Schedule for: 22w5085 - Deep Learning for Genetics, Genomics and Metagenomics: Latest developments and New Directions
Beginning on Sunday, June 5 and ending Friday June 10, 2022
All times in UBC Okanagan, Canada time, PDT (UTC-7).
Sunday, June 5 |
18:00 - 20:00 |
Check-in begins at 16:00 on Sunday and is open 24 hours (Front Desk Nechako Residence) |
Monday, June 6 |
08:00 - 08:45 |
Breakfast (Sunshine/ADM) |
08:45 - 09:00 |
Introduction and Welcome by UBCO-BIRS Staff (ART 386) |
09:00 - 09:40 |
Anshul Kundaje: Deep learning oracles for genomic discovery (Zoom) |
09:40 - 10:05 |
Yi Xing: Deep-learning augmented RNA-seq analysis of transcript splicing (ART 386) |
10:05 - 10:20 |
Coffee Break (ASC 310) |
10:20 - 10:45 |
Jian Zhou: Sequence-based modeling of three-dimensional genome architecture from kilobase to chromosome scale (Zoom) |
10:45 - 11:10 |
Julien Gagneur: A genetic algorithm with deep learning based guided mutations improves de novo peptide sequencing (ART 386) |
11:10 - 11:35 |
Mathieu Blanchette: Learning from Evolution (Zoom) |
11:35 - 12:00 |
Sara Mostafavi: Discussion morning session (Zoom) |
12:00 - 13:00 |
Lunch (Sunshine) |
13:00 - 14:00 |
Walkabout on Campus Trail (ASC 310) |
14:00 - 14:20 |
Group Photo (EME East Entrance) |
14:20 - 14:45 |
Camille Rochefort-Boulanger: Deep learning on genetic data with Diet Network and its application to a complex phenotype (ART 386) |
14:45 - 15:10 |
Joseph Szymborski: RAPPPID: Deep, Regularised Protein-Protein Interaction Prediction that Generalises to Unseen Proteins (ART 386) |
15:10 - 15:30 |
Coffee Break (ASC 310) |
15:30 - 16:10 |
James Zou: Geometric Deep Learning for Multiplex Spatial Biology (Zoom) |
16:10 - 16:35 |
Jian Tang: Geometric Deep Learning for Drug Discovery (Zoom) |
16:35 - 17:00 |
Anshul Kundaje: Discussion afternoon session (Zoom) |
17:00 - 17:25 |
Selin Jessa: Data-driven approaches to identify the origins of pediatric brain tumors (ART 386) |
17:25 - 17:50 |
Jesse Islam: Case-Base Neural Networks: survival analysis with time-varying, higher-order interactions (Zoom) |
18:00 - 20:00 |
Dinner (Sunshine) |
Tuesday, June 7 |
08:00 - 08:45 |
Breakfast (Sunshine/ADM) |
09:00 - 09:25 |
Wei Sun: Biologically-informed neural networks for scRNA-seq data (Zoom) |
09:25 - 09:50 |
Jingshu Wang: Model-Based Trajectory Inference for Single-Cell RNA Sequencing Using Deep Learning with a Mixture Prior (Zoom) |
09:50 - 10:15 |
Mingyao Li: Deciphering tissue microenvironment by integrative analysis of spatial transcriptomics with histology images and single cells (Zoom) |
10:15 - 10:30 |
Coffee Break (ASC 310) |
10:30 - 11:10 |
Ritambhara Singh: Towards spatial and temporal modeling of gene regulation using deep learning (ART 386) |
11:10 - 11:35 |
Claudia Kleinman: Assessing cell-type prediction methods for developmental single-cell RNA datasets (Zoom) |
11:35 - 12:00 |
Hongyu Zhao: Non-linear archetypal analysis of single-cell RNA-seq data by deep autoencoders (Zoom) |
12:00 - 12:25 |
Mengjie Chen: Discussion morning session (Zoom) |
12:30 - 14:00 |
Lunch (Sunshine) |
14:00 - 14:40 |
Jessica Li: An all-in-one statistical framework that simulates realistic single-cell omics data and infers cell heterogeneity structure (ART 386) |
14:40 - 15:05 |
Hongkai Ji: Cross-modality prediction and imputation of functional genome on single cells (Zoom) |
15:05 - 15:20 |
Coffee Break (ASC 310) |
15:20 - 15:45 |
Sara Mostafavi: Deep learning of immune cell differentiation (Zoom) |
15:45 - 16:10 |
Nancy Zhang: Deep neural networks for denoising and batch correction in single cell genomics (Zoom) |
16:10 - 16:35 |
Rui Jiang: Deep learning for cell type identification based on single-cell chromatin accessibility data (Zoom) |
16:35 - 17:00 |
Jesse Shapiro: Discussion afternoon session (Zoom) |
17:00 - 20:00 |
Dinner (Sunshine) |
Wednesday, June 8 |
08:00 - 08:45 |
Breakfast (Sunshine/ADM) |
09:00 - 09:25 |
Sach Mukherjee: A deep architecture for the large-scale learning of causal molecular networks (Zoom) |
09:25 - 09:50 |
Sriram Sankararaman: Interpretable deep learning for genomic discovery (ART 386) |
09:50 - 10:30 |
Michael Hoffman: Reproducibility standards for machine learning in the life sciences (Zoom) |
10:30 - 10:45 |
Coffee Break (ASC 310) |
10:45 - 11:10 |
Jessica Gronsbell: Leveraging electronic health records for genetic research (ART 386) |
11:10 - 11:35 |
Yue Li: Neural topic modeling of electronic health records (Zoom) |
11:35 - 12:00 |
James Zou: Discussion morning session (Zoom) |
12:00 - 13:30 |
Lunch (Sunshine) |
13:30 - 17:30 |
Free Afternoon (Kelowna) |
17:30 - 20:00 |
Dinner (Sunshine) |
Thursday, June 9 |
08:00 - 08:45 |
Breakfast (Sunshine/ADM) |
09:00 - 09:25 |
Kushal Dey: Evaluating the informativeness of deep learning annotations for human complex diseases (Zoom) |
09:25 - 09:50 |
Zihuai He: Deep neural networks with controlled variable selection for the identification of putative causal genetic variants (Zoom) |
09:50 - 10:05 |
Coffee Break (ASC 310) |
10:05 - 10:30 |
Valentina Boeva: Deciphering shared intratumor transcriptional heterogeneity of human tumors (Zoom) |
10:30 - 11:10 |
Amin Emad: Deep Learning in Cancer Precision Medicine (ART 386) |
11:10 - 11:35 |
Pingzhao Hu: Deep learning-empowered breast cancer radiogenomics for precision medicine (Zoom) |
11:35 - 12:00 |
Wei Sun: Discussion morning session (Zoom) |
12:00 - 13:30 |
Lunch (Sunshine) |
13:30 - 13:55 |
Lei Sun: Unusual suspects: Recent advances and new challenges in X chromosome-inclusive analyses (ART 386) |
13:55 - 14:20 |
Xihong Lin: Estimation of the number of ancestry PCs using bulk eigenvalue matching analysis (ART 386) |
14:20 - 14:45 |
Wei Pan: DeLIVR: A Deep Learning Approach to Testing for Non-linear Causal Effects in Transcriptome-Wide Association Studies (Zoom) |
14:45 - 15:10 |
Gabriela Cohen-Freue: Scaling up Mendelian randomization for high-dimensional -omics data (Zoom) |
15:10 - 15:30 |
Coffee Break (ASC 310) |
15:30 - 15:55 |
Shuangning Li: Searching for Robust Associations with a Multi-Environment Knockoff Filter (Zoom) |
15:55 - 16:20 |
Linxi Liu: Identifying putative causal loci in whole-genome sequencing studies via knockoff Statistics (Zoom) |
16:20 - 16:45 |
Fengzhu Sun: DeepLINK: Deep learning inference using knockoffs with applications to genomics (Zoom) |
16:45 - 17:15 |
Jingyi (Jessica) Li: Discussion afternoon session (ART 386) |
17:30 - 20:00 |
Dinner (Sunshine) |
Friday, June 10 |
08:00 - 08:45 |
Breakfast (Sunshine/ADM) |
09:00 - 10:30 |
General Discussion TBA (ART 386) |
10:30 - 11:00 |
Checkout by 11AM (Nechako Residence) |
11:30 - 13:00 |
Lunch (Sunshine) |