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 pptx pdf (1)Distill intros (2)Wu et al Prof. Gitter
5-Oct Graph neural network extensions Predicting protein function pptx pdf Graph attention networks Prof. Gitter
6 10-Oct Graph transformers Predicting chemical properties pptx pdf GraphGPS Prof. Gitter
12-Oct Graph transformers see 10-Oct Attention examples (pdf) (ipynb) Prof. Gitter
7 17-Oct Equivariant graph neural networks Predicting 3D chemical properties pptx pdf E(n) Equivariant GNN Prof. Gitter
19-Oct GANs and graph generative models Drug discovery pptx pdf MolGAN Prof. Gitter
8 24-Oct Graph topology and modules Degree distributions and modules Organizational properties of networks pptx pdf (1) Barabasi and Oltvai review (2) Girvan-Newman algorithm Prof. Roy
26-Oct Spectral and Louvain clustering Modules on graphs pptx pdf (1) Louvain clustering (2) Module detection challenge Prof. Roy
9 31-Oct Representation learning pptx pdf (1)Representation learning review(2)node2vec (3) OhmNet Prof. Roy
2-Nov Representing graphs with attributes pptx pdf (1)Variational GraphAutoEncoder (2)Deep Graph Infomax Prof. Roy
10 7-Nov Graph alignment Spectral and matrix factorization based alignment Aligning protein-protein interaction networks pptx pdf 1) IsoRank (2) FUSE Prof. Roy
9-Nov Graph alignment of single cell datasets Aligning and integrating single cell omic datasets pptx pdf (1) SCANORAMA (2) LIGER Prof. Roy
11 14-Nov Network-based data integration and interpretation Graph kernels for node prioritization Finding important genes of process/disease pptx pdf GeneWanderer Prof. Gitter
16-Nov Graph diffusion Finding pathways in cancer pptx pdf HotNet Prof. Gitter
12 21-Nov Graph diffusion Finding pathways in cancer see 16-Nov Prof. Gitter
23-Nov Thanksgiving
13 28-Nov Data integration using networks: Steiner forests Integrating data from few samples pptx pdf PCSF Prof. Gitter
30-Nov Data integration using networks: SNF Integrating data from many samples pptx pdf SNF Prof. Gitter
14 5-Dec Projects
7-Dec Projects
15 12-Dec Projects