EvoScientist 0.0.1.dev4__py3-none-any.whl → 0.1.0rc2__py3-none-any.whl

EvoScientist/skills/tensorboard/references/visualization.md

@@ -0,0 +1,620 @@
+# Comprehensive Visualization Guide
+
+Complete guide to visualizing ML experiments with TensorBoard.
+
+## Table of Contents
+- Scalars
+- Images
+- Histograms & Distributions
+- Graphs
+- Embeddings
+- Text
+- PR Curves
+- Custom Visualizations
+
+## Scalars
+
+### Basic Scalar Logging
+
+```python
+from torch.utils.tensorboard import SummaryWriter
+
+writer = SummaryWriter('runs/scalars_demo')
+
+# Log single metric
+for step in range(100):
+    loss = compute_loss()
+    writer.add_scalar('Loss', loss, step)
+
+writer.close()
+```
+
+### Multiple Scalars
+
+```python
+# Group related metrics
+writer.add_scalars('Loss', {
+    'train': train_loss,
+    'validation': val_loss,
+    'test': test_loss
+}, epoch)
+
+writer.add_scalars('Metrics/Classification', {
+    'accuracy': accuracy,
+    'precision': precision,
+    'recall': recall,
+    'f1_score': f1
+}, epoch)
+```
+
+### Time-Series Metrics
+
+```python
+# Track metrics over training
+for epoch in range(100):
+    # Training metrics
+    train_loss = 0.0
+    for batch in train_loader:
+        loss = train_batch(batch)
+        train_loss += loss
+
+    train_loss /= len(train_loader)
+
+    # Validation metrics
+    val_loss, val_acc = validate()
+
+    # Log
+    writer.add_scalar('Loss/train', train_loss, epoch)
+    writer.add_scalar('Loss/val', val_loss, epoch)
+    writer.add_scalar('Accuracy/val', val_acc, epoch)
+
+    # Log learning rate
+    current_lr = optimizer.param_groups[0]['lr']
+    writer.add_scalar('Learning_rate', current_lr, epoch)
+```
+
+### Custom Smoothing
+
+TensorBoard UI allows smoothing scalars:
+- Slider from 0 (no smoothing) to 1 (maximum smoothing)
+- Exponential moving average
+- Useful for noisy metrics
+
+## Images
+
+### Single Image
+
+```python
+import torch
+from torch.utils.tensorboard import SummaryWriter
+
+writer = SummaryWriter('runs/images_demo')
+
+# Log single image (C, H, W)
+img = torch.rand(3, 224, 224)
+writer.add_image('Sample_image', img, 0)
+```
+
+### Image Grid
+
+```python
+from torchvision.utils import make_grid
+
+# Create grid from batch
+images = torch.rand(64, 3, 224, 224)  # Batch of 64 images
+img_grid = make_grid(images, nrow=8)  # 8 images per row
+
+writer.add_image('Image_grid', img_grid, epoch)
+```
+
+### Training Visualizations
+
+```python
+# Visualize inputs, predictions, and ground truth
+for epoch in range(10):
+    # Get batch
+    images, labels = next(iter(val_loader))
+
+    # Predict
+    with torch.no_grad():
+        predictions = model(images)
+
+    # Visualize inputs
+    input_grid = make_grid(images[:16], nrow=4)
+    writer.add_image('Inputs', input_grid, epoch)
+
+    # Visualize predictions (if images)
+    if isinstance(predictions, torch.Tensor) and predictions.dim() == 4:
+        pred_grid = make_grid(predictions[:16], nrow=4)
+        writer.add_image('Predictions', pred_grid, epoch)
+```
+
+### Attention Maps
+
+```python
+# Visualize attention weights
+attention_maps = model.get_attention(images)  # (B, H, W)
+
+# Normalize to [0, 1]
+attention_maps = (attention_maps - attention_maps.min()) / (attention_maps.max() - attention_maps.min())
+
+# Add channel dimension
+attention_maps = attention_maps.unsqueeze(1)  # (B, 1, H, W)
+
+# Create grid
+attention_grid = make_grid(attention_maps[:16], nrow=4)
+writer.add_image('Attention_maps', attention_grid, epoch)
+```
+
+### TensorFlow Images
+
+```python
+import tensorflow as tf
+
+file_writer = tf.summary.create_file_writer('logs/images')
+
+with file_writer.as_default():
+    # Log image batch
+    tf.summary.image('Training_samples', images, step=epoch, max_outputs=25)
+
+    # Log single image
+    tf.summary.image('Sample', img[tf.newaxis, ...], step=epoch)
+```
+
+## Histograms & Distributions
+
+### Weight Histograms
+
+```python
+# PyTorch: Track weight distributions over time
+for epoch in range(100):
+    train_epoch()
+
+    # Log all model parameters
+    for name, param in model.named_parameters():
+        writer.add_histogram(f'Weights/{name}', param, epoch)
+
+    # Log gradients
+    for name, param in model.named_parameters():
+        if param.grad is not None:
+            writer.add_histogram(f'Gradients/{name}', param.grad, epoch)
+```
+
+### Activation Histograms
+
+```python
+# Hook to capture activations
+activations = {}
+
+def get_activation(name):
+    def hook(model, input, output):
+        activations[name] = output.detach()
+    return hook
+
+# Register hooks
+model.conv1.register_forward_hook(get_activation('conv1'))
+model.conv2.register_forward_hook(get_activation('conv2'))
+model.fc.register_forward_hook(get_activation('fc'))
+
+# Forward pass
+output = model(input)
+
+# Log activations
+for name, activation in activations.items():
+    writer.add_histogram(f'Activations/{name}', activation, epoch)
+```
+
+### Custom Distributions
+
+```python
+# Log prediction distributions
+predictions = model(test_data)
+writer.add_histogram('Predictions', predictions, epoch)
+
+# Log loss distributions across batches
+losses = []
+for batch in val_loader:
+    loss = compute_loss(batch)
+    losses.append(loss)
+
+losses = torch.tensor(losses)
+writer.add_histogram('Loss_distribution', losses, epoch)
+```
+
+### TensorFlow Histograms
+
+```python
+import tensorflow as tf
+
+file_writer = tf.summary.create_file_writer('logs/histograms')
+
+with file_writer.as_default():
+    # Log weight distributions
+    for layer in model.layers:
+        for weight in layer.weights:
+            tf.summary.histogram(weight.name, weight, step=epoch)
+```
+
+## Graphs
+
+### Model Architecture
+
+```python
+import torch
+from torch.utils.tensorboard import SummaryWriter
+
+# PyTorch model
+model = ResNet50(num_classes=1000)
+
+# Create dummy input (same shape as real input)
+dummy_input = torch.randn(1, 3, 224, 224)
+
+# Log graph
+writer = SummaryWriter('runs/graph_demo')
+writer.add_graph(model, dummy_input)
+writer.close()
+
+# View in TensorBoard "Graphs" tab
+```
+
+### TensorFlow Graph
+
+```python
+# TensorFlow automatically logs graph with Keras
+tensorboard_callback = tf.keras.callbacks.TensorBoard(
+    log_dir='logs',
+    write_graph=True  # Enable graph logging
+)
+
+model.fit(x, y, callbacks=[tensorboard_callback])
+```
+
+## Embeddings
+
+### Projecting Embeddings
+
+```python
+import torch
+from torch.utils.tensorboard import SummaryWriter
+
+writer = SummaryWriter('runs/embeddings_demo')
+
+# Get embeddings (e.g., word embeddings, image features)
+# Shape: (num_samples, embedding_dim)
+embeddings = model.get_embeddings(data)
+
+# Metadata (labels for each embedding)
+metadata = ['cat', 'dog', 'bird', 'cat', 'dog', ...]
+
+# Optional: Images for each embedding
+label_img = torch.stack([img1, img2, img3, ...])  # (num_samples, C, H, W)
+
+# Log embeddings
+writer.add_embedding(
+    embeddings,
+    metadata=metadata,
+    label_img=label_img,
+    global_step=epoch,
+    tag='Word_embeddings'
+)
+
+writer.close()
+```
+
+**In TensorBoard Projector:**
+- Choose PCA, t-SNE, or UMAP
+- Color by metadata labels
+- Search and filter points
+- Explore nearest neighbors
+
+### Image Embeddings
+
+```python
+# Extract features from CNN
+features = []
+labels = []
+images = []
+
+model.eval()
+with torch.no_grad():
+    for data, target in test_loader:
+        # Get features from penultimate layer
+        feature = model.get_features(data)  # (B, feature_dim)
+        features.append(feature)
+        labels.extend(target.cpu().numpy())
+        images.append(data)
+
+# Concatenate
+features = torch.cat(features)
+images = torch.cat(images)
+
+# Metadata (class names)
+class_names = ['airplane', 'car', 'bird', 'cat', 'deer', 'dog', 'frog', 'horse', 'ship', 'truck']
+metadata = [class_names[label] for label in labels]
+
+# Log to TensorBoard
+writer.add_embedding(
+    features,
+    metadata=metadata,
+    label_img=images,
+    tag='CIFAR10_features'
+)
+```
+
+### Text Embeddings
+
+```python
+# Word2Vec or BERT embeddings
+word_embeddings = model.word_embeddings.weight.data  # (vocab_size, embedding_dim)
+vocabulary = ['the', 'cat', 'dog', 'run', 'jump', ...]
+
+writer.add_embedding(
+    word_embeddings,
+    metadata=vocabulary,
+    tag='Word2Vec_embeddings'
+)
+```
+
+## Text
+
+### Basic Text Logging
+
+```python
+from torch.utils.tensorboard import SummaryWriter
+
+writer = SummaryWriter('runs/text_demo')
+
+# Log plain text
+writer.add_text('Config', str(config), 0)
+writer.add_text('Hyperparameters', f'lr={lr}, batch_size={batch_size}', 0)
+
+# Log predictions
+predictions_text = f"Epoch {epoch}:\n"
+for i, pred in enumerate(predictions[:5]):
+    predictions_text += f"Sample {i}: {pred}\n"
+
+writer.add_text('Predictions', predictions_text, epoch)
+```
+
+### Markdown Tables
+
+```python
+# Log results as markdown table
+results = f"""
+| Metric | Train | Validation | Test |
+|--------|-------|------------|------|
+| Accuracy | {train_acc:.4f} | {val_acc:.4f} | {test_acc:.4f} |
+| Loss | {train_loss:.4f} | {val_loss:.4f} | {test_loss:.4f} |
+| F1 Score | {train_f1:.4f} | {val_f1:.4f} | {test_f1:.4f} |
+"""
+
+writer.add_text('Results/Summary', results, epoch)
+```
+
+### Model Summaries
+
+```python
+# Log model architecture as text
+from torchinfo import summary
+
+model_summary = str(summary(model, input_size=(1, 3, 224, 224), verbose=0))
+writer.add_text('Model/Architecture', f'```\n{model_summary}\n```', 0)
+```
+
+## PR Curves
+
+### Precision-Recall Curves
+
+```python
+from torch.utils.tensorboard import SummaryWriter
+from sklearn.metrics import precision_recall_curve
+
+writer = SummaryWriter('runs/pr_curves')
+
+# Get predictions and ground truth
+y_true = []
+y_scores = []
+
+model.eval()
+with torch.no_grad():
+    for data, target in test_loader:
+        output = model(data)
+        probs = torch.softmax(output, dim=1)
+
+        y_true.extend(target.cpu().numpy())
+        y_scores.extend(probs.cpu().numpy())
+
+y_true = np.array(y_true)
+y_scores = np.array(y_scores)
+
+# Log PR curve for each class
+num_classes = y_scores.shape[1]
+for class_idx in range(num_classes):
+    # Binary classification: class vs rest
+    labels = (y_true == class_idx).astype(int)
+    scores = y_scores[:, class_idx]
+
+    # Add PR curve
+    writer.add_pr_curve(
+        f'PR_curve/class_{class_idx}',
+        labels,
+        scores,
+        global_step=epoch
+    )
+
+writer.close()
+```
+
+### ROC Curves
+
+```python
+# TensorBoard doesn't have built-in ROC, but we can log as image
+from sklearn.metrics import roc_curve, auc
+import matplotlib.pyplot as plt
+
+fig, ax = plt.subplots()
+
+for class_idx in range(num_classes):
+    labels = (y_true == class_idx).astype(int)
+    scores = y_scores[:, class_idx]
+
+    fpr, tpr, _ = roc_curve(labels, scores)
+    roc_auc = auc(fpr, tpr)
+
+    ax.plot(fpr, tpr, label=f'Class {class_idx} (AUC = {roc_auc:.2f})')
+
+ax.plot([0, 1], [0, 1], 'k--')
+ax.set_xlabel('False Positive Rate')
+ax.set_ylabel('True Positive Rate')
+ax.set_title('ROC Curves')
+ax.legend()
+
+# Convert to tensor and log
+fig.canvas.draw()
+img = np.frombuffer(fig.canvas.tostring_rgb(), dtype=np.uint8)
+img = img.reshape(fig.canvas.get_width_height()[::-1] + (3,))
+img = torch.from_numpy(img).permute(2, 0, 1)
+
+writer.add_image('ROC_curves', img, epoch)
+plt.close(fig)
+```
+
+## Custom Visualizations
+
+### Confusion Matrix
+
+```python
+import matplotlib.pyplot as plt
+import seaborn as sns
+from sklearn.metrics import confusion_matrix
+
+# Compute confusion matrix
+cm = confusion_matrix(y_true, y_pred)
+
+# Plot
+fig, ax = plt.subplots(figsize=(10, 10))
+sns.heatmap(cm, annot=True, fmt='d', cmap='Blues', ax=ax)
+ax.set_xlabel('Predicted')
+ax.set_ylabel('True')
+ax.set_title('Confusion Matrix')
+
+# Convert to tensor and log
+fig.canvas.draw()
+img = np.frombuffer(fig.canvas.tostring_rgb(), dtype=np.uint8)
+img = img.reshape(fig.canvas.get_width_height()[::-1] + (3,))
+img = torch.from_numpy(img).permute(2, 0, 1)
+
+writer.add_image('Confusion_matrix', img, epoch)
+plt.close(fig)
+```
+
+### Loss Landscape
+
+```python
+# Visualize loss surface around current parameters
+import numpy as np
+
+def compute_loss_landscape(model, data, target, param1, param2):
+    """Compute loss for a grid of parameter values."""
+    # Save original params
+    original_params = {name: param.clone() for name, param in model.named_parameters()}
+
+    # Grid
+    param1_range = np.linspace(-1, 1, 50)
+    param2_range = np.linspace(-1, 1, 50)
+    losses = np.zeros((50, 50))
+
+    for i, p1 in enumerate(param1_range):
+        for j, p2 in enumerate(param2_range):
+            # Perturb parameters
+            model.state_dict()[param1].add_(p1)
+            model.state_dict()[param2].add_(p2)
+
+            # Compute loss
+            with torch.no_grad():
+                output = model(data)
+                loss = F.cross_entropy(output, target)
+                losses[i, j] = loss.item()
+
+            # Restore parameters
+            model.load_state_dict(original_params)
+
+    return losses
+
+# Plot
+fig = plt.figure()
+ax = fig.add_subplot(111, projection='3d')
+X, Y = np.meshgrid(np.linspace(-1, 1, 50), np.linspace(-1, 1, 50))
+ax.plot_surface(X, Y, losses, cmap='viridis')
+ax.set_title('Loss Landscape')
+
+# Log
+fig.canvas.draw()
+img = np.frombuffer(fig.canvas.tostring_rgb(), dtype=np.uint8)
+img = img.reshape(fig.canvas.get_width_height()[::-1] + (3,))
+img = torch.from_numpy(img).permute(2, 0, 1)
+writer.add_image('Loss_landscape', img, epoch)
+plt.close(fig)
+```
+
+## Best Practices
+
+### 1. Use Hierarchical Tags
+
+```python
+# ✅ Good: Organized with hierarchy
+writer.add_scalar('Loss/train', train_loss, step)
+writer.add_scalar('Loss/val', val_loss, step)
+writer.add_scalar('Metrics/accuracy', accuracy, step)
+writer.add_scalar('Metrics/f1_score', f1, step)
+
+# ❌ Bad: Flat namespace
+writer.add_scalar('train_loss', train_loss, step)
+writer.add_scalar('val_loss', val_loss, step)
+```
+
+### 2. Log Regularly but Not Excessively
+
+```python
+# ✅ Good: Epoch-level + periodic batch-level
+for epoch in range(100):
+    for batch_idx, batch in enumerate(train_loader):
+        loss = train_step(batch)
+
+        # Log every 100 batches
+        if batch_idx % 100 == 0:
+            global_step = epoch * len(train_loader) + batch_idx
+            writer.add_scalar('Loss/train_batch', loss, global_step)
+
+    # Always log epoch metrics
+    writer.add_scalar('Loss/train_epoch', epoch_loss, epoch)
+
+# ❌ Bad: Every batch (creates huge logs)
+for batch in train_loader:
+    writer.add_scalar('Loss', loss, step)
+```
+
+### 3. Visualize Sample Predictions
+
+```python
+# Log predictions periodically
+if epoch % 5 == 0:
+    model.eval()
+    with torch.no_grad():
+        sample_images, sample_labels = next(iter(val_loader))
+        predictions = model(sample_images)
+
+        # Visualize
+        img_grid = make_grid(sample_images[:16], nrow=4)
+        writer.add_image('Samples/inputs', img_grid, epoch)
+
+        # Add predictions as text
+        pred_text = '\n'.join([f'{i}: {pred.argmax()}' for i, pred in enumerate(predictions[:16])])
+        writer.add_text('Samples/predictions', pred_text, epoch)
+```
+
+## Resources
+
+- **TensorBoard Documentation**: https://www.tensorflow.org/tensorboard
+- **PyTorch TensorBoard**: https://pytorch.org/docs/stable/tensorboard.html
+- **Projector Guide**: https://www.tensorflow.org/tensorboard/tensorboard_projector_plugin