GNNs

This course is designed to provide a comprehensive introduction to Graph Neural Networks (GNNs) and their applications in the Healthcare & Life Sciences industries. Participants will learn the fundamental concepts, architectures, and training techniques of GNNs, enabling them to develop and deploy graph-based models for various tasks relevant to the healthcare and life sciences domains, such as drug discovery, disease prediction, and biological network analysis.

• Understand the concepts and motivation behind Graph Neural Networks

• Represent and manipulate graph-structured data using Python libraries

• Implement and train various GNN architectures, such as Graph Convolutional Networks (GCNs) and Graph Attention Networks (GATs)

• Apply GNNs to solve node classification, edge prediction, and graph classification tasks in healthcare and life sciences

• Design and develop GNN-based solutions for drug discovery, disease prediction, and biological network analysis

1. Introduction to Graph Neural Networks

• Overview of graphs and their applications in the Healthcare & Life Sciences industries

• Limitations of traditional machine learning approaches for graph-structured data

• Introduction to Graph Neural Networks and their advantages

• Hands-on exercises: Representing and visualizing graphs using Python libraries (e.g., NetworkX, PyTorch Geometric)

2. Graph Convolutional Networks (GCNs)

• Spectral and spatial graph convolutions

• GCN architecture and propagation rules

• Training GCNs using backpropagation and gradient descent

• Hands-on exercises: Implementing and training GCNs for node classification tasks in biological networks

3. Graph Attention Networks (GATs) and Message Passing

• Attention mechanisms in graph neural networks

• GAT architecture and attention-based message passing

• Comparison of GATs with GCNs and other GNN variants

• Hands-on exercises: Implementing and training GATs for edge prediction tasks in drug-target interaction networks

4. Advanced GNN Architectures and Techniques

• Graph Recurrent Neural Networks (GRNNs) for capturing temporal dependencies in healthcare data

• Graph Autoencoders (GAEs) for unsupervised learning and graph generation in drug discovery

• Sampling techniques for large-scale graphs (e.g., GraphSAGE, Cluster-GCN)

• Hands-on exercises: Implementing advanced GNN architectures and techniques on healthcare and life sciences datasets

5. GNNs for Healthcare & Life Sciences Applications

• Case studies of GNNs in drug discovery and virtual screening

• Disease prediction and patient stratification using GNNs

• Biological network analysis and protein function prediction with GNNs

• Hands-on exercises: Developing a GNN-based solution for a specific Healthcare or Life Sciences use case

6. Deployment and Future Directions

• Deploying GNN models in production environments

• Scaling GNN training and inference for large-scale graphs

• Hybrid approaches combining GNNs with other machine learning techniques

• Future research directions and open challenges in GNNs for the Healthcare & Life Sciences industries

• Hands-on exercises: Deploying a GNN model using a cloud platform (e.g., AWS, GCP)

• Strong understanding of linear algebra, calculus, and probability theory

• Proficiency in programming with Python and deep learning frameworks (e.g., TensorFlow, PyTorch)

• Familiarity with basic machine learning concepts and techniques

• Knowledge of graph theory and network analysis is beneficial but not required