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 and generative modeling have 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 (June 23-27, 2025, Morningside Heights campus) for graduate students and postdoctoral fellows to learn more about methods in probabilistic data integration and optimal transport. Participants will learn about multi-modal and multi-donor single-cell data integration, probabilistic modeling, emerging technologies in spatial integration, and the theory and implementation of optimal transport. A one-day virtual bootcamp will be held prior to the workshop to review key prerequisites.
The one-week workshop will include lectures by instructors and guest speakers, hands-on problem sets, and networking lunches. The summer school will end with short group presentations and a mixer. The workshop will be preceded by an optional one-day virtual bootcamp (June 20, 2025). The virtual bootcamp will be an opportunity for participants to build the necessary skills and requirements to prepare for the workshop.
By the end of the workshop, participants will be familiar with the following concepts:
- Multi-modal and multi-donor single-cell data 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, time series, and spatial data
Audience and Requirements:
The workshop is aimed at graduate students and postdoctoral fellows (within and outside Columbia University).
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 June 23-27, 2025 on the Morningside Heights campus. The workshop will be preceded by an optional one-day virtual bootcamp (June 20, 2025).
Please note that the workshop is free to attend if you are selected. However, the Institute will not cover any travel or accommodation arrangements.
Instructors:
- Elham Azizi: Herbert and Florence Irving Associate Professor of Cancer Data Research and Associate Professor of Biomedical Engineering
- Andrew Blumberg: Herbert and Florence Irving Professor of Cancer Data Research and Professor of Mathematics and Computer Science
- Noah Bergam: PhD Student in Computer Science (Andrew Blumberg and Daniel Hsu's groups)
- Yining Liu: PhD Student in Computer Science (Andrew Blumberg and Itsik Pe'er’s groups)
- Joshua D. Myers: MS Student in Biomedical Engineering (Azizi group)
- Lingting Shi: Postdoctoral Research Scientist (Columbia University/IICD)
- Mingxuan Zhang: PhD Student in Molecular Therapeutics and Systems Biology (Elham Azizi and Andrea Califano's groups)
- Aaron Zweig: Postdoctoral Research Scientist in the Herbert and Florence Irving Institute for Cancer Dynamics (Elham Azizi and David Knowles's groups)
Confirmed guest lecturers:
- Genevera Allen: Professor of Statistics (Columbia University/IICD)
- Cassandra Burdziak: Postdoctoral Researcher (MSKCC)
- José L. McFaline-Figueroa: Assistant Professor of Biomedical Engineering (Columbia University/IICD)
- Dana Pe'er: Chair, Computational and Systems Biology Program (MSKCC); Investigator, Howard Hughes Medical Institute; Alan and Sandra Gerry Endowed Chair
- Nuttida Rungratsameetaweemana: Assistant Professor of Biomedical Engineering (Columbia University)
- Sanja Vickovic: Assistant Professor of Biomedical Engineering in the Herbert and Florence Irving Institute for Cancer Dynamics (Columbia University/IICD)
- Wesley Tansey: Principal Investigator and Assistant Attending Computational Oncologist (MSKCC)
Application deadline:
The deadline is April 21, 2025 (5 PM ET). The applications are open to researchers within and outside Columbia University.
How to apply:
- Application portal: https://fs25.formsite.com/cancerdynamics/2025_IICD_Workshop/
- 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”.