Preliminary AGENDA

This is a preliminary agenda and is subject to modification.

8 November 9 November 10 November
Day 1, 8 November
9:00 AM -
5:00 PM
2026 HCA Middle East In-Person, Pre-Symposium Workshop: Probabilistic Modeling for Single-Cell and Spatial Transcriptomics with scvi-tools
9:00 AM - 5:00 PM

 

Overview:

Recent advances in single-cell and spatial transcriptomics have transformed our ability to characterize complex tissues. However, extracting robust biological insights from increasingly large, heterogeneous datasets requires statistical models that explicitly account for technical noise, batch effects, and allow using these large datasets as reference for novel datasets. This workshop provides a practical introduction to probabilistic deep learning using scvi-tools, the leading open-source framework for generative modeling of single-cell and spatial omics data. Participants will learn both the theoretical foundations and practical workflows for reference mapping, cell type annotation, differential analysis, and analysis of spatial transcriptomics data using modern variational autoencoders. The workshop combines concise lectures with extensive hands-on sessions using reproducible Jupyter notebooks. Participants are expected to have basic familiarity with single-cell RNA-seq analysis and Python.

9:00 - 10:00 AM: Session I - Introduction to Probabilistic Modeling and scvi-tools

  • Topics to include:
    • Motivation for probabilistic modeling
    • Variational autoencoders for transcriptomics and latent representations
    • Batch correction
    • Current applications and reference atlases

10:00 - 12:00 PM: Session II - Introduction to Probabilistic Modeling and scvi-tools (continued)

  • Practical exercises to include:
    • Preparing AnnData objects
    • Training an scVI model
    • Exploring latent embeddings
    • Differential expression and abundance analysis
    • Semi-supervised annotation with scANVI and query mapping
    • Evaluating annotation confidence and uncertainty

12:00 - 1:30 PM: Lunch Break

1:30 - 3:30 PM: Session III - Hands-on: Spatial Transcriptomics with resolVI and scVIVA

  • Topics to include:
    • Introduction to probabilistic modeling for spatial transcriptomics
    • Addressing noise and cell type inference in spatial data
    • Infering spatial cell states

3:30 - 4:30 PM: Session IV - Outlook: AI-Native Analysis with scverse

  • Emerging directions include:
    • Agentic interfaces for computational biology
    • Natural language interaction with scverse workflows
    • Retrieval-Augmented Generation (RAG) for reference model discovery
       
Can Ergen-behr
Can Ergen-behr
Session Details
Time Zone: (UTC+03:30) Tehran [Change Time Zone]