Week Date Major Topic Computational concepts Biological application Slides Reading Lecturer
1 7-Sep Class overview What is Network Biology pptx pdf 1. Molecules of life 2. Topology of molecular networks Profs. Roy/Gitter
2 12-Sep Representing and learning networks from data Introductory concepts of graphs and PGMs Representing gene regulatory networks pptx pdf (1) Friedman et al (2) Sparse candidate (3) Markowetz and Spang (optional) Prof. Roy
14-Sep Learning directed PGMs from data Modeling time and prior knowledge for Gene regulatory networks pptx pdf (1) Cancer signaling and DBN (2) Werhli et al (optional) Prof. Roy
3 19-Sep Learning directed PGMs from data Modeling prior knowledge for GRNs pptx pdf Prof. Roy
21-Sep Learning dependency networks from data Linear and tree models for GRNs pptx pdf GENIE3 Prof. Roy
4 26-Sep Learning undirected models from data GGMs and multi-task learning pptx pdf GNAT Prof. Roy
28-Sep Causal graph learning Causality in GRNs pptx pdf Review Article Prof. Roy
5 3-Oct Supervised deep learning in network biology Graph neural networks Predicting protein interfaces (1)Distillintros(2)Wu et al Prof. Gitter
5-Oct Graph neural networks Prof. Gitter
6 10-Oct Graph transformers Predicting chemical properties Prof. Gitter
12-Oct Graph transformers Prof. Gitter
7 17-Oct Graph transformers Prof. Gitter
19-Oct GANs and graph generative models Drug discovery Prof. Gitter
8 24-Oct Graph topology and modules Degree distributions and modules Organizational properties of networks Prof. Roy
26-Oct Spectral and Louvain clustering Modules on graphs Prof. Roy
9 31-Oct Representation learning Clustering graphs with attributes Prof. Roy
2-Nov GNN methods for module finding Clustering graphs with attributes Prof. Roy
10 7-Nov Graph alignment Spectral and matrix factorization based alignment Aligning protein-protein interaction networks Prof. Roy
9-Nov Graph alignment of single cell datasets Aligning and integrating single cell omic datasets Prof. Roy
11 14-Nov Network-based data integration and interpretation Graph kernels for node prioritization Finding important genes of process/disease Prof. Gitter
16-Nov Graph diffusion Finding pathways in cancer HotNet Prof. Gitter
12 21-Nov More integration Prof. Gitter
23-Nov Thanksgiving
13 28-Nov Data integration using networks: Steiner forests Integrating data from few samples PCSF Prof. Gitter
30-Nov Data integration using networks: SNF Integrating data from many samples SNF Prof. Gitter
14 5-Dec Projects
7-Dec Projects
15 12-Dec Projects