SURE-tools 2.4.5__py3-none-any.whl → 2.4.17__py3-none-any.whl

SURE/EfficientTranscriptomeDecoder.py

@@ -0,0 +1,552 @@
+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, List, Optional, Tuple
+import math
+import warnings
+warnings.filterwarnings('ignore')
+
+class EfficientTranscriptomeDecoder:
+    """
+    High-performance, memory-efficient transcriptome decoder
+    Fixed version with corrected RMSNorm implementation
+    """
+    
+    def __init__(self, 
+                 latent_dim: int = 100,
+                 gene_dim: int = 60000,
+                 hidden_dims: List[int] = [512, 1024, 2048],
+                 bottleneck_dim: int = 256,
+                 num_experts: int = 4,
+                 dropout_rate: float = 0.1,
+                 device: str = None):
+        """
+        Advanced decoder combining multiple state-of-the-art techniques
+        
+        Args:
+            latent_dim: Latent variable dimension
+            gene_dim: Number of genes (full transcriptome)
+            hidden_dims: Hidden layer dimensions
+            bottleneck_dim: Bottleneck dimension for memory efficiency
+            num_experts: Number of mixture-of-experts
+            dropout_rate: Dropout rate
+            device: Computation device
+        """
+        self.latent_dim = latent_dim
+        self.gene_dim = gene_dim
+        self.hidden_dims = hidden_dims
+        self.bottleneck_dim = bottleneck_dim
+        self.num_experts = num_experts
+        self.dropout_rate = dropout_rate
+        self.device = device or ('cuda' if torch.cuda.is_available() else 'cpu')
+        
+        # Initialize model with corrected architecture
+        self.model = self._build_corrected_model()
+        self.model.to(self.device)
+        
+        # Training state
+        self.is_trained = False
+        self.training_history = None
+        self.best_val_loss = float('inf')
+        
+        print(f"🚀 EfficientTranscriptomeDecoder Initialized:")
+        print(f"   - Latent Dimension: {latent_dim}")
+        print(f"   - Gene Dimension: {gene_dim}")
+        print(f"   - Hidden Dimensions: {hidden_dims}")
+        print(f"   - Bottleneck Dimension: {bottleneck_dim}")
+        print(f"   - Number of Experts: {num_experts}")
+        print(f"   - Parameters: {sum(p.numel() for p in self.model.parameters()):,}")
+    
+    class CorrectedRMSNorm(nn.Module):
+        """Corrected RMS Normalization with proper dimension handling"""
+        def __init__(self, dim: int, eps: float = 1e-8):
+            super().__init__()
+            self.eps = eps
+            self.dim = dim
+            self.weight = nn.Parameter(torch.ones(dim))  # Correct: weight has same dim as input
+        
+        def forward(self, x):
+            # Ensure input has the right dimension
+            if x.size(-1) != self.dim:
+                raise ValueError(f"Input dimension {x.size(-1)} doesn't match RMSNorm dimension {self.dim}")
+            
+            # Calculate RMS
+            rms = torch.sqrt(torch.mean(x ** 2, dim=-1, keepdim=True) + self.eps)
+            # Normalize and apply weight
+            return x / rms * self.weight
+    
+    class SimplifiedSwiGLU(nn.Module):
+        """Simplified SwiGLU activation"""
+        def forward(self, x):
+            # Split into two parts
+            x, gate = x.chunk(2, dim=-1)
+            return x * F.silu(gate)
+    
+    class MemoryEfficientBottleneck(nn.Module):
+        """Memory-efficient bottleneck with corrected dimensions"""
+        def __init__(self, input_dim: int, bottleneck_dim: int, output_dim: int):
+            super().__init__()
+            # Ensure proper dimension matching
+            self.compress = nn.Linear(input_dim, bottleneck_dim)
+            self.norm1 = EfficientTranscriptomeDecoder.CorrectedRMSNorm(bottleneck_dim)
+            self.expand = nn.Linear(bottleneck_dim, output_dim)
+            self.norm2 = EfficientTranscriptomeDecoder.CorrectedRMSNorm(output_dim)
+            self.activation = nn.SiLU()
+            self.dropout = nn.Dropout(0.1)
+            
+        def forward(self, x):
+            # Compress
+            compressed = self.compress(x)
+            compressed = self.norm1(compressed)
+            compressed = self.activation(compressed)
+            compressed = self.dropout(compressed)
+            
+            # Expand
+            expanded = self.expand(compressed)
+            expanded = self.norm2(expanded)
+            
+            return expanded
+    
+    class StableMixtureOfExperts(nn.Module):
+        """Stable mixture of experts without dimension issues"""
+        def __init__(self, input_dim: int, num_experts: int = 4):
+            super().__init__()
+            self.num_experts = num_experts
+            self.input_dim = input_dim
+            
+            # Shared expert with different scaling factors
+            self.shared_expert = nn.Sequential(
+                nn.Linear(input_dim, input_dim * 2),
+                nn.SiLU(),
+                nn.Dropout(0.1),
+                nn.Linear(input_dim * 2, input_dim)
+            )
+            
+            # Gating network
+            self.gate = nn.Sequential(
+                nn.Linear(input_dim, num_experts * 4),
+                nn.SiLU(),
+                nn.Linear(num_experts * 4, num_experts)
+            )
+            
+        def forward(self, x):
+            # Get gate weights
+            gate_weights = F.softmax(self.gate(x), dim=-1)  # [batch, num_experts]
+            
+            # Process through shared expert
+            expert_output = self.shared_expert(x)  # [batch, input_dim]
+            
+            # Apply expert-specific scaling
+            weighted_output = torch.zeros_like(expert_output)
+            for i in range(self.num_experts):
+                expert_scale = 0.5 + 0.5 * i  # Different scaling for each expert
+                expert_contribution = expert_output * expert_scale
+                expert_weight = gate_weights[:, i].unsqueeze(-1)  # [batch, 1]
+                weighted_output += expert_weight * expert_contribution
+            
+            # Residual connection
+            return x + weighted_output
+    
+    class CorrectedDecoder(nn.Module):
+        """Corrected decoder with proper dimension handling"""
+        
+        def __init__(self, latent_dim: int, gene_dim: int, hidden_dims: List[int], 
+                     bottleneck_dim: int, num_experts: int, dropout_rate: float):
+            super().__init__()
+            
+            # Input projection
+            self.input_projection = nn.Sequential(
+                nn.Linear(latent_dim, hidden_dims[0]),
+                EfficientTranscriptomeDecoder.CorrectedRMSNorm(hidden_dims[0]),
+                nn.SiLU(),
+                nn.Dropout(dropout_rate)
+            )
+            
+            # Main processing blocks
+            self.blocks = nn.ModuleList()
+            current_dim = hidden_dims[0]
+            
+            for i, next_dim in enumerate(hidden_dims[1:], 1):
+                block = nn.ModuleDict({
+                    'swiglu': nn.Sequential(
+                        nn.Linear(current_dim, current_dim * 2),
+                        EfficientTranscriptomeDecoder.SimplifiedSwiGLU(),
+                        nn.Dropout(dropout_rate),
+                        nn.Linear(current_dim, current_dim)  # Project back to same dimension
+                    ),
+                    'bottleneck': EfficientTranscriptomeDecoder.MemoryEfficientBottleneck(
+                        current_dim, bottleneck_dim, next_dim
+                    ),
+                    'experts': EfficientTranscriptomeDecoder.StableMixtureOfExperts(
+                        next_dim, num_experts
+                    )
+                })
+                self.blocks.append(block)
+                current_dim = next_dim
+            
+            # Final projection to gene dimension
+            self.final_projection = nn.Sequential(
+                nn.Linear(current_dim, current_dim * 2),
+                nn.SiLU(),
+                nn.Dropout(dropout_rate),
+                nn.Linear(current_dim * 2, gene_dim)
+            )
+            
+            # Output parameters
+            self.output_scale = nn.Parameter(torch.ones(1))
+            self.output_bias = nn.Parameter(torch.zeros(1))
+            
+            self._init_weights()
+        
+        def _init_weights(self):
+            """Proper 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)
+        
+        def forward(self, x):
+            # Input projection
+            x = self.input_projection(x)
+            
+            # Process through blocks
+            for block in self.blocks:
+                # SwiGLU with residual
+                residual = x
+                x_swiglu = block['swiglu'](x)
+                x = x + x_swiglu  # Residual connection
+                
+                # Bottleneck
+                x = block['bottleneck'](x)
+                
+                # Mixture of Experts with residual
+                x = block['experts'](x)
+            
+            # Final projection
+            x = self.final_projection(x)
+            
+            # Ensure non-negative output
+            x = F.softplus(x * self.output_scale + self.output_bias)
+            
+            return x
+    
+    def _build_corrected_model(self):
+        """Build the corrected model"""
+        return self.CorrectedDecoder(
+            self.latent_dim, self.gene_dim, self.hidden_dims,
+            self.bottleneck_dim, self.num_experts, self.dropout_rate
+        )
+    
+    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') -> Dict:
+        """
+        Train the corrected decoder
+        """
+        print("🚀 Starting Training...")
+        
+        # Data preparation
+        train_dataset = self._create_dataset(train_latent, train_expression)
+        
+        if val_latent is not None and val_expression is not None:
+            val_dataset = self._create_dataset(val_latent, val_expression)
+            train_loader = DataLoader(train_dataset, batch_size=batch_size, shuffle=True, pin_memory=True)
+            val_loader = DataLoader(val_dataset, batch_size=batch_size, shuffle=False, pin_memory=True)
+            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, pin_memory=True)
+            val_loader = DataLoader(val_subset, batch_size=batch_size, shuffle=False, pin_memory=True)
+            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
+        optimizer = optim.AdamW(
+            self.model.parameters(),
+            lr=learning_rate,
+            weight_decay=0.01,
+            betas=(0.9, 0.999)
+        )
+        
+        # Scheduler
+        scheduler = optim.lr_scheduler.CosineAnnealingLR(optimizer, T_max=num_epochs)
+        
+        # Loss function
+        def combined_loss(pred, target):
+            mse_loss = F.mse_loss(pred, target)
+            poisson_loss = (pred - target * torch.log(pred + 1e-8)).mean()
+            correlation = self._pearson_correlation(pred, target)
+            correlation_loss = 1 - correlation
+            return mse_loss + 0.3 * poisson_loss + 0.1 * correlation_loss
+        
+        # Training history
+        history = {
+            'train_loss': [], 'val_loss': [],
+            'train_mse': [], 'val_mse': [],
+            'train_correlation': [], 'val_correlation': [],
+            'learning_rates': []
+        }
+        
+        best_val_loss = float('inf')
+        patience = 20
+        patience_counter = 0
+        
+        print("\n📈 Starting training loop...")
+        for epoch in range(1, num_epochs + 1):
+            # Training
+            train_metrics = self._train_epoch(train_loader, optimizer, combined_loss)
+            
+            # Validation
+            val_metrics = self._validate_epoch(val_loader, combined_loss)
+            
+            # Update scheduler
+            scheduler.step()
+            current_lr = optimizer.param_groups[0]['lr']
+            
+            # Record history
+            history['train_loss'].append(train_metrics['loss'])
+            history['val_loss'].append(val_metrics['loss'])
+            history['train_mse'].append(train_metrics['mse'])
+            history['val_mse'].append(val_metrics['mse'])
+            history['train_correlation'].append(train_metrics['correlation'])
+            history['val_correlation'].append(val_metrics['correlation'])
+            history['learning_rates'].append(current_lr)
+            
+            # Print progress
+            if epoch % 10 == 0 or epoch == 1:
+                print(f"📍 Epoch {epoch:3d}/{num_epochs} | "
+                      f"Train Loss: {train_metrics['loss']:.4f} | "
+                      f"Val Loss: {val_metrics['loss']:.4f} | "
+                      f"Correlation: {val_metrics['correlation']:.4f} | "
+                      f"LR: {current_lr:.2e}")
+            
+            # Early stopping
+            if val_metrics['loss'] < best_val_loss:
+                best_val_loss = val_metrics['loss']
+                patience_counter = 0
+                self._save_checkpoint(epoch, optimizer, scheduler, best_val_loss, history, checkpoint_path)
+                if epoch % 20 == 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}")
+        
+        return history
+    
+    def _create_dataset(self, latent_data, expression_data):
+        """Create dataset"""
+        class SimpleDataset(Dataset):
+            def __init__(self, latent, expression):
+                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 _pearson_correlation(self, pred, target):
+        """Calculate Pearson correlation"""
+        pred_centered = pred - pred.mean(dim=1, keepdim=True)
+        target_centered = target - target.mean(dim=1, keepdim=True)
+        
+        numerator = (pred_centered * target_centered).sum(dim=1)
+        denominator = torch.sqrt(torch.sum(pred_centered ** 2, dim=1)) * torch.sqrt(torch.sum(target_centered ** 2, dim=1))
+        
+        return (numerator / (denominator + 1e-8)).mean()
+    
+    def _train_epoch(self, train_loader, optimizer, loss_fn):
+        """Train one epoch"""
+        self.model.train()
+        total_loss = 0
+        total_mse = 0
+        total_correlation = 0
+        
+        for latent, target in train_loader:
+            latent = latent.to(self.device, non_blocking=True)
+            target = target.to(self.device, non_blocking=True)
+            
+            optimizer.zero_grad()
+            pred = self.model(latent)
+            
+            loss = loss_fn(pred, target)
+            loss.backward()
+            
+            # Gradient clipping
+            torch.nn.utils.clip_grad_norm_(self.model.parameters(), max_norm=1.0)
+            optimizer.step()
+            
+            # Calculate metrics
+            mse_loss = F.mse_loss(pred, target).item()
+            correlation = self._pearson_correlation(pred, target).item()
+            
+            total_loss += loss.item()
+            total_mse += mse_loss
+            total_correlation += correlation
+        
+        num_batches = len(train_loader)
+        return {
+            'loss': total_loss / num_batches,
+            'mse': total_mse / num_batches,
+            'correlation': total_correlation / num_batches
+        }
+    
+    def _validate_epoch(self, val_loader, loss_fn):
+        """Validate one epoch"""
+        self.model.eval()
+        total_loss = 0
+        total_mse = 0
+        total_correlation = 0
+        
+        with torch.no_grad():
+            for latent, target in val_loader:
+                latent = latent.to(self.device, non_blocking=True)
+                target = target.to(self.device, non_blocking=True)
+                
+                pred = self.model(latent)
+                loss = loss_fn(pred, target)
+                mse_loss = F.mse_loss(pred, target).item()
+                correlation = self._pearson_correlation(pred, target).item()
+                
+                total_loss += loss.item()
+                total_mse += mse_loss
+                total_correlation += correlation
+        
+        num_batches = len(val_loader)
+        return {
+            'loss': total_loss / num_batches,
+            'mse': total_mse / num_batches,
+            'correlation': total_correlation / num_batches
+        }
+    
+    def _save_checkpoint(self, epoch, optimizer, scheduler, best_loss, history, path):
+        """Save 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_dims': self.hidden_dims,
+                'bottleneck_dim': self.bottleneck_dim,
+                'num_experts': self.num_experts
+            }
+        }, path)
+    
+    def predict(self, latent_data: np.ndarray, batch_size: int = 32) -> np.ndarray:
+        """Predict gene expression"""
+        if not self.is_trained:
+            warnings.warn("⚠️ Model not trained. Predictions may be inaccurate.")
+        
+        self.model.eval()
+        
+        if isinstance(latent_data, np.ndarray):
+            latent_data = torch.FloatTensor(latent_data)
+        
+        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)
+        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! Best val 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_dims': self.hidden_dims,
+            'device': str(self.device)
+        }
+
+'''
+# Example usage
+def example_usage():
+    """Example demonstration"""
+    
+    # Initialize decoder
+    decoder = EfficientTranscriptomeDecoder(
+        latent_dim=100,
+        gene_dim=2000,  # Reduced for example
+        hidden_dims=[256, 512, 1024],
+        bottleneck_dim=128,
+        num_experts=4,
+        dropout_rate=0.1
+    )
+    
+    # Generate example data
+    n_samples = 1000
+    latent_data = np.random.randn(n_samples, 100).astype(np.float32)
+    
+    # Simulate 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)
+    
+    print(f"📊 Data shapes: Latent {latent_data.shape}, Expression {expression_data.shape}")
+    
+    # Train
+    history = decoder.train(
+        train_latent=latent_data,
+        train_expression=expression_data,
+        batch_size=32,
+        num_epochs=50
+    )
+    
+    # Predict
+    test_latent = np.random.randn(10, 100).astype(np.float32)
+    predictions = decoder.predict(test_latent)
+    print(f"🔮 Prediction shape: {predictions.shape}")
+    
+    return decoder
+
+if __name__ == "__main__":
+    example_usage()
+'''