IICD Intensive Workshop: Methods in Single-Cell Data Integration and Optimal Transport

IICD Intensive Workshop: Methods in Single-Cell Data Integration and Optimal Transport

 

Summary:

The Irving Institute for Cancer Dynamics offers a five-day in-person intensive workshop (July 8th-12th, 2024, Columbia University Morningside Heights Campus) for graduate students and postdoctoral fellows to learn about data integration and optimal transport methods (at no cost for participants). Participants will learn about multi-modal single-cell genomic data integration, probabilistic modeling, emerging technologies in spatial integration, and the theory and implementation of optimal transport.

 

Overview: 

Data integration methods are used to combine and align multiple genomic datasets within the same cells, allowing researchers to identify patterns and interactions that may not be apparent in a single dataset. Data integration is essential in machine learning to analyze imaging technologies, single‐cell RNA/DNA sequencing, etc.

Optimal transport is a mathematical framework used to formulate probabilistic matching and alignment problems. Optimal transport has a variety of applications in diverse areas including economics, computer science, neuroscience, and image processing. In recent years, optimal transport has seen renewed attention in the machine learning community as advances in algorithms and computational power have allowed applications to problems involving high-dimensional data.

The Institute offers a 5-day intensive workshop (July 8th-12th, 2024, Morningside Heights campus) for graduate students and postdoctoral fellows to learn more about methods in data integration and optimal transport. Participants will learn about multi-modal single-cell integration, probabilistic modeling, emerging technologies in spatial integration, and the theory and implementation of optimal transport.

The one-week workshop will include morning lectures and hands-on problem sets in the afternoon, and each day will conclude with a guest lecturer. The summer school will end with short group presentations and a mixer.

By the end of the workshop, participants will be familiar with the following concepts:

  • Multi-modal single-cell integration
  • Probabilistic modeling and representation learning for high-dimensional data
  • Emerging technologies in spatial and imaging integration
  • Theory and implementation of optimal transport
  • Applications of optimal transport for multi-modal single-cell integration and spatial data

 

Audience and Requirements:

The workshop is aimed at students and postdoctoral fellows.

To attend the one-week workshop, participants are required to have:

  • comfort with programming in Python or R
  • elementary knowledge in linear algebra, probability, statistics

 

When and Where:

The 5-day intensive workshop will take place in person from July 8th-12th, 2024 on the Morningside Heights campus.

 

Instructors:

  • Elham Azizi: Herbert and Florence Irving Assistant Professor of Cancer Data Research and Assistant Professor of Biomedical Engineering
  • Andrew Blumberg: Herbert and Florence Irving Professor of Cancer Data Research and Professor of Mathematics and Computer Science
  • Joy Fan: PhD student in biomedical engineering (Elham Azizi’s group)
  • Valerio Galanti: PhD student in computer science (Andrew Blumberg’s group)
  • Justin Hong: PhD student in computer science (Elham Azizi’s group)
  • Yining Liu: PhD student in computer science (Andrew Blumberg and Itsik Pe'er’s group)
  • Achille Nazaret: PhD student in computer science (Elham Azizi’s group)

 

Confirmed guest lecturers:

  • Khanh Dinh: Associate Research Scientist in the Herbert and Florence Irving Institute for Cancer Dynamics and in the Department of Statistics (Columbia University)
  • Bianca Dumitrascu: Assistant Professor of Statistics and Herbert and Florence Irving Assistant Professor of Cancer Data Research (Columbia University)
  • Jellert Gaublomme: Assistant Professor of Biological Sciences (Columbia University)
  • Ritambhara Singh: Assistant Professor of Computer Science, Assistant Professor of Data Science (Brown University)

 

The list will be updated as guest speakers are confirmed.

 

Application deadline: The application portal is now close.

UPDATE MARCH 27th, 2024: The deadline has been extended to April 5th, 2024 (5 PM ET). The applications are now open to researchers outside Columbia University.

 

How to apply:

- Application portal: https://fs25.formsite.com/cancerdynamics/IICD_Intensive_Workshop/index

- For your application, you will need:

  • CV
  • Statement of interest which outlines your research background and why attending the workshop would offer a valuable opportunity for your professional development (1-2 paragraphs)
  • A brief signed paragraph from your research advisor explaining why they support your attendance and how the experience will contribute to your professional development

 

Next steps after application:

  • Applications will be reviewed after the closing date.
  • Selected participants will receive an official offer letter from the program coordinator by the end of April/early May.
  • All the applicants will receive the final notification by May 31st. 

 

Any questions?

Please send an email to [email protected] using the subject line “IICD Intensive Workshop”.