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Workshop
Learning Meaningful Representations of Life (LMRL.org)
Elizabeth Wood · Debora Marks · Thouis Jones · Adji Bousso Dieng · Alan Aspuru-Guzik · Anshul Kundaje · Barbara Engelhardt · Chang Liu · Edward Boyden · Kresten Lindorff-Larsen · Mor Nitzan · Smita Krishnaswamy · Wouter Boomsma · Yixin Wang · David Van Valen · Orr Ashenberg

Fri Dec 11 06:00 AM -- 06:15 PM (PST) @ None
Event URL: http://www.lmrl.org »

There now exists a unique opportunity to unlock the secrets of biological systems at all scales. Mapping structural molecular detail to organismal phenotype and function; predicting emergent effects of human genetic variation; designing novel interventions including prevention, diagnostics, therapeutics, and the development of new synthetic biotechnologies for causal investigations are just some of the challenges that hinge on appropriate formal structures to make them accessible to the broadest possible community of computer scientists, statisticians, and their tools.

This workshop is designed to bring together trainees and experts in machine learning with those in the very forefront of biological research today for this purpose. Our full-day workshop will advance the joint project of the CS and biology communities with the goal of "Learning Meaningful Representations of Life" (LMRL), emphasizing interpretable representation learning of structure and principle. As last year, the workshop will be oriented around five layers of biological abstraction: genome, molecule, cell, synthetic system, and phenotype. This year will have a special talk in each layer dedicated to COVID responses, successful or not, at that level of biological scale from some of the world's foremost experts and first-line responders.

Fri 6:00 a.m. -
Pamela Silver - TBD (Keynote) [ Video ] Video
Pam Silver
Fri 8:00 a.m. - 8:45 a.m.
Suchi Saria - TBD (Opening Remarks) Video
Suchi Saria
Fri 8:45 a.m. - 9:30 a.m.
Tamara Broderick - TBD (Opening Remarks) Video
Tamara Broderick
Fri 9:30 a.m. - 10:15 a.m.
Daniela Witten - TBD (Opening Remarks) Video
Daniela M Witten
Fri 10:15 a.m. - 10:45 a.m.
Synth - David Baker - TBD (Synth Talk) Video
David Baker
Fri 10:45 a.m. - 11:05 a.m.
Molecule - David Ryan Koes - TBD (Molecule Talk) Video
Dave Koes
Fri 10:45 a.m. - 11:15 a.m.
Synth - Viviana Gradinaru - TBD (Synth Talk) Video
Viviana Gradinaru
Fri 10:45 a.m. - 11:05 a.m.
Cell - Juan Caicedo and Shantanu Singh (Cell Talk) Video
Shantanu Singh, Juan Caicedo
Fri 10:45 a.m. - 11:15 a.m.
Phenotype - Akiko Iwasaki (Phenotype Talk) Video
Akiko Iwasaki
Fri 11:05 a.m. - 11:25 a.m.
Molecule - Cecilia Clementi - TBD (Molecule Talk) Video
Cecilia Clementi
Fri 11:05 a.m. - 11:25 a.m.
Cell - Barak Raveh - TBD (Cell Talk) Video
Barak Raveh
Fri 11:15 a.m. - 11:45 a.m.
Phenotype - Eran Segal - TBD (Phenotype Talk) Video
Eran Segal
Fri 11:25 a.m. - 11:45 a.m.
Molecule - Pedro Beltrao - TBD (Molecule Talk) Video
Pedro Beltrao
Fri 11:25 a.m. - 11:45 a.m.
Cell - Leeat Keren - TBD (Cell Talk) Video
Leeat Keren
Fri 11:45 a.m. - 12:10 p.m.
Synth - Lin Tian - TBD (Synth Talk) Video
Lin Tian
Fri 11:45 a.m. - 12:05 p.m.
Cell - David Zeevi - TBD (Cell Talk) Video
David Zeevi
Fri 11:45 a.m. - 12:15 p.m.
Phenotype - Harlan Krumholz - TBD (Phenotype Talk) Video
Harlan Krumholz
Fri 11:55 a.m. - 12:15 p.m.
Christine Peter - TBD (Molecule Talk) Video
Christine Peter
Fri 12:05 p.m. - 12:25 p.m.
Cell - Jesse Bloom - TBD (Cell Talk) Video
Jesse D Bloom
Fri 12:10 p.m. - 12:35 p.m.
Synth - Kate Adamala - TBD (Synth Talk) Video
Kate Adamala
Fri 12:15 p.m. - 12:30 p.m.
John Chodera - TBD (Molecule Talk) Video
John D Chodera
Fri 12:15 p.m. - 12:30 p.m.
Hirunima Jayasekara - TBD (Phenotype Talk) Video
Hirunima Jayasekara
Fri 12:25 p.m. - 12:45 p.m.
Cell - Geoffrey Schiebinger - TBD (Cell Talk) Video
Geoffrey Schiebinger
Fri 12:30 p.m. - 12:45 p.m.
Jack Lanchantin - TBD (Phenotype Talk) Video
Jack Lanchantin
Fri 12:35 p.m. - 12:55 p.m.
Synth - Eli Weinstein - TBD (Synth Talk) Video
Eli Weinstein
Fri 12:45 p.m. - 1:05 p.m.
Cell - Nuria Lopez-Bigas - TBD (Cell Talk) Video
Nuria Lopez-Bigas
Fri 12:45 p.m. - 12:55 p.m.
James T Morton - TBD (Molecule Talk) Video
James Morton
Fri 12:45 p.m. - 1:00 p.m.
Caroline V Weis - TBD (Phenotype Talk) Video
Caroline Weis
Fri 12:55 p.m. - 1:10 p.m.
Synth - Surojit Biswas - TBD (Synth Talk) Video
Surge Biswas, Surge Biswas
Fri 12:55 p.m. - 1:05 p.m.
Maria Littmann - TBD (Molecule Talk) Video
Maria Littmann
Fri 1:00 p.m. - 1:15 p.m.
Manik Kuchroo - TBD (Phenotype Talk) Video
Manik Kuchroo
Fri 1:05 p.m. - 1:15 p.m.
Max Shen - TBD (Molecule Talk) Video
Max Shen
Fri 1:10 p.m. - 1:45 p.m.
Jose Miguel Hernandez Lobato - TBD (Synth Talk) Video
Jose Miguel Hernández-Lobato
Fri 1:15 p.m. - 1:25 p.m.
Eli Draizen - TBD (Molecule Talk) Video
Eli Draizen
Fri 1:15 p.m. - 1:45 p.m.
Phenotype Panel (Phenotype -- Panel)
Fri 1:25 p.m. - 1:35 p.m.
Hattie Chung - TBD (Molecule Talk) Video
Hattie Chung
Fri 1:25 p.m. - 1:45 p.m.
Sam Riesenfeld - TBA (Cell Talk) Video
Samantha Riesenfeld
Fri 1:35 p.m. - 1:45 p.m.
Martin Voegele - TBD (Molecule Talk) Video
Martin Voegele
Fri 2:00 p.m. - 3:00 p.m.
Poster Session I - All Posters (Poster Session)
Fri 4:00 p.m. - 4:45 p.m.
Christina Leslie - TBD (Closing Remarks) Video
Christina Leslie
Fri 4:45 p.m. - 5:30 p.m.
Hilary Finucane - TBD (Closing Remarks) Video
Hilary Finucane
Fri 5:30 p.m. - 6:15 p.m.
Jennifer Listgarten - TBD (Closing Remarks) Video
Jennifer Listgarten

Author Information

Elizabeth Wood (Broad Institute)

Elizabeth Wood co-founded and co-runs JURA Bio, Inc., an early-stage therapeutics start up focusing on developing and delivering cell-based therapies for the treatment of autoimmune and immune-related neurodegenerative disease. Before founding JURA, Wood was a post-doc in the lab of Adam Cohen at Harvard, after completing her PhD studies with Angela Belcher and Markus Buehler at MIT, and Claus Helix-Neilsen at The Technical University of Denmark. She has also worked at the University of Copenhagen’s Biocenter with Kresten Lindorff-Larsen, integrating computational methods with experimental studies to understand how the ability of proteins to change their shape help modulate their function. Elizabeth Wood is a visiting scientist at the Broad Institute, where she serves on the steering committee of the Machine Inference Algorithm’s Initiative.

Debora Marks
Thouis Jones (Broad Institute)
Adji Dieng (Columbia University)
Alan Aspuru-Guzik (University of Toronto)
Anshul Kundaje (Stanford University)
Barbara Engelhardt (Princeton University)

Barbara E. Engelhardt is an associate professor in the Princeton Computer Science Department, on leave in 2019-2020 working as a principal scientist at Genomics Plc. Previously, she was an assistant professor at Duke University in Biostatistics and Bioinformatics and Statistical Sciences. She graduated from Stanford University and received her Ph.D. from the University of California, Berkeley, advised by Professor Michael Jordan. She did postdoctoral research at the University of Chicago, working with Professor Matthew Stephens. Interspersed among her academic experiences, she spent two years working at the Jet Propulsion Laboratory, a summer at Google Research, and a year at 23andMe, a DNA ancestry service. Professor Engelhardt received an NSF Graduate Research Fellowship, the Google Anita Borg Memorial Scholarship, and the Walter M. Fitch Prize from the Society for Molecular Biology and Evolution. As a faculty member, she received the NIH NHGRI K99/R00 Pathway to Independence Award, a Sloan Faculty Fellowship, and an NSF CAREER Award. Professor Engelhardt’s research interests involve developing statistical models and methods for the analysis of high-dimensional biomedical data, with a goal of understanding the underlying biological mechanisms and dynamics of complex phenotypes and human disease.

Chang Liu (UC Irvine)

Professor Liu’s research is in the fields of synthetic biology, chemical biology, and directed evolution. He is particularly interested in engineering specialized genetic systems for rapid mutation and evolution of genes in vivo. These systems can then be widely applied for the engineering, discovery, and understanding of biological function.

Edward Boyden (Massachusetts Institute of Technology)
Kresten Lindorff-Larsen (University of Copenhagen)

Kresten Lindorff-Larsen trained as a biochemist at the University of Copenhagen and Carlsberg Laboratory, and completed his Ph.D. at the University of Cambridge in 2004. He then moved on to become an assistant professor in Copenhagen before joining D. E. Shaw Research in New York in 2007. He returned to Copenhagen in 2011, where he now serves as a Professor of Computational Protein Biophysics. He received the Danish Independent Research Councils’ Young Researchers’ Award in 2006, was a co-recipient of the 2009 Gordon Bell Prize, and has received several prestigious grants including a Hallas-Møller stipend (2011), a Sapere Aude grant (2012), and most recently a Novo Nordisk Foundation challenge programme grant (2019). His current research interests include developing and applying computational methods for integrative structural biology, and the integration of biophysics and genomics research.

Mor Nitzan (Broad Institute)
Smita Krishnaswamy (Yale University)
Wouter Boomsma (University of Copenhagen)
Yixin Wang (Columbia University)
David Van Valen (Caltech)
Orr Ashenberg (Broad Institute)

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