Inaugural IICD Intensive Workshop Focusing on Data Integration and Optimal Transport
From July 8th to 12th, 2024, the Irving Institute for Cancer Dynamics (IICD) held for the first time a five-day intensive workshop at Columbia University's Morningside Heights campus, focusing on data integration and optimal transport methods. This no-cost workshop, aimed at graduate students and postdoctoral fellows, successfully provided participants with cutting-edge knowledge and hands-on experience in these critical areas of research.
The workshop covered essential topics in data integration, a method used to combine and align multiple genomic datasets within the same cells, revealing patterns and interactions that single datasets might miss. Participants explored multi-modal single-cell genomic data integration, probabilistic modeling, emerging technologies in spatial integration, and the theory and implementation of optimal transport, a mathematical framework used in various fields, including economics, computer science, neuroscience, and image processing.
The workshop was tailored for graduate students and postdoctoral fellows with a background in programming (Python or R) and a foundational knowledge of linear algebra, probability, and statistics. It was led by two faculty members - Elham Azizi (Herbert and Florence Irving Assistant Professor of Cancer Data Research and Assistant Professor of Biomedical Engineering) and Andrew Blumberg (Herbert and Florence Irving Professor of Cancer Data Research and Professor of Mathematics and Computer Science) - and six graduate students from their respective labs.
"The IICD Intensive Workshop gave the opportunity to deep dive into probabilistic modeling and optimal transport for current problems in single-cell data integration. Participants gained hands-on experience in this one-week crash course and learned from exceptional invited lecturers who showcased real-world applications from different perspectives," Elham Azizi said.
The program included morning lectures followed by hands-on problem sets in the afternoons. Each day concluded with a guest lecture from leading experts, including Ritambhara Singh (Brown University), Smita Krishnaswamy (Yale University), Jellert Gaublomme (Columbia University), Cassandra Burdziak (MSKCC), and Caleb Lareau (MSKCC). The week culminated in short group presentations and a mixer, fostering collaboration and networking among participants.
"The IICD workshop experience was incredibly informative and inspirational. Not only was a plethora of technical knowledge shared, but the lectures helped promote new ideas for methods I plan to apply to my own research," said Ethan Earlie, a PhD student in computational biology and medicine, at Weill Cornell Medicine.
By the end of the workshop, participants were well-versed in multi-modal single-cell integration, probabilistic modeling, and representation learning for high-dimensional data, emerging technologies in spatial and imaging integration, the theory and implementation of optimal transport, and its applications for multi-modal single-cell integration and spatial data.
"I had a fantastic time at the IICD workshop. I wanted to learn more about optimal transport in cancer biology and I did so from the very people who have been advancing the field. The consistently high quality of the speakers and the diverse group of attendees created an ideal environment for learning and discussion." explains Alessandro Grande, a postdoctoral research fellow at MSKCC and Columbia University.
The 2024 IICD Intensive Workshop was a success. It provided a rich learning environment and facilitated a collaborative community among participants and instructors. Attendees left equipped with new skills and knowledge, ready to apply data integration and optimal transport methods in their research endeavors. The IICD looks forward to hosting similar events in the future to continue advancing the frontiers of cancer dynamics research.