Introduction to Deep Learning Tools in Genomics

This workshop will introduce the applications of deep neural networks to genomics including variant calling, motif discovery, analysis of gene expression, single cell and image analysis using deepVariant, deepBind, cellpose, etc. We will introduce basic concepts in ML and discuss common model architectures and training. We will also touch upon foundation models in single cell analysis such as scGPT. A hands-on session is emphasized and will showcase how to use Python to train a simple model on HPC3 and perform common analysis tasks in genomics.

Attendees are encouraged to bring their own project data for analysis and discussion.

Instruction by Jenny Wu, PhD and Ivan Chang, PhD