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 | |
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| 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) |
