gh-k-dense-ai-claude-scientific-skills-scientific-skills/skills/torchdrug/references/models_architectures.md

Models and Architectures

Overview

TorchDrug provides a comprehensive collection of pre-built model architectures for various graph-based learning tasks. This reference catalogs all available models with their characteristics, use cases, and implementation details.

Graph Neural Networks

GCN (Graph Convolutional Network)

Type: Spatial message passing Paper: Semi-Supervised Classification with Graph Convolutional Networks (Kipf & Welling, 2017)

Characteristics:

• Simple and efficient aggregation
• Normalized adjacency matrix convolution
• Works well for homophilic graphs
• Good baseline for many tasks

Best For:

• Initial experiments and baselines
• When computational efficiency is important
• Graphs with clear local structure

Parameters:

• input_dim: Node feature dimension
• hidden_dims: List of hidden layer dimensions
• edge_input_dim: Edge feature dimension (optional)
• batch_norm: Apply batch normalization
• activation: Activation function (relu, elu, etc.)
• dropout: Dropout rate

Use Cases:

• Molecular property prediction
• Citation network classification
• Social network analysis

GAT (Graph Attention Network)

Type: Attention-based message passing Paper: Graph Attention Networks (Veličković et al., 2018)

Characteristics:

• Learns attention weights for neighbors
• Different importance for different neighbors
• Multi-head attention for robustness
• Handles varying node degrees naturally

Best For:

• When neighbor importance varies
• Heterogeneous graphs
• Interpretable predictions

Parameters:

• input_dim, hidden_dims: Standard dimensions
• num_heads: Number of attention heads
• negative_slope: LeakyReLU slope
• concat: Concatenate or average multi-head outputs

Use Cases:

• Protein-protein interaction prediction
• Molecule generation with attention to reactive sites
• Knowledge graph reasoning with relation importance

GIN (Graph Isomorphism Network)

Type: Maximally powerful message passing Paper: How Powerful are Graph Neural Networks? (Xu et al., 2019)

Characteristics:

• Theoretically most expressive GNN architecture
• Injective aggregation function
• Can distinguish graph structures GCN cannot
• Often best performance on molecular tasks

Best For:

• Molecular property prediction (state-of-the-art)
• Tasks requiring structural discrimination
• Graph classification

Parameters:

• input_dim, hidden_dims: Standard dimensions
• edge_input_dim: Include edge features
• batch_norm: Typically use true
• readout: Graph pooling ("sum", "mean", "max")
• eps: Learnable or fixed epsilon

Use Cases:

• Drug property prediction (BBBP, HIV, etc.)
• Molecular generation
• Reaction prediction

RGCN (Relational Graph Convolutional Network)

Type: Multi-relational message passing Paper: Modeling Relational Data with Graph Convolutional Networks (Schlichtkrull et al., 2018)

Characteristics:

• Handles multiple edge/relation types
• Relation-specific weight matrices
• Basis decomposition for parameter efficiency
• Essential for knowledge graphs

Best For:

• Knowledge graph reasoning
• Heterogeneous molecular graphs
• Multi-relational data

Parameters:

• num_relation: Number of relation types
• hidden_dims: Layer dimensions
• num_bases: Basis decomposition (reduce parameters)

Use Cases:

• Knowledge graph completion
• Retrosynthesis (different bond types)
• Protein interaction networks

MPNN (Message Passing Neural Network)

Type: General message passing framework Paper: Neural Message Passing for Quantum Chemistry (Gilmer et al., 2017)

Characteristics:

• Flexible message and update functions
• Edge features in message computation
• GRU updates for node hidden states
• Set2Set readout for graph representation

Best For:

• Quantum chemistry predictions
• Tasks with important edge information
• When node states evolve over multiple iterations

Parameters:

• input_dim, hidden_dim: Feature dimensions
• edge_input_dim: Edge feature dimension
• num_layer: Message passing iterations
• num_mlp_layer: MLP layers in message function

Use Cases:

• QM9 quantum property prediction
• Molecular dynamics
• 3D conformation-aware tasks

SchNet (Continuous-Filter Convolutional Network)

Type: 3D geometry-aware convolution Paper: SchNet: A continuous-filter convolutional neural network (Schütt et al., 2017)

Characteristics:

• Operates on 3D atomic coordinates
• Continuous filter convolutions
• Rotation and translation invariant
• Excellent for quantum chemistry

Best For:

• 3D molecular structure tasks
• Quantum property prediction
• Protein structure analysis
• Energy and force prediction

Parameters:

• input_dim: Atom features
• hidden_dims: Layer dimensions
• num_gaussian: RBF basis functions for distances
• cutoff: Interaction cutoff distance

Use Cases:

• QM9 property prediction
• Molecular dynamics simulations
• Protein-ligand binding with structures
• Crystal property prediction

ChebNet (Chebyshev Spectral CNN)

Type: Spectral convolution Paper: Convolutional Neural Networks on Graphs (Defferrard et al., 2016)

Characteristics:

• Spectral graph convolution
• Chebyshev polynomial approximation
• Captures global graph structure
• Computationally efficient

Best For:

• Tasks requiring global information
• When graph Laplacian is informative
• Theoretical analysis

Parameters:

• input_dim, hidden_dims: Dimensions
• num_cheb: Order of Chebyshev polynomial

Use Cases:

• Citation network classification
• Brain network analysis
• Signal processing on graphs

NFP (Neural Fingerprint)

Type: Molecular fingerprint learning Paper: Convolutional Networks on Graphs for Learning Molecular Fingerprints (Duvenaud et al., 2015)

Characteristics:

• Learns differentiable molecular fingerprints
• Alternative to hand-crafted fingerprints (ECFP)
• Circular convolutions like ECFP
• Interpretable learned features

Best For:

• Molecular similarity learning
• Property prediction with limited data
• When interpretability is important

Parameters:

• input_dim, output_dim: Feature dimensions
• hidden_dims: Layer dimensions
• num_layer: Circular convolution depth

Use Cases:

• Virtual screening
• Molecular similarity search
• QSAR modeling

Protein-Specific Models

GearNet (Geometry-Aware Relational Graph Network)

Type: Protein structure encoder Paper: Protein Representation Learning by Geometric Structure Pretraining (Zhang et al., 2023)

Characteristics:

• Incorporates 3D geometric information
• Multiple edge types (sequential, spatial, KNN)
• Designed specifically for proteins
• State-of-the-art on protein tasks

Best For:

• Protein structure prediction
• Protein function prediction
• Protein-protein interaction
• Any task with protein 3D structures

Parameters:

• input_dim: Residue features
• hidden_dims: Layer dimensions
• num_relation: Edge types (sequence, radius, KNN)
• edge_input_dim: Geometric features (distances, angles)
• batch_norm: Typically true

Use Cases:

• Enzyme function prediction (EnzymeCommission)
• Protein fold recognition
• Contact prediction
• Binding site identification

ESM (Evolutionary Scale Modeling)

Type: Protein language model (transformer) Paper: Biological structure and function emerge from scaling unsupervised learning (Rives et al., 2021)

Characteristics:

• Pre-trained on 250M+ protein sequences
• Captures evolutionary and structural information
• Transformer architecture
• Transfer learning for downstream tasks

Best For:

• Any sequence-based protein task
• When no structure available
• Transfer learning with limited data

Variants:

• ESM-1b: 650M parameters
• ESM-2: Multiple sizes (8M to 15B parameters)

Use Cases:

• Protein function prediction
• Variant effect prediction
• Protein design
• Structure prediction (ESMFold)

ProteinBERT

Type: Masked language model for proteins

Characteristics:

• BERT-style pre-training
• Masked amino acid prediction
• Bidirectional context
• Good for sequence-based tasks

Use Cases:

• Function annotation
• Subcellular localization
• Stability prediction

ProteinCNN / ProteinResNet

Type: Convolutional networks for sequences

Characteristics:

• 1D convolutions on sequences
• Local pattern recognition
• Faster than transformers
• Good for motif detection

Use Cases:

• Binding site prediction
• Secondary structure prediction
• Domain identification

ProteinLSTM

Type: Recurrent network for sequences

Characteristics:

• Bidirectional LSTM
• Captures long-range dependencies
• Sequential processing
• Good baseline for sequence tasks

Use Cases:

• Order prediction
• Sequential annotation
• Time-series protein data

Knowledge Graph Models

TransE (Translation Embedding)

Type: Translation-based embedding Paper: Translating Embeddings for Modeling Multi-relational Data (Bordes et al., 2013)

Characteristics:

• h + r ≈ t (head + relation ≈ tail)
• Simple and interpretable
• Works well for 1-to-1 relations
• Memory efficient

Best For:

• Large knowledge graphs
• Initial experiments
• Interpretable embeddings

Parameters:

• num_entity, num_relation: Graph size
• embedding_dim: Embedding dimensions (typically 50-500)

RotatE (Rotation Embedding)

Type: Rotation in complex space Paper: RotatE: Knowledge Graph Embedding by Relational Rotation in Complex Space (Sun et al., 2019)

Characteristics:

• Relations as rotations in complex space
• Handles symmetric, antisymmetric, inverse, composition
• State-of-the-art on many benchmarks

Best For:

• Most knowledge graph tasks
• Complex relation patterns
• When accuracy is critical

Parameters:

• num_entity, num_relation: Graph size
• embedding_dim: Must be even (complex embeddings)
• max_score: Score clipping value

DistMult

Type: Bilinear model

Characteristics:

• Symmetric relation modeling
• Fast and efficient
• Cannot model antisymmetric relations

Best For:

• Symmetric relations (e.g., "similar to")
• When speed is critical
• Large-scale graphs

ComplEx

Type: Complex-valued embeddings

Characteristics:

• Handles asymmetric and symmetric relations
• Better than DistMult for most graphs
• Good balance of expressiveness and efficiency

Best For:

• General knowledge graph completion
• Mixed relation types
• When RotatE is too complex

SimplE

Type: Enhanced embedding model

Characteristics:

• Two embeddings per entity (canonical + inverse)
• Fully expressive
• Slightly more parameters than ComplEx

Best For:

• When full expressiveness needed
• Inverse relations are important

Generative Models

GraphAutoregressiveFlow

Type: Normalizing flow for molecules

Characteristics:

• Exact likelihood computation
• Invertible transformations
• Stable training (no adversarial)
• Conditional generation support

Best For:

• Molecular generation
• Density estimation
• Interpolation between molecules

Parameters:

• input_dim: Atom features
• hidden_dims: Coupling layers
• num_flow: Number of flow transformations

Use Cases:

• De novo drug design
• Chemical space exploration
• Property-targeted generation

Pre-training Models

InfoGraph

Type: Contrastive learning

Characteristics:

• Maximizes mutual information
• Graph-level and node-level contrast
• Unsupervised pre-training
• Good for small datasets

Use Cases:

• Pre-train molecular encoders
• Few-shot learning
• Transfer learning

MultiviewContrast

Type: Multi-view contrastive learning for proteins

Characteristics:

• Contrasts different views of proteins
• Geometric pre-training
• Uses 3D structure information
• Excellent for protein models

Use Cases:

• Pre-train GearNet on protein structures
• Transfer to property prediction
• Limited labeled data scenarios

Model Selection Guide

By Task Type

Molecular Property Prediction:

1. GIN (first choice)
2. GAT (interpretability)
3. SchNet (3D available)

Protein Tasks:

1. ESM (sequence only)
2. GearNet (structure available)
3. ProteinBERT (sequence, lighter than ESM)

Knowledge Graphs:

1. RotatE (best performance)
2. ComplEx (good balance)
3. TransE (large graphs, efficiency)

Molecular Generation:

1. GraphAutoregressiveFlow (exact likelihood)
2. GCPN with GIN backbone (property optimization)

Retrosynthesis:

1. GIN (synthon completion)
2. RGCN (center identification with bond types)

By Dataset Size

Small (< 1k):

• Use pre-trained models (ESM for proteins)
• Simpler architectures (GCN, ProteinCNN)
• Heavy regularization

Medium (1k-100k):

• GIN for molecules
• GAT for interpretability
• Standard training

Large (> 100k):

• Any model works
• Deeper architectures
• Can train from scratch

By Computational Budget

Low:

• GCN (simplest)
• DistMult (KG)
• ProteinLSTM

Medium:

• GIN
• GAT
• ComplEx

High:

• ESM (large)
• SchNet (3D)
• RotatE with high dim

Implementation Tips

1. Start Simple: Begin with GCN or GIN baseline
2. Use Pre-trained: ESM for proteins, InfoGraph for molecules
3. Tune Depth: 3-5 layers typically sufficient
4. Batch Normalization: Usually helps (except KG embeddings)
5. Residual Connections: Important for deep networks
6. Readout Function: "mean" usually works well
7. Edge Features: Include when available (bonds, distances)
8. Regularization: Dropout, weight decay, early stopping