Agenda
Day 1: April 3, 2023 (all times EDT)
11:00 - 11:30 Welcome and opening remarks
NCI: Origin and purpose of the workshop
Opening presentation: Caroline Uhler, Broad and MIT “Cancer Research and AI - A 2-Way Street”
11:30 - 1:00 Session 1: Expanding classical structure prediction with machine learning towards drug discovery
Session Chair: Trey Ideker, UC San Diego Introductory comments from the chair (5 min)
Anima Anandkumar, Cal Tech and NVIDIA
“Role of generative AI in chemistry and biology” (15 min)
Andrej Sali, UC San Francisco
“From integrative structural biology to cell biology” (15 min)
Jure Leskovec, Stanford University
“Machine learning for cell-type discovery and identification in spatially resolved single-cell data” (15 min)
Rick Stevens, Argonne National Laboratory (5 min) Sergey Ovchinnikov, Harvard (5 min)
Discussion (30 min)
1:00 - 1:15 BREAK
1:15 - 2:45 Session 2: Chemical, genetic, and mechanical perturbations for understanding mechanisms in cancer: Extrapolating beyond existing data
Session Chair: Fabian Theis, Helmholtz Munich Introductory comments from the chair (5 min)
Yoshua Bengio, Université de Montréal “Causal Discovery with GFlowNets” (15 min)
GV "Shiva" Shivashankar, ETH Zurich
“Mechano-Genomics of Tumor Microenvironment” (15 min)
Smita Krishnaswamy, Yale University
“Learning generalizable perturbation models with manifold learning and dynamics” (15 min)
Panel discussion (speakers + additional panelists)
Paquita Vazquez, Broad Institute (5 min)
Byung-Jun Yoon, Texas A&M University and Brookhaven National Laboratory (5 min)
Discussion (30 min)
2:45 - 3:00 BREAK
3:00 - 4:30 Session 3: Multimodal learning in data limited contexts: Leveraging tissue-level data for understanding cell-cell interactions in cancer
Session Chair: Dana Pe’er, Memorial Sloan Kettering Introductory comments from the chair (5 min)
Atul Deshpande, Johns Hopkins University
“Mapping molecular interactions in tumor microenvironments through latent space analysis of spatial transcriptomics” (15 min)
Elham Azizi, Columbia University
“Probabilistic modeling of dynamics in the tumor microenvironment” (15 min)
Livnat Jerby, Stanford University
“Structure, location, and function: From natural to engineered cellular circuits” (15 min)
Marianna Rapsomaniki, IBM Research (5 min) Arjun Krishnan, University of Colorado (5 min) Discussion (30 min)
Day 2: April 4, 2023 (all times EDT)
11:00 - 11:05 Welcome to Day 2
11:05 - 12:35 Session 4: Making use of large-scale, structured clinical research data and image repositories
Session Chair: Ziad Obermeyer, UC Berkeley Introductory comments from the chair (5 min)
Chris Probert, InSitro
“Learned Embeddings Enable Multi-Modal Clinical Data Fusion” (15 min)
James Zou, Stanford University
“Advancing precision oncology with real-world clinico-genomics and spatial omics” (15 min)
Mihaela van der Schaar, University of Cambridge
“How can we build digital twins from complex, messy, incomplete and private real-world clinical data” (15 min)
Panel discussion (speakers + additional panelists)
Lily Peng, Verily (5 min)
Matthew Lungren, Microsoft/UCSF (5 min) Discussion (30 min)
12:35 - 12:45 BREAK
12:45 - 2:15 Session 5: Improving modeling of real-world evidence data in clinical research and clinical trial design
Session chair: Tianxi Cai, Harvard T.H. Chan School of Public Health Introductory comments from the chair (5 min)
Sean Khozin, MIT
“Addressing external validity deficits in conventional cancer clinical trials with real-world evidence” (15 min)
Limor Appelbaum Beth Israel Deaconess and Martin Rinard, MIT “Challenges and solutions for building cancer predictive models with EHR data” (15 min)
Ryan Copping, Roche & Genentech
“Getting more out of Real-World Data with Advanced Analytics” (15 min)
Panel discussion (speakers + additional panelists)
Donna Rivera, FDA (5 min)
Khaled El Emam, University of Ottawa (5 min) Discussion (30 min)
2:15 - 2:25 BREAK
2:25 - 3:15 Session 6: Cross-cutting discussion with session chairs Session chair: Olivier Gevaert, Stanford University
Introductory comments from the chair (10 min)
Panel Discussion (40 min)
Caroline Uhler Trey Ideker Dana Pe’er Ziad Obermeyer Tianxi Cai
3:15 - 3:30 Closing Remarks
Workshop Chairs:
Caroline Uhler, MIT and Broad Institute Olivier Gevaert, Stanford University
NCI Planning Committee:
Juli Klemm Jennifer Couch Sean Hanlon Natalie Abrams Keyvan Farahani Emily Greenspan Paul Han Roxanne Jensen Jerry Li
Catherine Schweppe