Week Date Major Topic Computational concepts Biological application Slides Reading Lecturer
1 8-Sep Class overview What is Network Biology pptx pdf molbio_graphtheory_background probability_background 1. Molecules of life 2. Topology of molecular networks Profs. Roy/Gitter
2 13-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
15-Sep Learning directed PGMs from data Gene network inference with and without priors pptx pdf (1) Werhli et al (2) Cancer signaling and DBN Prof. Roy
3 20-Sep Learning directed PGMs from data and priors pptx pdf Prof. Roy
22-Sep Learning dependency networks from data Linear and tree models for GRNs pptx pdf (1) GENIE3 (2) Inferelator Prof. Roy
4 27-Sep Learning undirected models from data GGMs and multi-task learning pptx pdf GNAT Prof. Roy
29-Sep Recent advances in graph learning Single cell GRNs and causality pptx pdf (1) PIDC (2) NOTEARS Prof. Roy
5 4-Oct Deep learning in network biology Network embedding and representation learning Tissue-specific gene function pptx pdf (1)Representation learning review(2)node2vec Prof. Gitter
6-Oct Graph convolutional networks Predicting protein interfaces pptx pdf (1)Distillintros(2)Wu et al Prof. Gitter
6 11-Oct Graph transformers Predicting chemical properties pptx pdf GraphGPS Prof. Gitter
13-Oct Graph transformers Attention examples (pdf) (ipynb) Prof. Gitter
7 18-Oct Graph transformers Prof. Gitter
20-Oct GANs and graph generative models Drug discovery pptx pdf MolGAN Prof. Gitter
8 25-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
27-Oct Spectral and Louvain clustering Modules on graphs pptx pdf (1) Louvain clustering (2) Module detection challenge Prof. Roy
9 1-Nov GNN methods for module finding Clustering graphs with attributes pptx pdf (1)DNR (2) Senet Prof. Roy
3-Nov Dynamic modules Examining topology changes pptx pdf PisCES Prof. Roy
10 8-Nov Network-based data integration and interpretation Graph kernels for node prioritization Finding important genes of process/disease pptx pdf GeneWanderer Prof. Gitter
10-Nov Graph diffusion Finding pathways in cancer pptx pdf HotNet Prof. Gitter
11 15-Nov Data integration using networks: Steiner forests Integrating data from few samples pptx pdf PCSF Prof. Gitter
17-Nov Data integration using networks: SNF Integrating data from many samples pptx pdf SNF Prof. Gitter
12 22-Nov Graph alignment Spectal and matrix factorization based alignment Aligning protein-protein interaction networks pptx pdf (1) IsoRank (2) FUSE Prof. Roy
24-Nov Thanksgiving
13 29-Nov Graph alignment of single cell datasets Aligning and integrating single cell omic datasets pptx pdf (1) SCANORAMA (2) LIGER Prof. Roy
1-Dec Dana Pe'er seminar
14 6-Dec Projects
8-Dec Projects
15 13-Dec Projects