Wednesday, November 2, 2022

CCMB Seminar: Marinka Zitnik, Ph.D.

4:00 PM to 5:00 PM

Palmer Commons, Great Lakes South

Round tables w/hearty hors d'ouevres

"Graph Artificial Intelligence to Enable Precision Medicine"


Graph representation learning leverages knowledge, geometry, and structure to develop powerful machine learning methods. First, I will introduce Shepherd, a graph neural network for personalized diagnosis of patients with rare genetic diseases. Diagnostic delay is pervasive in patients with rare genetic conditions. It can lead to numerous problems, including redundant testing and unnecessary procedures, delays in obtaining disease-appropriate management and therapies, and even irreversible disease progression. Shepherd uses knowledge-guided geometric deep learning to gather information from different parts of a knowledge graph and logically connect a patient's clinical-genomic information to the region in the knowledge graph relevant to diagnosis. Evaluation of patients from the Undiagnosed Diseases Network shows that Shepherd accurately identifies causal disease genes, finds other patients with the same causal gene and disease, and provides interpretable characterizations of novel diseases. Second, I will describe applications of graph neural networks in drug discovery. These are available through Therapeutics Data Commons (, an initiative to access and evaluate AI capability across therapeutic modalities and stages of drug discovery. The Commons supports the development of machine learning methods, with a strong bent towards developing the foundations for which methods are most suitable for drug discovery and why.


M Zitnik

Marinka Zitnik, Ph.D.

Assistant Professor of Biomedical Informatics, Harvard Medical School

Marinka Zitnik ( is an Assistant Professor at Harvard University with appointments in the Department of Biomedical Informatics, Broad Institute of MIT and Harvard, and Harvard Data Science. Dr. Zitnik has published extensively in top ML venues and leading scientific journals. She has organized conferences and workshops in graph representation learning, drug discovery, and precision medicine at leading conferences (NeurIPS, ICLR, ICML, ISMB, AAAI, WWW), where she is also on the organizing committees. She is an ELLIS Scholar in the European Laboratory for Learning and Intelligent Systems (ELLIS) Society and a member of the Science Working Group at NASA Space Biology. Her research won paper and research awards from the International Society for Computational Biology, Bayer Early Excellence in Science, Amazon Faculty Research, Roche Alliance with Distinguished Scientists, Rising Star Award in Electrical Engineering and Computer Science, and Next Generation in Biomedicine Recognition, being the only young scientist with such recognition in both EECS and Biomedicine. She co-founded Therapeutics Data Commons and also AI for Science community initiative.