SURE-tools 2.2.24__py3-none-any.whl → 2.4.34__py3-none-any.whl

SURE/TranscriptomeDecoder.py

@@ -0,0 +1,511 @@
+import torch
+import torch.nn as nn
+import torch.nn.functional as F
+import torch.optim as optim
+from torch.utils.data import Dataset, DataLoader
+import numpy as np
+from typing import Dict, Optional
+import warnings
+warnings.filterwarnings('ignore')
+
+class TranscriptomeDecoder:
+    """Transcriptome decoder"""
+    
+    def __init__(self, 
+                 latent_dim: int = 100,
+                 gene_dim: int = 60000,
+                 hidden_dim: int = 512,
+                 device: str = None):
+        """
+        Simple but powerful decoder for latent to transcriptome mapping
+        
+        Args:
+            latent_dim: Latent variable dimension (typically 50-100)
+            gene_dim: Number of genes (full transcriptome ~60,000)
+            hidden_dim: Hidden dimension optimized
+            device: Computation device
+        """
+        self.latent_dim = latent_dim
+        self.gene_dim = gene_dim
+        self.hidden_dim = hidden_dim
+        self.device = device or ('cuda' if torch.cuda.is_available() else 'cpu')
+        
+        # Initialize model
+        self.model = self._build_model()
+        self.model.to(self.device)
+        
+        # Training state
+        self.is_trained = False
+        self.training_history = None
+        self.best_val_loss = float('inf')
+        
+        print(f"🚀 SimpleTranscriptomeDecoder Initialized:")
+        print(f"   - Latent Dimension: {latent_dim}")
+        print(f"   - Gene Dimension: {gene_dim}")
+        print(f"   - Hidden Dimension: {hidden_dim}")
+        print(f"   - Device: {self.device}")
+        print(f"   - Parameters: {sum(p.numel() for p in self.model.parameters()):,}")
+    
+    class Decoder(nn.Module):
+        """Memory-efficient decoder architecture with dimension handling"""
+        
+        def __init__(self, latent_dim: int, gene_dim: int, hidden_dim: int):
+            super().__init__()
+            self.latent_dim = latent_dim
+            self.gene_dim = gene_dim
+            self.hidden_dim = hidden_dim
+            
+            # Stage 1: Latent variable expansion
+            self.latent_expansion = nn.Sequential(
+                nn.Linear(latent_dim, hidden_dim * 2),
+                nn.BatchNorm1d(hidden_dim * 2),
+                nn.GELU(),
+                nn.Dropout(0.1),
+                nn.Linear(hidden_dim * 2, hidden_dim),
+                nn.BatchNorm1d(hidden_dim),
+                nn.GELU(),
+            )
+            
+            # Stage 2: Direct projection to gene dimension (simpler approach)
+            self.gene_projector = nn.Sequential(
+                nn.Linear(hidden_dim, hidden_dim * 2),
+                nn.GELU(),
+                nn.Dropout(0.1),
+                nn.Linear(hidden_dim * 2, gene_dim),  # Direct projection to gene_dim
+            )
+            
+            # Stage 3: Lightweight gene interaction
+            self.gene_interaction = nn.Sequential(
+                nn.Conv1d(1, 32, kernel_size=3, padding=1),
+                nn.GELU(),
+                nn.Dropout1d(0.1),
+                nn.Conv1d(32, 1, kernel_size=3, padding=1),
+            )
+            
+            # Output scaling
+            self.output_scale = nn.Parameter(torch.ones(1))
+            self.output_bias = nn.Parameter(torch.zeros(1))
+            
+            self._init_weights()
+        
+        def _init_weights(self):
+            """Weight initialization"""
+            for module in self.modules():
+                if isinstance(module, nn.Linear):
+                    nn.init.xavier_uniform_(module.weight)
+                    if module.bias is not None:
+                        nn.init.zeros_(module.bias)
+                elif isinstance(module, nn.Conv1d):
+                    nn.init.kaiming_uniform_(module.weight)
+                    if module.bias is not None:
+                        nn.init.zeros_(module.bias)
+        
+        def forward(self, latent: torch.Tensor) -> torch.Tensor:
+            batch_size = latent.shape[0]
+            
+            # 1. Expand latent variables
+            latent_features = self.latent_expansion(latent)  # [batch_size, hidden_dim]
+            
+            # 2. Direct projection to gene dimension
+            gene_output = self.gene_projector(latent_features)  # [batch_size, gene_dim]
+            
+            # 3. Gene interaction with dimension safety
+            if self.gene_dim > 1:  # Only apply if gene_dim > 1
+                gene_output = gene_output.unsqueeze(1)  # [batch_size, 1, gene_dim]
+                interaction_output = self.gene_interaction(gene_output)  # [batch_size, 1, gene_dim]
+                gene_output = gene_output + interaction_output  # Residual connection
+                gene_output = gene_output.squeeze(1)  # [batch_size, gene_dim]
+            
+            # 4. Final activation (ensure non-negative)
+            gene_output = F.softplus(gene_output * self.output_scale + self.output_bias)
+            
+            return gene_output
+    
+    def _build_model(self):
+        """Build the decoder model"""
+        return self.Decoder(self.latent_dim, self.gene_dim, self.hidden_dim)
+    
+    def _create_dataset(self, latent_data, expression_data):
+        """Create dataset with dimension validation"""
+        class SimpleDataset(Dataset):
+            def __init__(self, latent, expression):
+                # Ensure dimensions match
+                assert latent.shape[0] == expression.shape[0], "Sample count mismatch"
+                assert latent.shape[1] == self.latent_dim, f"Latent dim mismatch: expected {self.latent_dim}, got {latent.shape[1]}"
+                assert expression.shape[1] == self.gene_dim, f"Gene dim mismatch: expected {self.gene_dim}, got {expression.shape[1]}"
+                
+                self.latent = torch.FloatTensor(latent)
+                self.expression = torch.FloatTensor(expression)
+            
+            def __len__(self):
+                return len(self.latent)
+            
+            def __getitem__(self, idx):
+                return self.latent[idx], self.expression[idx]
+        
+        return SimpleDataset(latent_data, expression_data)
+    
+    def train(self,
+              train_latent: np.ndarray,
+              train_expression: np.ndarray,
+              val_latent: np.ndarray = None,
+              val_expression: np.ndarray = None,
+              batch_size: int = 32,
+              num_epochs: int = 100,
+              learning_rate: float = 1e-4,
+              checkpoint_path: str = 'transcriptome_decoder.pth'):
+        """
+        Train the decoder model with dimension safety
+        
+        Args:
+            train_latent: Training latent variables [n_samples, latent_dim]
+            train_expression: Training expression data [n_samples, gene_dim]
+            val_latent: Validation latent variables (optional)
+            val_expression: Validation expression data (optional)
+            batch_size: Batch size optimized for memory
+            num_epochs: Number of training epochs
+            learning_rate: Learning rate
+            checkpoint_path: Path to save the best model
+        """
+        print("🚀 Starting training...")
+        
+        # Dimension validation
+        self._validate_data_dimensions(train_latent, train_expression, "Training")
+        if val_latent is not None and val_expression is not None:
+            self._validate_data_dimensions(val_latent, val_expression, "Validation")
+        
+        # Data preparation
+        train_dataset = self._create_safe_dataset(train_latent, train_expression)
+        
+        if val_latent is not None and val_expression is not None:
+            val_dataset = self._create_safe_dataset(val_latent, val_expression)
+            train_loader = DataLoader(train_dataset, batch_size=batch_size, shuffle=True, num_workers=2)
+            val_loader = DataLoader(val_dataset, batch_size=batch_size, shuffle=False, num_workers=2)
+            print(f"📈 Using provided validation data: {len(val_dataset)} samples")
+        else:
+            # Auto split
+            train_size = int(0.9 * len(train_dataset))
+            val_size = len(train_dataset) - train_size
+            train_subset, val_subset = torch.utils.data.random_split(train_dataset, [train_size, val_size])
+            train_loader = DataLoader(train_subset, batch_size=batch_size, shuffle=True, num_workers=2)
+            val_loader = DataLoader(val_subset, batch_size=batch_size, shuffle=False, num_workers=2)
+            print(f"📈 Auto-split validation: {val_size} samples")
+        
+        print(f"📊 Training samples: {len(train_loader.dataset)}")
+        print(f"📊 Validation samples: {len(val_loader.dataset)}")
+        print(f"📊 Batch size: {batch_size}")
+        
+        # Optimizer configuration
+        optimizer = optim.AdamW(
+            self.model.parameters(),
+            lr=learning_rate,
+            weight_decay=0.01,
+            betas=(0.9, 0.999)
+        )
+        
+        # Learning rate scheduler
+        scheduler = optim.lr_scheduler.CosineAnnealingLR(optimizer, T_max=num_epochs)
+        
+        # Loss function with dimension safety
+        def safe_loss(pred, target):
+            # Ensure dimensions match
+            if pred.shape != target.shape:
+                print(f"⚠️ Dimension mismatch: pred {pred.shape}, target {target.shape}")
+                # Truncate to minimum dimension (safety measure)
+                min_dim = min(pred.shape[1], target.shape[1])
+                pred = pred[:, :min_dim]
+                target = target[:, :min_dim]
+                
+            def correlation_loss(pred, target):
+                pred_centered = pred - pred.mean(dim=1, keepdim=True)
+                target_centered = target - target.mean(dim=1, keepdim=True)
+        
+                correlation = (pred_centered * target_centered).sum(dim=1) / (
+                    torch.sqrt(torch.sum(pred_centered ** 2, dim=1)) * 
+                    torch.sqrt(torch.sum(target_centered ** 2, dim=1)) + 1e-8
+                )
+        
+                return 1 - correlation.mean()
+            
+            mse_loss = F.mse_loss(pred, target)
+            poisson_loss = (pred - target * torch.log(pred + 1e-8)).mean()
+            corr_loss = correlation_loss(pred, target)
+            return mse_loss + 0.5 * poisson_loss + 0.3 * corr_loss
+        
+        # Training history
+        history = {
+            'train_loss': [],
+            'val_loss': [],
+            'learning_rate': []
+        }
+        
+        best_val_loss = float('inf')
+        patience = 15
+        patience_counter = 0
+        
+        print("\n📈 Starting training loop...")
+        for epoch in range(1, num_epochs + 1):
+            # Training phase
+            train_loss = self._train_epoch(train_loader, optimizer, safe_loss)
+            
+            # Validation phase
+            val_loss = self._validate_epoch(val_loader, safe_loss)
+            
+            # Update scheduler
+            scheduler.step()
+            current_lr = scheduler.get_last_lr()[0]
+            
+            # Record history
+            history['train_loss'].append(train_loss)
+            history['val_loss'].append(val_loss)
+            history['learning_rate'].append(current_lr)
+            
+            # Print progress
+            if epoch % 5 == 0 or epoch == 1:
+                print(f"📍 Epoch {epoch:3d}/{num_epochs} | "
+                      f"Train Loss: {train_loss:.4f} | "
+                      f"Val Loss: {val_loss:.4f} | "
+                      f"LR: {current_lr:.2e}")
+            
+            # Early stopping and model saving
+            if val_loss < best_val_loss:
+                best_val_loss = val_loss
+                patience_counter = 0
+                self._save_checkpoint(epoch, optimizer, scheduler, best_val_loss, history, checkpoint_path)
+                if epoch % 10 == 0:
+                    print(f"💾 Best model saved (Val Loss: {best_val_loss:.4f})")
+            else:
+                patience_counter += 1
+                if patience_counter >= patience:
+                    print(f"🛑 Early stopping at epoch {epoch}")
+                    break
+        
+        # Training completed
+        self.is_trained = True
+        self.training_history = history
+        self.best_val_loss = best_val_loss
+        
+        print(f"\n🎉 Training completed!")
+        print(f"🏆 Best validation loss: {best_val_loss:.4f}")
+        print(f"📊 Final training loss: {history['train_loss'][-1]:.4f}")
+        
+        return history
+    
+    def _validate_data_dimensions(self, latent_data, expression_data, data_type):
+        """Validate input data dimensions"""
+        assert latent_data.shape[1] == self.latent_dim, (
+            f"{data_type} latent dimension mismatch: expected {self.latent_dim}, got {latent_data.shape[1]}")
+        assert expression_data.shape[1] == self.gene_dim, (
+            f"{data_type} gene dimension mismatch: expected {self.gene_dim}, got {expression_data.shape[1]}")
+        assert latent_data.shape[0] == expression_data.shape[0], (
+            f"{data_type} sample count mismatch: latent {latent_data.shape[0]}, expression {expression_data.shape[0]}")
+        print(f"✅ {data_type} data dimensions validated")
+    
+    def _create_safe_dataset(self, latent_data, expression_data):
+        """Create dataset with safety checks"""
+        class SafeDataset(Dataset):
+            def __init__(self, latent, expression):
+                self.latent = torch.FloatTensor(latent)
+                self.expression = torch.FloatTensor(expression)
+                
+                # Safety check
+                if self.latent.shape[0] != self.expression.shape[0]:
+                    raise ValueError(f"Sample count mismatch: latent {self.latent.shape[0]}, expression {self.expression.shape[0]}")
+            
+            def __len__(self):
+                return len(self.latent)
+            
+            def __getitem__(self, idx):
+                return self.latent[idx], self.expression[idx]
+        
+        return SafeDataset(latent_data, expression_data)
+    
+    def _train_epoch(self, train_loader, optimizer, loss_fn):
+        """Train for one epoch with dimension safety"""
+        self.model.train()
+        total_loss = 0
+        
+        for batch_idx, (latent, target) in enumerate(train_loader):
+            latent = latent.to(self.device)
+            target = target.to(self.device)
+            
+            # Dimension check
+            if latent.shape[1] != self.latent_dim:
+                print(f"⚠️ Batch {batch_idx}: Latent dim mismatch {latent.shape[1]} != {self.latent_dim}")
+                continue
+                
+            optimizer.zero_grad()
+            pred = self.model(latent)
+            
+            # Final dimension check before loss calculation
+            if pred.shape[1] != target.shape[1]:
+                min_dim = min(pred.shape[1], target.shape[1])
+                pred = pred[:, :min_dim]
+                target = target[:, :min_dim]
+                if batch_idx == 0:  # Only warn once
+                    print(f"⚠️ Truncating to min dimension: {min_dim}")
+            
+            loss = loss_fn(pred, target)
+            loss.backward()
+            
+            # Gradient clipping for stability
+            torch.nn.utils.clip_grad_norm_(self.model.parameters(), max_norm=1.0)
+            optimizer.step()
+            
+            total_loss += loss.item()
+        
+        return total_loss / len(train_loader)
+    
+    def _validate_epoch(self, val_loader, loss_fn):
+        """Validate for one epoch with dimension safety"""
+        self.model.eval()
+        total_loss = 0
+        
+        with torch.no_grad():
+            for batch_idx, (latent, target) in enumerate(val_loader):
+                latent = latent.to(self.device)
+                target = target.to(self.device)
+                
+                pred = self.model(latent)
+                
+                # Dimension safety
+                if pred.shape[1] != target.shape[1]:
+                    min_dim = min(pred.shape[1], target.shape[1])
+                    pred = pred[:, :min_dim]
+                    target = target[:, :min_dim]
+                
+                loss = loss_fn(pred, target)
+                total_loss += loss.item()
+        
+        return total_loss / len(val_loader)
+    
+    def _save_checkpoint(self, epoch, optimizer, scheduler, best_loss, history, path):
+        """Save model checkpoint"""
+        torch.save({
+            'epoch': epoch,
+            'model_state_dict': self.model.state_dict(),
+            'optimizer_state_dict': optimizer.state_dict(),
+            'scheduler_state_dict': scheduler.state_dict(),
+            'best_val_loss': best_loss,
+            'training_history': history,
+            'model_config': {
+                'latent_dim': self.latent_dim,
+                'gene_dim': self.gene_dim,
+                'hidden_dim': self.hidden_dim
+            }
+        }, path)
+    
+    def predict(self, latent_data: np.ndarray, batch_size: int = 32) -> np.ndarray:
+        """
+        Predict gene expression from latent variables
+        
+        Args:
+            latent_data: Latent variables [n_samples, latent_dim]
+            batch_size: Prediction batch size
+        
+        Returns:
+            expression: Predicted expression [n_samples, gene_dim]
+        """
+        if not self.is_trained:
+            warnings.warn("⚠️ Model not trained. Predictions may be inaccurate.")
+        
+        self.model.eval()
+        
+        # Input validation
+        if latent_data.shape[1] != self.latent_dim:
+            raise ValueError(f"Latent dimension mismatch: expected {self.latent_dim}, got {latent_data.shape[1]}")
+        
+        if isinstance(latent_data, np.ndarray):
+            latent_data = torch.FloatTensor(latent_data)
+        
+        # Predict in batches to save memory
+        predictions = []
+        with torch.no_grad():
+            for i in range(0, len(latent_data), batch_size):
+                batch_latent = latent_data[i:i+batch_size].to(self.device)
+                batch_pred = self.model(batch_latent)
+                predictions.append(batch_pred.cpu())
+        
+        return torch.cat(predictions).numpy()
+    
+    def load_model(self, model_path: str):
+        """Load pre-trained model"""
+        checkpoint = torch.load(model_path, map_location=self.device)
+        
+        # Check model configuration
+        if 'model_config' in checkpoint:
+            config = checkpoint['model_config']
+            if (config['latent_dim'] != self.latent_dim or 
+                config['gene_dim'] != self.gene_dim):
+                print("⚠️ Model configuration mismatch. Reinitializing model.")
+                self.model = self._build_model()
+                self.model.to(self.device)
+        
+        self.model.load_state_dict(checkpoint['model_state_dict'])
+        self.is_trained = True
+        self.training_history = checkpoint.get('training_history')
+        self.best_val_loss = checkpoint.get('best_val_loss', float('inf'))
+        
+        print(f"✅ Model loaded successfully!")
+        print(f"🏆 Best validation loss: {self.best_val_loss:.4f}")
+    
+    def get_model_info(self) -> Dict:
+        """Get model information"""
+        return {
+            'is_trained': self.is_trained,
+            'best_val_loss': self.best_val_loss,
+            'parameters': sum(p.numel() for p in self.model.parameters()),
+            'latent_dim': self.latent_dim,
+            'gene_dim': self.gene_dim,
+            'hidden_dim': self.hidden_dim,
+            'device': str(self.device)
+        }
+'''
+# Example usage
+def example_usage():
+    """Example demonstration with dimension safety"""
+    
+    # 1. Initialize decoder
+    decoder = SimpleTranscriptomeDecoder(
+        latent_dim=100,
+        gene_dim=2000,  # Reduced for example
+        hidden_dim=256
+    )
+    
+    # 2. Generate example data with correct dimensions
+    n_samples = 1000
+    latent_data = np.random.randn(n_samples, 100).astype(np.float32)
+    
+    # Create simulated expression data
+    weights = np.random.randn(100, 2000) * 0.1
+    expression_data = np.tanh(latent_data.dot(weights))
+    expression_data = np.maximum(expression_data, 0)  # Non-negative
+    
+    print(f"📊 Data shapes: Latent {latent_data.shape}, Expression {expression_data.shape}")
+    
+    # 3. Train the model
+    history = decoder.train(
+        train_latent=latent_data,
+        train_expression=expression_data,
+        batch_size=32,
+        num_epochs=50,
+        learning_rate=1e-4
+    )
+    
+    # 4. Make predictions
+    test_latent = np.random.randn(10, 100).astype(np.float32)
+    predictions = decoder.predict(test_latent)
+    print(f"🔮 Prediction shape: {predictions.shape}")
+    
+    # 5. Get model info
+    info = decoder.get_model_info()
+    print(f"\n📋 Model Info:")
+    for key, value in info.items():
+        print(f"   {key}: {value}")
+    
+    return decoder
+
+if __name__ == "__main__":
+    example_usage()
+    
+'''