@synsci/cli-darwin-x64-baseline 1.1.77 → 1.1.78

package/bin/skills/torch_geometric/references/layers_reference.md

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+# PyTorch Geometric Neural Network Layers Reference
+
+This document provides a comprehensive reference of all neural network layers available in `torch_geometric.nn`.
+
+## Layer Capability Flags
+
+When selecting layers, consider these capability flags:
+
+- **SparseTensor**: Supports `torch_sparse.SparseTensor` format for efficient sparse operations
+- **edge_weight**: Handles one-dimensional edge weight data
+- **edge_attr**: Processes multi-dimensional edge feature information
+- **Bipartite**: Works with bipartite graphs (different source/target node dimensions)
+- **Static**: Operates on static graphs with batched node features
+- **Lazy**: Enables initialization without specifying input channel dimensions
+
+## Convolutional Layers
+
+### Standard Graph Convolutions
+
+**GCNConv** - Graph Convolutional Network layer
+- Implements spectral graph convolution with symmetric normalization
+- Supports: SparseTensor, edge_weight, Bipartite, Lazy
+- Use for: Citation networks, social networks, general graph learning
+- Example: `GCNConv(in_channels, out_channels, improved=False, cached=True)`
+
+**SAGEConv** - GraphSAGE layer
+- Inductive learning via neighborhood sampling and aggregation
+- Supports: SparseTensor, Bipartite, Lazy
+- Use for: Large graphs, inductive learning, heterogeneous features
+- Example: `SAGEConv(in_channels, out_channels, aggr='mean')`
+
+**GATConv** - Graph Attention Network layer
+- Multi-head attention mechanism for adaptive neighbor weighting
+- Supports: SparseTensor, edge_attr, Bipartite, Static, Lazy
+- Use for: Tasks requiring variable neighbor importance
+- Example: `GATConv(in_channels, out_channels, heads=8, dropout=0.6)`
+
+**GraphConv** - Simple graph convolution (Morris et al.)
+- Basic message passing with optional edge weights
+- Supports: SparseTensor, edge_weight, Bipartite, Lazy
+- Use for: Baseline models, simple graph structures
+- Example: `GraphConv(in_channels, out_channels, aggr='add')`
+
+**GINConv** - Graph Isomorphism Network layer
+- Maximally powerful GNN for graph isomorphism testing
+- Supports: Bipartite
+- Use for: Graph classification, molecular property prediction
+- Example: `GINConv(nn.Sequential(nn.Linear(in_channels, out_channels), nn.ReLU()))`
+
+**TransformerConv** - Graph Transformer layer
+- Combines graph structure with transformer attention
+- Supports: SparseTensor, Bipartite, Lazy
+- Use for: Long-range dependencies, complex graphs
+- Example: `TransformerConv(in_channels, out_channels, heads=8, beta=True)`
+
+**ChebConv** - Chebyshev spectral graph convolution
+- Uses Chebyshev polynomials for efficient spectral filtering
+- Supports: SparseTensor, edge_weight, Bipartite, Lazy
+- Use for: Spectral graph learning, efficient convolutions
+- Example: `ChebConv(in_channels, out_channels, K=3)`
+
+**SGConv** - Simplified Graph Convolution
+- Pre-computes fixed number of propagation steps
+- Supports: SparseTensor, edge_weight, Bipartite, Lazy
+- Use for: Fast training, shallow models
+- Example: `SGConv(in_channels, out_channels, K=2)`
+
+**APPNP** - Approximate Personalized Propagation of Neural Predictions
+- Separates feature transformation from propagation
+- Supports: SparseTensor, edge_weight, Lazy
+- Use for: Deep propagation without oversmoothing
+- Example: `APPNP(K=10, alpha=0.1)`
+
+**ARMAConv** - ARMA graph convolution
+- Uses ARMA filters for graph filtering
+- Supports: SparseTensor, edge_weight, Bipartite, Lazy
+- Use for: Advanced spectral methods
+- Example: `ARMAConv(in_channels, out_channels, num_stacks=3, num_layers=2)`
+
+**GATv2Conv** - Improved Graph Attention Network
+- Fixes static attention computation issue in GAT
+- Supports: SparseTensor, edge_attr, Bipartite, Static, Lazy
+- Use for: Better attention learning than original GAT
+- Example: `GATv2Conv(in_channels, out_channels, heads=8)`
+
+**SuperGATConv** - Self-supervised Graph Attention
+- Adds self-supervised attention mechanism
+- Supports: SparseTensor, edge_attr, Bipartite, Static, Lazy
+- Use for: Self-supervised learning, limited labels
+- Example: `SuperGATConv(in_channels, out_channels, heads=8)`
+
+**GMMConv** - Gaussian Mixture Model Convolution
+- Uses Gaussian kernels in pseudo-coordinate space
+- Supports: Bipartite
+- Use for: Point clouds, spatial data
+- Example: `GMMConv(in_channels, out_channels, dim=3, kernel_size=5)`
+
+**SplineConv** - Spline-based convolution
+- B-spline basis functions for spatial filtering
+- Supports: Bipartite
+- Use for: Irregular grids, continuous spaces
+- Example: `SplineConv(in_channels, out_channels, dim=2, kernel_size=5)`
+
+**NNConv** - Neural Network Convolution
+- Edge features processed by neural networks
+- Supports: edge_attr, Bipartite
+- Use for: Rich edge features, molecular graphs
+- Example: `NNConv(in_channels, out_channels, nn=edge_nn, aggr='mean')`
+
+**CGConv** - Crystal Graph Convolution
+- Designed for crystalline materials
+- Supports: Bipartite
+- Use for: Materials science, crystal structures
+- Example: `CGConv(in_channels, dim=3, batch_norm=True)`
+
+**EdgeConv** - Edge Convolution (Dynamic Graph CNN)
+- Dynamically computes edges based on feature space
+- Supports: Static
+- Use for: Point clouds, dynamic graphs
+- Example: `EdgeConv(nn=edge_nn, aggr='max')`
+
+**PointNetConv** - PointNet++ convolution
+- Local and global feature learning for point clouds
+- Use for: 3D point cloud processing
+- Example: `PointNetConv(local_nn, global_nn)`
+
+**ResGatedGraphConv** - Residual Gated Graph Convolution
+- Gating mechanism with residual connections
+- Supports: edge_attr, Bipartite, Lazy
+- Use for: Deep GNNs, complex features
+- Example: `ResGatedGraphConv(in_channels, out_channels)`
+
+**GENConv** - Generalized Graph Convolution
+- Generalizes multiple GNN variants
+- Supports: SparseTensor, edge_weight, edge_attr, Bipartite, Lazy
+- Use for: Flexible architecture exploration
+- Example: `GENConv(in_channels, out_channels, aggr='softmax', num_layers=2)`
+
+**FiLMConv** - Feature-wise Linear Modulation
+- Conditions on global features
+- Supports: Bipartite, Lazy
+- Use for: Conditional generation, multi-task learning
+- Example: `FiLMConv(in_channels, out_channels, num_relations=5)`
+
+**PANConv** - Path Attention Network
+- Attention over multi-hop paths
+- Supports: SparseTensor, Lazy
+- Use for: Complex connectivity patterns
+- Example: `PANConv(in_channels, out_channels, filter_size=3)`
+
+**ClusterGCNConv** - Cluster-GCN convolution
+- Efficient training via graph clustering
+- Supports: edge_attr, Lazy
+- Use for: Very large graphs
+- Example: `ClusterGCNConv(in_channels, out_channels)`
+
+**MFConv** - Multi-scale Feature Convolution
+- Aggregates features at multiple scales
+- Supports: SparseTensor, Lazy
+- Use for: Multi-scale patterns
+- Example: `MFConv(in_channels, out_channels)`
+
+**RGCNConv** - Relational Graph Convolution
+- Handles multiple edge types
+- Supports: SparseTensor, edge_weight, Lazy
+- Use for: Knowledge graphs, heterogeneous graphs
+- Example: `RGCNConv(in_channels, out_channels, num_relations=10)`
+
+**FAConv** - Frequency Adaptive Convolution
+- Adaptive filtering in spectral domain
+- Supports: SparseTensor, Lazy
+- Use for: Spectral graph learning
+- Example: `FAConv(in_channels, eps=0.1, dropout=0.5)`
+
+### Molecular and 3D Convolutions
+
+**SchNet** - Continuous-filter convolutional layer
+- Designed for molecular dynamics
+- Use for: Molecular property prediction, 3D molecules
+- Example: `SchNet(hidden_channels=128, num_filters=64, num_interactions=6)`
+
+**DimeNet** - Directional Message Passing
+- Uses directional information and angles
+- Use for: 3D molecular structures, chemical properties
+- Example: `DimeNet(hidden_channels=128, out_channels=1, num_blocks=6)`
+
+**PointTransformerConv** - Point cloud transformer
+- Transformer for 3D point clouds
+- Use for: 3D vision, point cloud segmentation
+- Example: `PointTransformerConv(in_channels, out_channels)`
+
+### Hypergraph Convolutions
+
+**HypergraphConv** - Hypergraph convolution
+- Operates on hyperedges (edges connecting multiple nodes)
+- Supports: Lazy
+- Use for: Multi-way relationships, chemical reactions
+- Example: `HypergraphConv(in_channels, out_channels)`
+
+**HGTConv** - Heterogeneous Graph Transformer
+- Transformer for heterogeneous graphs with multiple types
+- Supports: Lazy
+- Use for: Heterogeneous networks, knowledge graphs
+- Example: `HGTConv(in_channels, out_channels, metadata, heads=8)`
+
+## Aggregation Operators
+
+**Aggr** - Base aggregation class
+- Flexible aggregation across nodes
+
+**SumAggregation** - Sum aggregation
+- Example: `SumAggregation()`
+
+**MeanAggregation** - Mean aggregation
+- Example: `MeanAggregation()`
+
+**MaxAggregation** - Max aggregation
+- Example: `MaxAggregation()`
+
+**SoftmaxAggregation** - Softmax-weighted aggregation
+- Learnable attention weights
+- Example: `SoftmaxAggregation(learn=True)`
+
+**PowerMeanAggregation** - Power mean aggregation
+- Learnable power parameter
+- Example: `PowerMeanAggregation(learn=True)`
+
+**LSTMAggregation** - LSTM-based aggregation
+- Sequential processing of neighbors
+- Example: `LSTMAggregation(in_channels, out_channels)`
+
+**SetTransformerAggregation** - Set Transformer aggregation
+- Transformer for permutation-invariant aggregation
+- Example: `SetTransformerAggregation(in_channels, out_channels)`
+
+**MultiAggregation** - Multiple aggregations
+- Combines multiple aggregation methods
+- Example: `MultiAggregation(['mean', 'max', 'std'])`
+
+## Pooling Layers
+
+### Global Pooling
+
+**global_mean_pool** - Global mean pooling
+- Averages node features per graph
+- Example: `global_mean_pool(x, batch)`
+
+**global_max_pool** - Global max pooling
+- Max over node features per graph
+- Example: `global_max_pool(x, batch)`
+
+**global_add_pool** - Global sum pooling
+- Sums node features per graph
+- Example: `global_add_pool(x, batch)`
+
+**global_sort_pool** - Global sort pooling
+- Sorts and concatenates top-k nodes
+- Example: `global_sort_pool(x, batch, k=30)`
+
+**GlobalAttention** - Global attention pooling
+- Learnable attention weights for aggregation
+- Example: `GlobalAttention(gate_nn)`
+
+**Set2Set** - Set2Set pooling
+- LSTM-based attention mechanism
+- Example: `Set2Set(in_channels, processing_steps=3)`
+
+### Hierarchical Pooling
+
+**TopKPooling** - Top-k pooling
+- Keeps top-k nodes based on projection scores
+- Example: `TopKPooling(in_channels, ratio=0.5)`
+
+**SAGPooling** - Self-Attention Graph Pooling
+- Uses self-attention for node selection
+- Example: `SAGPooling(in_channels, ratio=0.5)`
+
+**ASAPooling** - Adaptive Structure Aware Pooling
+- Structure-aware node selection
+- Example: `ASAPooling(in_channels, ratio=0.5)`
+
+**PANPooling** - Path Attention Pooling
+- Attention over paths for pooling
+- Example: `PANPooling(in_channels, ratio=0.5)`
+
+**EdgePooling** - Edge contraction pooling
+- Pools by contracting edges
+- Example: `EdgePooling(in_channels)`
+
+**MemPooling** - Memory-based pooling
+- Learnable cluster assignments
+- Example: `MemPooling(in_channels, out_channels, heads=4, num_clusters=10)`
+
+**avg_pool** / **max_pool** - Average/Max pool with clustering
+- Pools nodes within clusters
+- Example: `avg_pool(cluster, data)`
+
+## Normalization Layers
+
+**BatchNorm** - Batch normalization
+- Normalizes features across batch
+- Example: `BatchNorm(in_channels)`
+
+**LayerNorm** - Layer normalization
+- Normalizes features per sample
+- Example: `LayerNorm(in_channels)`
+
+**InstanceNorm** - Instance normalization
+- Normalizes per sample and graph
+- Example: `InstanceNorm(in_channels)`
+
+**GraphNorm** - Graph normalization
+- Graph-specific normalization
+- Example: `GraphNorm(in_channels)`
+
+**PairNorm** - Pair normalization
+- Prevents oversmoothing in deep GNNs
+- Example: `PairNorm(scale_individually=False)`
+
+**MessageNorm** - Message normalization
+- Normalizes messages during passing
+- Example: `MessageNorm(learn_scale=True)`
+
+**DiffGroupNorm** - Differentiable Group Normalization
+- Learnable grouping for normalization
+- Example: `DiffGroupNorm(in_channels, groups=10)`
+
+## Model Architectures
+
+### Pre-Built Models
+
+**GCN** - Complete Graph Convolutional Network
+- Multi-layer GCN with dropout
+- Example: `GCN(in_channels, hidden_channels, num_layers, out_channels)`
+
+**GraphSAGE** - Complete GraphSAGE model
+- Multi-layer SAGE with dropout
+- Example: `GraphSAGE(in_channels, hidden_channels, num_layers, out_channels)`
+
+**GIN** - Complete Graph Isomorphism Network
+- Multi-layer GIN for graph classification
+- Example: `GIN(in_channels, hidden_channels, num_layers, out_channels)`
+
+**GAT** - Complete Graph Attention Network
+- Multi-layer GAT with attention
+- Example: `GAT(in_channels, hidden_channels, num_layers, out_channels, heads=8)`
+
+**PNA** - Principal Neighbourhood Aggregation
+- Combines multiple aggregators and scalers
+- Example: `PNA(in_channels, hidden_channels, num_layers, out_channels)`
+
+**EdgeCNN** - Edge Convolution CNN
+- Dynamic graph CNN for point clouds
+- Example: `EdgeCNN(out_channels, num_layers=3, k=20)`
+
+### Auto-Encoders
+
+**GAE** - Graph Auto-Encoder
+- Encodes graphs into latent space
+- Example: `GAE(encoder)`
+
+**VGAE** - Variational Graph Auto-Encoder
+- Probabilistic graph encoding
+- Example: `VGAE(encoder)`
+
+**ARGA** - Adversarially Regularized Graph Auto-Encoder
+- GAE with adversarial regularization
+- Example: `ARGA(encoder, discriminator)`
+
+**ARGVA** - Adversarially Regularized Variational Graph Auto-Encoder
+- VGAE with adversarial regularization
+- Example: `ARGVA(encoder, discriminator)`
+
+### Knowledge Graph Embeddings
+
+**TransE** - Translating embeddings
+- Learns entity and relation embeddings
+- Example: `TransE(num_nodes, num_relations, hidden_channels)`
+
+**RotatE** - Rotational embeddings
+- Embeddings in complex space
+- Example: `RotatE(num_nodes, num_relations, hidden_channels)`
+
+**ComplEx** - Complex embeddings
+- Complex-valued embeddings
+- Example: `ComplEx(num_nodes, num_relations, hidden_channels)`
+
+**DistMult** - Bilinear diagonal model
+- Simplified bilinear model
+- Example: `DistMult(num_nodes, num_relations, hidden_channels)`
+
+## Utility Layers
+
+**Sequential** - Sequential container
+- Chains multiple layers
+- Example: `Sequential('x, edge_index', [(GCNConv(16, 64), 'x, edge_index -> x'), nn.ReLU()])`
+
+**JumpingKnowledge** - Jumping knowledge connections
+- Combines representations from all layers
+- Modes: 'cat', 'max', 'lstm'
+- Example: `JumpingKnowledge(mode='cat')`
+
+**DeepGCNLayer** - Deep GCN layer wrapper
+- Enables very deep GNNs with skip connections
+- Example: `DeepGCNLayer(conv, norm, act, block='res+', dropout=0.1)`
+
+**MLP** - Multi-layer perceptron
+- Standard feedforward network
+- Example: `MLP([in_channels, 64, 64, out_channels], dropout=0.5)`
+
+**Linear** - Lazy linear layer
+- Linear transformation with lazy initialization
+- Example: `Linear(in_channels, out_channels, bias=True)`
+
+## Dense Layers
+
+For dense (non-sparse) graph representations:
+
+**DenseGCNConv** - Dense GCN layer
+**DenseSAGEConv** - Dense SAGE layer
+**DenseGINConv** - Dense GIN layer
+**DenseGraphConv** - Dense graph convolution
+
+These are useful when working with small, fully-connected, or densely represented graphs.
+
+## Usage Tips
+
+1. **Start simple**: Begin with GCNConv or GATConv for most tasks
+2. **Consider data type**: Use molecular layers (SchNet, DimeNet) for 3D structures
+3. **Check capabilities**: Match layer capabilities to your data (edge features, bipartite, etc.)
+4. **Deep networks**: Use normalization (PairNorm, LayerNorm) and JumpingKnowledge for deep GNNs
+5. **Large graphs**: Use scalable layers (SAGE, Cluster-GCN) with neighbor sampling
+6. **Heterogeneous**: Use RGCNConv, HGTConv, or to_hetero() conversion
+7. **Lazy initialization**: Use lazy layers when input dimensions vary or are unknown
+
+## Common Patterns
+
+### Basic GNN
+```python
+from torch_geometric.nn import GCNConv, global_mean_pool
+
+class GNN(torch.nn.Module):
+    def __init__(self, in_channels, hidden_channels, out_channels):
+        super().__init__()
+        self.conv1 = GCNConv(in_channels, hidden_channels)
+        self.conv2 = GCNConv(hidden_channels, out_channels)
+
+    def forward(self, x, edge_index, batch):
+        x = self.conv1(x, edge_index).relu()
+        x = self.conv2(x, edge_index)
+        return global_mean_pool(x, batch)
+```
+
+### Deep GNN with Normalization
+```python
+class DeepGNN(torch.nn.Module):
+    def __init__(self, in_channels, hidden_channels, num_layers, out_channels):
+        super().__init__()
+        self.convs = torch.nn.ModuleList()
+        self.norms = torch.nn.ModuleList()
+
+        self.convs.append(GCNConv(in_channels, hidden_channels))
+        self.norms.append(LayerNorm(hidden_channels))
+
+        for _ in range(num_layers - 2):
+            self.convs.append(GCNConv(hidden_channels, hidden_channels))
+            self.norms.append(LayerNorm(hidden_channels))
+
+        self.convs.append(GCNConv(hidden_channels, out_channels))
+        self.jk = JumpingKnowledge(mode='cat')
+
+    def forward(self, x, edge_index, batch):
+        xs = []
+        for conv, norm in zip(self.convs[:-1], self.norms):
+            x = conv(x, edge_index)
+            x = norm(x)
+            x = F.relu(x)
+            xs.append(x)
+
+        x = self.convs[-1](x, edge_index)
+        xs.append(x)
+
+        x = self.jk(xs)
+        return global_mean_pool(x, batch)
+```