benchmarks/DeepLoc/membrane_localization_predictor.py

import torch
import torch.nn as nn
import torch.optim as optim
from torch.utils.data import DataLoader, Dataset
from sklearn.metrics import accuracy_score, precision_score, recall_score, f1_score, roc_auc_score

from tqdm import tqdm
from datetime import datetime
import pandas as pd
import numpy as np
import pickle
import os

# Hyperparameters dictionary
path = "/home/a03-sgoel/MDpLM"

hyperparams = {
    "batch_size": 1,
    "learning_rate": 4e-5,
    "num_epochs": 5,
    "max_length": 2000,
    "train_data": path + "/benchmarks/membrane_type_train.csv",
    "test_data" : path + "/benchmarks/membrane_type_test.csv",
    "val_data": "", # none
    "embeddings_pkl": "" # Need to generate ESM embeddings
}

# Dataset class can load pickle file
class LocalizationDataset(Dataset):
    def __init__(self, csv_file, embeddings_pkl, max_length=2000):
        self.data = pd.read_csv(csv_file)
        self.max_length = max_length

        # Map sequences to embeddings
        with open(embeddings_pkl, 'rb') as f:
            self.embeddings_dict = pickle.load(f)
        self.data['embedding'] = self.data['Sequence'].map(self.embeddings_dict)

        # Ensure sequences and embeddings are of the same length
        assert len(self.data) == len(self.data['embedding']), "CSV data and embeddings length mismatch"

        # Create multi-class label list
        self.data['label'] = self.data.iloc[:, 2:7].value.tolist()

    def __len__(self):
        return len(self.data)

    def __getitem__(self, idx):
        embeddings = torch.tensor(self.data['embedding'][idx], dtype=torch.float)
        labels = torch.tensor(self.data['label'][idx], dtype=torch.long)

        return embeddings, labels

# Multi-class localization predictor
class LocalizationPredictor(nn.Module):
    def __init__(self, input_dim, num_classes):
        super(LocalizationPredictor, self).__init__()
        self.classifier = nn.Linear(input_dim, num_classes) # 1280 x 4

    def forward(self, embeddings):
        avg_embedding = torch.mean(embeddings, dim=0) # Average embedding dimension: 1280
        logits = self.classifier(avg_embedding)
        return logits # pass logits of dimension 1x4 (4-class distribution) to CE loss

# Training function
def train(model, dataloader, optimizer, criterion, device):
    model.train()
    total_loss = 0
    for embeddings, labels in tqdm(dataloader):
        embeddings, labels = embeddings.to(device), labels.to(device)
        optimizer.zero_grad()
        outputs = model(embeddings)
        loss = criterion(outputs, labels)
        loss.backward()
        optimizer.step()
        total_loss += loss.item()
    return total_loss / len(dataloader)

# Evaluation function
def evaluate(model, dataloader, device):
    model.eval()
    preds, true_labels = [], []
    with torch.no_grad():
        for embeddings, labels in tqdm(dataloader):
            embeddings, labels = embeddings.to(device), labels.to(device)
            outputs = model(embeddings)
            preds.append(outputs.cpu().numpy())
            true_labels.append(labels.cpu().numpy())
    return preds, true_labels

# Metrics calculation
def calculate_metrics(preds, labels, threshold=0.5):
    flat_binary_preds, flat_labels = [], []

    for pred, label in zip(preds, labels):
        flat_binary_preds.extend((pred > threshold).astype(int).flatten())
        flat_labels.extend(label.flatten())

    flat_binary_preds = np.array(flat_binary_preds)
    flat_labels = np.array(flat_labels)

    accuracy = accuracy_score(flat_labels, flat_binary_preds)
    precision = precision_score(flat_labels, flat_binary_preds, average='macro')
    recall = recall_score(flat_labels, flat_binary_preds, average='macro')
    f1 = f1_score(flat_labels, flat_binary_preds, average='macro')

    return accuracy, precision, recall, f1


device = torch.device("cuda" if torch.cuda.is_available() else "cpu")

train_dataset = LocalizationDataset(hyperparams["train_data"], hyperparams["embeddings_pkl"], max_length=hyperparams["max_length"])
test_dataset = LocalizationDataset(hyperparams["test_data"], hyperparams["embeddings_pkl"], max_length=hyperparams["max_length"])

train_dataloader = DataLoader(train_dataset, batch_size=hyperparams["batch_size"], shuffle=True)
test_dataloader = DataLoader(test_dataset, batch_size=hyperparams["batch_size"], shuffle=False)

model = LocalizationPredictor(input_dim=1280, num_classes=4).to(device)
optimizer = optim.Adam(model.parameters(), lr=hyperparams["learning_rate"])
criterion = nn.CrossEntropyLoss()

# Train the model
for epoch in range(hyperparams["num_epochs"]):
    train_loss = train(model, train_dataloader, optimizer, criterion, device)
    print(f"EPOCH {epoch+1}/{hyperparams['num_epochs']}")
    print(f"TRAIN LOSS: {train_loss:.4f}")
    print("\n")

# Evaluate model on test dataset
print("Test set")
test_preds, test_labels = evaluate(model, test_dataloader, device)
test_metrics = calculate_metrics(test_preds, test_labels)
print("TEST METRICS:")
print(f"Accuracy: {test_metrics[0]:.4f}")
print(f"Precision: {test_metrics[1]:.4f}")
print(f"Recall: {test_metrics[2]:.4f}")
print(f"F1 Score: {test_metrics[3]:.4f}")