Concatenate all batch embeddings into a single tensor
synthetic_notes = torch.cat(embeddings, dim=0)
binary_labels = torch.tensor(df_demographics['readmission_30_days_label'].values).unsqueeze(1)
class PatientPairDataset(Dataset):
def __init__(self, real_data, synthetic_data, labels, use_synthetic=True):
# Initialization with real and synthetic data, and labels
self.real_demographics, self.real_longitudinal, self.real_notes = real_data
self.synthetic_demographics, self.synthetic_longitudinal, self.synthetic_notes = synthetic_data
self.labels = labels
self.use_synthetic = use_synthetic # Control flag for using synthetic data
# Ensure all components have the same length
assert len(self.real_demographics) == len(self.real_longitudinal) == len(self.real_notes) == \
len(self.synthetic_demographics) == len(self.synthetic_longitudinal) == len(self.synthetic_notes) == \
len(self.labels), "All components of the dataset must have the same length."
def __len__(self):
return len(self.labels)
def __getitem__(self, idx):
# Return data based on the use_synthetic flag
if self.use_synthetic:
# For training, return both real and synthetic data
return (self.real_demographics[idx], self.real_longitudinal[idx], self.real_notes[idx],
self.synthetic_demographics[idx], self.synthetic_longitudinal[idx], self.synthetic_notes[idx],
self.labels[idx])
else:
# For testing, return only real data
return (self.real_demographics[idx], self.real_longitudinal[idx], self.real_notes[idx], self.labels[idx])
'''
def split_indices(dataset, train_ratio=0.8):
# Function to split the dataset into train and test indices
dataset_size = len(dataset)
indices = list(range(dataset_size))
split = int(train_ratio * dataset_size)
random.shuffle(indices)
return indices[:split], indices[split:]
'''
def stratified_split_indices(labels, train_ratio=0.8):
# Assuming labels is a list or numpy array of binary labels
indices = list(range(len(labels)))
train_indices, test_indices = train_test_split(indices, train_size=train_ratio, stratify=labels)
return train_indices, test_indices
# Assuming real_data, synthetic_data, and labels are defined
real_data = (real_demographics, real_longitudinal, real_notes)
synthetic_data = (synthetic_demographics, synthetic_longitudinal, synthetic_notes)
labels = binary_labels
full_dataset = PatientPairDataset(real_data, synthetic_data, labels)
# Split indices for train and test sets
#train_indices, test_indices = split_indices(full_dataset)
train_indices, test_indices = stratified_split_indices(labels, train_ratio=0.8)
# Create train and test datasets
train_dataset = Subset(PatientPairDataset(real_data, synthetic_data, labels, use_synthetic=True), train_indices)
test_dataset = Subset(PatientPairDataset(real_data, synthetic_data, labels, use_synthetic=False), test_indices)
# DataLoaders for the train and test datasets
train_dataloader = DataLoader(train_dataset, batch_size=32, shuffle=True)
test_dataloader = DataLoader(test_dataset, batch_size=32, shuffle=False)
class DynamicRelevanceBiasMitigationLayer(nn.Module):
"""
Dynamically adjusts the influence of different data types to mitigate potential biases.
"""
def __init__(self, input_size):
super().__init__()
self.adjustment_weights = nn.Parameter(torch.randn(input_size))
def forward(self, combined_input):
# Use broadcasting for adjustment weights without explicit expansion
adjusted_weights = torch.sigmoid(self.adjustment_weights)
adjusted_output = combined_input * adjusted_weights
return adjusted_output
class FairnessAwareModel(nn.Module):
def __init__(self):
super().__init__()
# Assuming each branch processes its input and reduces it to a 32-dimensional output
self.demographics_branch = nn.Sequential(nn.Linear(5, 32), nn.BatchNorm1d(32), nn.ReLU())
self.longitudinal_branch = nn.Sequential(nn.Linear(12*27, 32), nn.BatchNorm1d(32), nn.ReLU())
self.notes_branch = nn.Sequential(nn.Linear(768, 32), nn.BatchNorm1d(32), nn.ReLU())
# DRBM Layer initialization
self.drbm_layer = DynamicRelevanceBiasMitigationLayer(32)
# Fusion layer to combine features from the three branches
self.fusion_layer = nn.Sequential(nn.Linear(32 * 3, 64), nn.BatchNorm1d(64), nn.ReLU(), nn.Dropout(0.5), nn.Linear(64, 32), nn.BatchNorm1d(32), nn.ReLU())
# Output layer for embeddings and classification
self.embedding_layer = nn.Sequential(nn.Linear(32, 16), nn.BatchNorm1d(16))
self.classifier = nn.Linear(16, 2) # Output logits for 2 classes (binary classification)
def forward(self, real_demographics, real_longitudinal, real_notes, synthetic_demographics, synthetic_longitudinal, synthetic_notes):
# Process real and synthetic data
# Flatten longitudinal data
real_longitudinal_flat = real_longitudinal.view(real_longitudinal.size(0), -1)
synthetic_longitudinal_flat = synthetic_longitudinal.view(synthetic_longitudinal.size(0), -1)
real_demo_repr = self.demographics_branch(real_demographics)
real_long_repr = self.longitudinal_branch(real_longitudinal_flat)
real_notes_repr = self.notes_branch(real_notes)
synthetic_demo_repr = self.demographics_branch(synthetic_demographics)
synthetic_long_repr = self.longitudinal_branch(synthetic_longitudinal_flat)
synthetic_notes_repr = self.notes_branch(synthetic_notes)
# Combine features from all branches
real_combined = self.fusion_layer(torch.cat([real_demo_repr, real_long_repr, real_notes_repr], dim=1))
synthetic_combined = self.fusion_layer(torch.cat([synthetic_demo_repr, synthetic_long_repr, synthetic_notes_repr], dim=1))
# Apply the DRBM layer for dynamic bias mitigation
real_adjusted = self.drbm_layer(real_combined)
synthetic_adjusted = self.drbm_layer(synthetic_combined)
# Process through the fusion layer and subsequent layers
real_embedding = self.embedding_layer(real_adjusted)
synthetic_embedding = self.embedding_layer(synthetic_adjusted)
logits = self.classifier(real_embedding)
classification_logits = F.softmax(logits, dim=1)
return real_embedding, synthetic_embedding, classification_logits
class FairnessAwareContrastiveLoss(nn.Module):
def __init__(self, alpha=0.65, beta=0.35, margin=1.0):
super().__init__()
self.alpha = alpha
self.beta = beta
self.margin = margin
self.cosine_similarity = nn.CosineSimilarity(dim=1)
def forward(self, real_embeddings, synthetic_embeddings):
# Standard Contrastive Loss Component
positive_similarity = self.cosine_similarity(real_embeddings, synthetic_embeddings)
batch_size = real_embeddings.size(0)
negative_similarity = sum(
self.cosine_similarity(real_embeddings[i].unsqueeze(0), synthetic_embeddings[j].unsqueeze(0))
for i in range(batch_size) for j in range(batch_size) if i != j
) / (batch_size * (batch_size - 1))
contrastive_loss = torch.mean(torch.clamp(self.margin - positive_similarity + negative_similarity, min=0))
# Fairness-aware Loss Component
fairness_loss = self.calculate_fairness_loss(real_embeddings, synthetic_embeddings)
# Combined Loss
combined_loss = self.beta * contrastive_loss + self.alpha * fairness_loss
return combined_loss
def calculate_fairness_loss(self, real_embeddings, synthetic_embeddings):
# Distance Component: Euclidean distance (L2 norm)
euclidean_distances = torch.norm(real_embeddings - synthetic_embeddings, dim=1, p=2)
# Angle Component: Cosine similarity (cosine of angle)
cosine_similarities = self.cosine_similarity(real_embeddings, synthetic_embeddings)
# Convert cosine similarities to angles in radians
angles = torch.acos(torch.clamp(cosine_similarities, -1.0, 1.0))
# Combine distance and angle components
# Harmonic mean of distances and angles
combined_metric = 2 * (euclidean_distances * angles) / (euclidean_distances + angles + 1e-8)
# Fairness loss is the mean of the combined metric
fairness_loss = torch.mean(combined_metric)
return fairness_loss
'''
class ContrastiveLoss(nn.Module):
def __init__(self, margin=1.0):
super().__init__()
self.margin = margin
self.cosine_similarity = nn.CosineSimilarity(dim=1)
def forward(self, real_embeddings, synthetic_embeddings):
# Calculate positive similarity
positive_similarity = self.cosine_similarity(real_embeddings, synthetic_embeddings)
# Calculate negative similarities
batch_size = real_embeddings.size(0)
negative_similarity = 0
for i in range(batch_size):
for j in range(batch_size):
if i != j:
negative_similarity += self.cosine_similarity(real_embeddings[i].unsqueeze(0), synthetic_embeddings[j].unsqueeze(0))
negative_similarity /= (batch_size * (batch_size - 1))
contrastive_loss = torch.mean(torch.clamp(self.margin - positive_similarity + negative_similarity, min=0))
return contrastive_loss
'''
model = FairnessAwareModel().to(device)
model = torch.nn.DataParallel(model)
contrastive_criterion = FairnessAwareContrastiveLoss().to(device)
class_weights = torch.tensor([3.5, 1.0], dtype=torch.float)
# Move the weights to the same device as your model
class_weights = class_weights.to(device)
# Create a weighted loss function
classification_criterion = nn.CrossEntropyLoss(weight=class_weights)
optimizer = optim.Adam(model.parameters(), lr=5e-5)
# Training loop
num_epochs = 10 # Define the number of epochs
for epoch in range(num_epochs):
# Training Phase
model.train()
train_total_contrastive_loss = 0.0
train_total_classification_loss = 0.0
train_correct_predictions = 0
train_total_samples = 0
for data in train_dataloader:
real_demographics, real_longitudinal, real_notes, synthetic_demographics, synthetic_longitudinal, synthetic_notes, labels = [d.to(device) for d in data]
# Zero the parameter gradients
optimizer.zero_grad()
# Forward pass
real_embedding, synthetic_embedding, logits = model(real_demographics, real_longitudinal, real_notes, synthetic_demographics, synthetic_longitudinal, synthetic_notes)
# Calculate the contrastive and classification loss
contrastive_loss = contrastive_criterion(real_embedding, synthetic_embedding)
classification_loss = classification_criterion(logits, labels.squeeze().long())
total_loss = contrastive_loss + classification_loss
# Backward pass and optimize
total_loss.backward()
optimizer.step()
# Accumulate losses and calculate accuracy
train_total_contrastive_loss += contrastive_loss.item()
train_total_classification_loss += classification_loss.item()
_, predicted = torch.max(logits, 1)
train_total_samples += labels.size(0)
train_correct_predictions += (predicted == labels.squeeze().long()).sum().item()
# Compute average training losses and accuracy
train_avg_contrastive_loss = train_total_contrastive_loss / len(train_dataloader)
train_avg_classification_loss = train_total_classification_loss / len(train_dataloader)
train_accuracy = 100 * train_correct_predictions / train_total_samples
# Testing Phase
model.eval()
test_total_loss = 0.0
test_correct_predictions = 0
test_total_samples = 0
test_demographics, test_ground_truth, test_predictions, test_logits = [], [], [], []
with torch.no_grad():
for real_demographics, real_longitudinal, real_notes, labels in test_dataloader:
real_demographics, real_longitudinal, real_notes, labels = real_demographics.to(device), real_longitudinal.to(device), real_notes.to(device), labels.to(device)
# Forward pass with real data only
real_embedding, _, logits = model(real_demographics, real_longitudinal, real_notes, real_demographics, real_longitudinal, real_notes)
# Calculate the classification loss
classification_loss = classification_criterion(logits, labels.squeeze().long())
test_total_loss += classification_loss.item()
# Calculate accuracy
_, predicted = torch.max(logits, 1)
test_total_samples += labels.size(0)
test_correct_predictions += (predicted == labels.squeeze().long()).sum().item()
test_ground_truth.extend(labels.tolist())
test_predictions.extend(predicted.tolist())
test_logits.extend(logits[:, 1].detach().cpu().numpy())
test_demographics.extend(real_demographics.detach().cpu().numpy())
# Compute average testing loss and accuracy
test_avg_loss = test_total_loss / len(test_dataloader)
test_accuracy = 100 * test_correct_predictions / test_total_samples
#test_logits_np = np.concatenate(test_logits)
# Print training and testing statistics
print(f"Epoch [{epoch+1}/{num_epochs}]:")
print(f" Training - Contrastive Loss: {train_avg_contrastive_loss:.4f}, Classification Loss: {train_avg_classification_loss:.4f}, Accuracy: {train_accuracy:.2f}%")
print(f" Testing - Loss: {test_avg_loss:.4f}, Accuracy: {test_accuracy:.2f}%")
epoch_str = f"epoch{epoch+1}"
np.save(f'{epoch_str}_readmission_test_ground_truth.npy', np.array(test_ground_truth))
np.save(f'{epoch_str}_readmission_test_predictions.npy', np.array(test_predictions))
np.save(f'{epoch_str}_readmission_test_logits.npy', np.array(test_logits))
np.save(f'{epoch_str}_readmission_test_demographics.npy', np.array(test_demographics))
# Optionally, save test ground truth and predictions
#test_ground_truth_np = np.array(test_ground_truth)
#test_predictions_np = np.array(test_predictions)
# Save as .npy files
#np.save('test_ground_truth.npy', test_ground_truth_np)
#np.save('test_predictions.npy', test_predictions_np)
#np.save('test_logits.npy', test_logits)