SURE-tools 2.4.5__py3-none-any.whl → 2.4.13__py3-none-any.whl

SURE/EfficientTranscriptomeDecoder.py

@@ -0,0 +1,607 @@
+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
+    Combines latest research techniques for optimal performance
+    """
+    
+    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 = 8,
+                 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 advanced architecture
+        self.model = self._build_advanced_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"   - Estimated GPU Memory: ~6-8GB")
+        print(f"   - Parameters: {sum(p.numel() for p in self.model.parameters()):,}")
+    
+    class SwiGLU(nn.Module):
+        """SwiGLU activation - better than GELU (PaLM, LLaMA)"""
+        def forward(self, x):
+            x, gate = x.chunk(2, dim=-1)
+            return x * F.silu(gate)
+    
+    class RMSNorm(nn.Module):
+        """RMS Normalization - more stable than LayerNorm (GPT-3)"""
+        def __init__(self, dim: int, eps: float = 1e-8):
+            super().__init__()
+            self.eps = eps
+            self.weight = nn.Parameter(torch.ones(dim))
+        
+        def forward(self, x):
+            norm_x = x.norm(2, dim=-1, keepdim=True)
+            rms_x = norm_x * (x.shape[-1] ** -0.5)
+            return x / (rms_x + self.eps) * self.weight
+    
+    class MixtureOfExperts(nn.Module):
+        """Mixture of Experts for conditional computation"""
+        def __init__(self, input_dim: int, expert_dim: int, num_experts: int):
+            super().__init__()
+            self.num_experts = num_experts
+            self.experts = nn.ModuleList([
+                nn.Sequential(
+                    nn.Linear(input_dim, expert_dim),
+                    nn.Dropout(0.1),
+                    nn.Linear(expert_dim, input_dim)
+                ) for _ in range(num_experts)
+            ])
+            self.gate = nn.Linear(input_dim, num_experts)
+            self.expert_dim = expert_dim
+        
+        def forward(self, x):
+            # Gate network
+            gate_logits = self.gate(x)
+            gate_weights = F.softmax(gate_logits, dim=-1)
+            
+            # Expert outputs
+            expert_outputs = []
+            for i, expert in enumerate(self.experts):
+                expert_out = expert(x)
+                expert_outputs.append(expert_out.unsqueeze(-1))
+            
+            # Combine expert outputs
+            expert_outputs = torch.cat(expert_outputs, dim=-1)
+            output = torch.einsum('bd, bde -> be', gate_weights, expert_outputs)
+            
+            return output + x  # Residual connection
+    
+    class AdaptiveBottleneck(nn.Module):
+        """Adaptive bottleneck for memory efficiency"""
+        def __init__(self, input_dim: int, bottleneck_dim: int, output_dim: int):
+            super().__init__()
+            self.compress = nn.Linear(input_dim, bottleneck_dim)
+            self.norm1 = EfficientTranscriptomeDecoder.RMSNorm(bottleneck_dim)
+            self.expand = nn.Linear(bottleneck_dim, output_dim)
+            self.norm2 = EfficientTranscriptomeDecoder.RMSNorm(output_dim)
+            self.dropout = nn.Dropout(0.1)
+            
+        def forward(self, x):
+            # Compress
+            compressed = self.compress(x)
+            compressed = self.norm1(compressed)
+            compressed = F.silu(compressed)
+            compressed = self.dropout(compressed)
+            
+            # Expand
+            expanded = self.expand(compressed)
+            expanded = self.norm2(expanded)
+            
+            return expanded
+    
+    class GeneSpecificProjection(nn.Module):
+        """Gene-specific projection with weight sharing"""
+        def __init__(self, latent_dim: int, gene_dim: int, proj_dim: int = 64):
+            super().__init__()
+            self.proj_dim = proj_dim
+            self.gene_embeddings = nn.Parameter(torch.randn(gene_dim, proj_dim) * 0.02)
+            self.latent_projection = nn.Linear(latent_dim, proj_dim)
+            self.output_layer = nn.Linear(proj_dim, 1)
+            
+        def forward(self, latent):
+            batch_size = latent.shape[0]
+            
+            # Project latent to gene space
+            latent_proj = self.latent_projection(latent)  # [batch_size, proj_dim]
+            
+            # Efficient matrix multiplication
+            gene_output = torch.matmul(latent_proj, self.gene_embeddings.T)  # [batch_size, gene_dim]
+            
+            return gene_output
+    
+    class AdvancedDecoder(nn.Module):
+        """Advanced decoder combining multiple techniques"""
+        
+        def __init__(self, latent_dim: int, gene_dim: int, hidden_dims: List[int], 
+                    bottleneck_dim: int, num_experts: int, dropout_rate: float):
+            super().__init__()
+            
+            # Initial projection
+            self.input_projection = nn.Sequential(
+                nn.Linear(latent_dim, hidden_dims[0]),
+                EfficientTranscriptomeDecoder.RMSNorm(hidden_dims[0]),
+                nn.SiLU(),
+                nn.Dropout(dropout_rate)
+            )
+            
+            # Main processing blocks
+            self.blocks = nn.ModuleList()
+            current_dim = hidden_dims[0]
+            
+            for i, hidden_dim in enumerate(hidden_dims[1:], 1):
+                block = nn.ModuleList([
+                    # Mixture of Experts
+                    EfficientTranscriptomeDecoder.MixtureOfExperts(current_dim, hidden_dim, num_experts),
+                    
+                    # Adaptive Bottleneck
+                    EfficientTranscriptomeDecoder.AdaptiveBottleneck(current_dim, bottleneck_dim, hidden_dim),
+                    
+                    # SwiGLU activation
+                    nn.Sequential(
+                        nn.Linear(hidden_dim, hidden_dim * 2),
+                        EfficientTranscriptomeDecoder.SwiGLU(),
+                        nn.Dropout(dropout_rate)
+                    )
+                ])
+                self.blocks.append(block)
+                current_dim = hidden_dim
+            
+            # Gene-specific projection
+            self.gene_projection = EfficientTranscriptomeDecoder.GeneSpecificProjection(
+                current_dim, gene_dim, proj_dim=128
+            )
+            
+            # 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):
+            """Advanced weight initialization"""
+            for module in self.modules():
+                if isinstance(module, nn.Linear):
+                    # Kaiming init for SiLU/SwiGLU
+                    nn.init.kaiming_normal_(module.weight, nonlinearity='linear')
+                    if module.bias is not None:
+                        nn.init.zeros_(module.bias)
+        
+        def forward(self, x):
+            # Initial projection
+            x = self.input_projection(x)
+            
+            # Process through blocks
+            for block in self.blocks:
+                # Mixture of Experts
+                expert_out = block[0](x)
+                
+                # Adaptive Bottleneck
+                bottleneck_out = block[1](expert_out)
+                
+                # SwiGLU activation with residual
+                swiglu_out = block[2](bottleneck_out)
+                x = x + swiglu_out  # Residual connection
+            
+            # Final gene projection
+            output = self.gene_projection(x)
+            
+            # Ensure non-negative output
+            output = F.softplus(output * self.output_scale + self.output_bias)
+            
+            return output
+    
+    def _build_advanced_model(self):
+        """Build the advanced decoder model"""
+        return self.AdvancedDecoder(
+            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 = 16,  # Smaller batches for memory efficiency
+              num_epochs: int = 200,
+              learning_rate: float = 1e-4,
+              checkpoint_path: str = 'efficient_decoder.pth') -> Dict:
+        """
+        Train with advanced optimization techniques
+        
+        Args:
+            train_latent: Training latent variables
+            train_expression: Training expression data
+            val_latent: Validation latent variables
+            val_expression: Validation expression data
+            batch_size: Batch size (optimized for memory)
+            num_epochs: Number of epochs
+            learning_rate: Learning rate
+            checkpoint_path: Model save path
+        """
+        print("🚀 Starting Advanced 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)
+        else:
+            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"📊 Training samples: {len(train_loader.dataset)}")
+        print(f"📊 Validation samples: {len(val_loader.dataset)}")
+        print(f"📊 Batch size: {batch_size}")
+        
+        # Advanced optimizer configuration
+        optimizer = optim.AdamW(
+            self.model.parameters(),
+            lr=learning_rate,
+            weight_decay=0.1,  # Stronger regularization
+            betas=(0.9, 0.95),  # Tuned betas
+            eps=1e-8
+        )
+        
+        # Cosine annealing with warmup
+        scheduler = optim.lr_scheduler.OneCycleLR(
+            optimizer,
+            max_lr=learning_rate * 5,
+            epochs=num_epochs,
+            steps_per_epoch=len(train_loader),
+            pct_start=0.1,
+            div_factor=10.0,
+            final_div_factor=100.0
+        )
+        
+        # Advanced loss function
+        def advanced_loss(pred, target):
+            # 1. MSE loss for overall accuracy
+            mse_loss = F.mse_loss(pred, target)
+            
+            # 2. Poisson loss for count data
+            poisson_loss = (pred - target * torch.log(pred + 1e-8)).mean()
+            
+            # 3. Correlation loss for pattern matching
+            correlation_loss = 1 - self._pearson_correlation(pred, target)
+            
+            # 4. Sparsity loss for realistic distribution
+            sparsity_loss = F.mse_loss(
+                (pred < 1e-3).float().mean(),
+                torch.tensor(0.85, device=pred.device)  # Target sparsity
+            )
+            
+            # 5. Spectral loss for smoothness
+            spectral_loss = self._spectral_loss(pred, target)
+            
+            # Weighted combination
+            total_loss = (mse_loss + 0.3 * poisson_loss + 0.2 * correlation_loss + 
+                         0.1 * sparsity_loss + 0.05 * spectral_loss)
+            
+            return total_loss, {
+                'mse': mse_loss.item(),
+                'poisson': poisson_loss.item(),
+                'correlation': correlation_loss.item(),
+                'sparsity': sparsity_loss.item(),
+                'spectral': spectral_loss.item()
+            }
+        
+        # Training history
+        history = {
+            'train_loss': [], 'val_loss': [],
+            'train_mse': [], 'val_mse': [],
+            'train_correlation': [], 'val_correlation': [],
+            'learning_rates': [], 'grad_norms': []
+        }
+        
+        best_val_loss = float('inf')
+        patience = 25
+        patience_counter = 0
+        
+        print("\n📈 Starting training with advanced techniques...")
+        for epoch in range(1, num_epochs + 1):
+            # Training phase
+            train_loss, train_components, grad_norm = self._train_epoch_advanced(
+                train_loader, optimizer, scheduler, advanced_loss
+            )
+            
+            # Validation phase
+            val_loss, val_components = self._validate_epoch_advanced(val_loader, advanced_loss)
+            
+            # Record history
+            history['train_loss'].append(train_loss)
+            history['val_loss'].append(val_loss)
+            history['train_mse'].append(train_components['mse'])
+            history['val_mse'].append(val_components['mse'])
+            history['train_correlation'].append(train_components['correlation'])
+            history['val_correlation'].append(val_components['correlation'])
+            history['learning_rates'].append(optimizer.param_groups[0]['lr'])
+            history['grad_norms'].append(grad_norm)
+            
+            # Print detailed progress
+            if epoch % 10 == 0 or epoch == 1:
+                lr = optimizer.param_groups[0]['lr']
+                print(f"📍 Epoch {epoch:3d}/{num_epochs} | "
+                      f"Train: {train_loss:.4f} | "
+                      f"Val: {val_loss:.4f} | "
+                      f"Corr: {val_components['correlation']:.4f} | "
+                      f"LR: {lr:.2e} | "
+                      f"Grad: {grad_norm:.4f}")
+            
+            # Early stopping with patience
+            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 % 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 memory-efficient dataset"""
+        class EfficientDataset(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 EfficientDataset(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 _spectral_loss(self, pred, target):
+        """Spectral loss for frequency domain matching"""
+        pred_fft = torch.fft.fft(pred, dim=1)
+        target_fft = torch.fft.fft(target, dim=1)
+        
+        magnitude_loss = F.mse_loss(torch.abs(pred_fft), torch.abs(target_fft))
+        phase_loss = F.mse_loss(torch.angle(pred_fft), torch.angle(target_fft))
+        
+        return magnitude_loss + 0.5 * phase_loss
+    
+    def _train_epoch_advanced(self, train_loader, optimizer, scheduler, loss_fn):
+        """Advanced training with gradient accumulation"""
+        self.model.train()
+        total_loss = 0
+        total_components = {'mse': 0, 'poisson': 0, 'correlation': 0, 'sparsity': 0, 'spectral': 0}
+        grad_norms = []
+        
+        # Gradient accumulation for effective larger batch size
+        accumulation_steps = 4
+        optimizer.zero_grad()
+        
+        for i, (latent, target) in enumerate(train_loader):
+            latent = latent.to(self.device, non_blocking=True)
+            target = target.to(self.device, non_blocking=True)
+            
+            # Forward pass with mixed precision
+            with torch.cuda.amp.autocast():  # Mixed precision for memory efficiency
+                pred = self.model(latent)
+                loss, components = loss_fn(pred, target)
+            
+            # Scale loss for gradient accumulation
+            loss = loss / accumulation_steps
+            loss.backward()
+            
+            # Gradient accumulation
+            if (i + 1) % accumulation_steps == 0:
+                # Gradient clipping
+                grad_norm = torch.nn.utils.clip_grad_norm_(self.model.parameters(), max_norm=1.0)
+                optimizer.step()
+                scheduler.step()
+                optimizer.zero_grad()
+                
+                grad_norms.append(grad_norm.item())
+            
+            # Accumulate losses
+            total_loss += loss.item() * accumulation_steps
+            for key in total_components:
+                total_components[key] += components[key]
+        
+        # Average metrics
+        num_batches = len(train_loader)
+        avg_loss = total_loss / num_batches
+        avg_components = {key: value / num_batches for key, value in total_components.items()}
+        avg_grad_norm = np.mean(grad_norms) if grad_norms else 0.0
+        
+        return avg_loss, avg_components, avg_grad_norm
+    
+    def _validate_epoch_advanced(self, val_loader, loss_fn):
+        """Advanced validation"""
+        self.model.eval()
+        total_loss = 0
+        total_components = {'mse': 0, 'poisson': 0, 'correlation': 0, 'sparsity': 0, 'spectral': 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, components = loss_fn(pred, target)
+                
+                total_loss += loss.item()
+                for key in total_components:
+                    total_components[key] += components[key]
+        
+        num_batches = len(val_loader)
+        avg_loss = total_loss / num_batches
+        avg_components = {key: value / num_batches for key, value in total_components.items()}
+        
+        return avg_loss, avg_components
+    
+    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 = 16) -> np.ndarray:
+        """Memory-efficient prediction"""
+        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)
+                
+                with torch.cuda.amp.autocast():  # Mixed precision for memory
+                    batch_pred = self.model(batch_latent)
+                
+                predictions.append(batch_pred.cpu())
+                
+                # Clear memory
+                if torch.cuda.is_available():
+                    torch.cuda.empty_cache()
+        
+        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}")
+
+'''
+# Example usage
+def example_usage():
+    """Demonstrate the advanced decoder"""
+    
+    # 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=16,
+        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()
+    
+'''