Schedule

Week	Date	Major Topic	Computational Concepts	Biological Application	Slides	Reading	Lecturer
1	3-Sep	Class overview		What is Network Biology	pptx, pdf	1. Molecules of life 2. Topology of molecular networks 3. Current and Future Directions in Network Biology	Profs. Roy/Gitter
2	8-Sep	Learning graphs from data	Introductory concepts of graphs and PGMs	Representing gene regulatory networks			Prof. Roy
	10-Sep		Bayesian networks	Learning GRNs from expression			Prof. Roy
3	15-Sep		Bayesian networks contd/Dependency networks				Prof. Roy
	17-Sep		Dependency networks	Cycles and predictive relationships			Prof. Roy
4	22-Sep		Dynamic and Causal graph learning	Dynamic GRNs			Prof. Roy
	24-Sep		Dynamic and Causal graph learning	Causal GRNs			Prof. Roy
5	29-Sep	Graph Laplacian and applications	Intro Lin Algebra, Connected components, clustering	Topological properties of graphs			Prof. Roy
	1-Oct	Graph clustering	Spectral and louvain clustering	Detecting modules on graphs			Prof. Roy
6	6-Oct	Shallow representation learning (RL) for graphs	Node embedding, random walk, node2vec	Function prediction in multi-layer networks			Prof. Roy
	8-Oct	Deep RL for graphs	Graph neural networks				Prof. Gitter
7	13-Oct		Graph neural networks				Prof. Gitter
	15-Oct		Graph transformers				Prof. Gitter
8	20-Oct		Graph transformers				Prof. Gitter
	22-Oct		Experimental design & evaluation for graph ML				Prof. Gitter
9	27-Oct	Unsupervised Deep RL for graphs	Variational Graph AutoEncoders	Generalizing to new examples			Prof. Roy
	29-Oct	Graph comparison and alignment	Graph Alignment	Aligning protein-protein interaction networks			Prof. Roy
10	3-Nov		Graph Alignment				Prof. Roy
	5-Nov	Network-based applications (NBA): prioritization	Graph kernels for node prioritization	Finding important genes of a process/disease			Prof. Gitter
11	10-Nov		Graph diffusion	Finding disease pathways associated with cancer			Prof. Gitter
	12-Nov		Graph diffusion	More integration			Prof. Gitter
12	17-Nov		Data integration using networks: Steiner tree	Integrating data from small samples			Prof. Gitter
	19-Nov		Data integration using networks: SNF	Integrating data from large samples			Prof. Gitter
13	24-Nov		Data integration using networks: BIONIC	Integrating complementary networks			Prof. Gitter
	26-Nov	Thanksgiving
14	1-Dec	Projects
	3-Dec	Projects
15	8-Dec	Projects