Workshop
Learning Meaningful Representations of Life (LMRL)
Elizabeth Wood · Adji Bousso Dieng · Aleksandrina Goeva · Anshul Kundaje · Barbara Engelhardt · Chang Liu · David Van Valen · Debora Marks · Edward Boyden · Eli N Weinstein · Lorin Crawford · Mor Nitzan · Romain Lopez · Tamara Broderick · Ray Jones · Wouter Boomsma · Yixin Wang
Tue 14 Dec, 4 a.m. PST
One of the greatest challenges facing biologists and the statisticians that work with them is the goal of representation learning to discover and define appropriate representation of data in order to perform complex, multi-scale machine learning tasks. This workshop is designed to bring together trainee and expert machine learning scientists with those in the very forefront of biological research 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.
We will organize around the theme "From Genomes to Phenotype, and Back Again": an extension of a long-standing effort in the biological sciences to assign biochemical and cellular functions to the millions of as-yet uncharacterized gene products discovered by genome sequencing. ML methods to predict phenotype from genotype are rapidly advancing and starting to achieve widespread success. At the same time, large scale gene synthesis and genome editing technologies have rapidly matured, and become the foundation for new scientific insight as well as biomedical and industrial advances. ML-based methods have the potential to accelerate and extend these technologies' application, by providing tools for solving the key problem of going "back again," from a desired phenotype to the genotype necessary to achieve that desired set of observable characteristics. We will focus on this foundational design problem and its application to areas ranging from protein engineering to phylogeny, immunology, vaccine design and next generation therapies.
Generative modeling, semi-supervised learning, optimal experimental design, Bayesian optimization, & many other areas of machine learning have the potential to address the phenotype-to-genotype problem, and we propose to bring together experts in these fields as well as many others.
LMRL will take place on Dec 13, 2021.
Schedule
Tue 4:00 a.m. - 5:00 a.m.
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All LMRL Events are accessible from our Gather.Town! ( GatherTown ) > link | 🔗 |
Tue 5:00 a.m. - 5:30 a.m.
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Fritz Obermeyer ( Live Talk, Zoom 2 ) > link | 🔗 |
Tue 5:00 a.m. - 5:30 a.m.
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Dagmar Kainmueller
(
Live Talk, Zoom 1
)
>
link
SlidesLive Video |
🔗 |
Tue 5:30 a.m. - 6:00 a.m.
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Mo Lotfollahi ( Live Talk, Zoom 2 ) > link | Mohammad Lotfollahi 🔗 |
Tue 5:59 a.m. - 6:00 a.m.
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8:30-9:00 EST Steve Frank - The evolutionary paradox of robustness, genome overwiring, and analogies with deep learning
(
Live Talk, Zoom 1
)
>
link
SlidesLive Video |
Steven Frank 🔗 |
Tue 6:00 a.m. - 6:30 a.m.
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Nancy Zhang - Data Denoising and Transfer Learning in Single Cell Transcriptomics
(
Live Talk, Zoom 1
)
>
link
SlidesLive Video |
🔗 |
Tue 6:00 a.m. - 6:30 a.m.
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Matt Raybould ( Live Talk, Zoom 2 ) > link | 🔗 |
Tue 6:30 a.m. - 6:45 a.m.
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15 min Break - Check out the posters on Gather Town! ( GatherTown ) > link | 🔗 |
Tue 6:45 a.m. - 7:15 a.m.
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Frank Noe
(
Live Talk, Zoom 1
)
>
link
SlidesLive Video |
🔗 |
Tue 6:45 a.m. - 7:15 a.m.
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Jennifer Wei - Machine Learning for Chemical Sensing ( Live Talk, Zoom 2 ) > link | 🔗 |
Tue 7:15 a.m. - 7:45 a.m.
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Su-In Lee ( Live Talk, Zoom 2 ) > link | 🔗 |
Tue 7:15 a.m. - 7:45 a.m.
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Lyla Atta - RNA velocity-informed embeddings for visualizing cellular trajectories
(
Live Talk, Zoom 1
)
>
link
SlidesLive Video |
Lyla Atta 🔗 |
Tue 7:45 a.m. - 8:15 a.m.
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Jean-Phillippe Vert - Deep learning for DNA and proteins: equivariance and alignment
(
Live Talk, Zoom 1
)
>
link
SlidesLive Video |
🔗 |
Tue 7:45 a.m. - 8:15 a.m.
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Kristin Branson ( Live Talk, Zoom 2 ) > link | 🔗 |
Tue 8:15 a.m. - 8:30 a.m.
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15 min Break - Check out the posters on Gather Town! ( GatherTown ) > link | 🔗 |
Tue 8:30 a.m. - 9:00 a.m.
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Milo Lin - Distilling generalizable rules from data using Essence Neural Networks
(
Live Talk, Zoom 1
)
>
link
SlidesLive Video |
🔗 |
Tue 8:30 a.m. - 9:00 a.m.
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Georg Seelig - Machine learning-guided design of functional DNA, RNA and protein sequences ( Live Talk, Zoom 2 ) > link | 🔗 |
Tue 9:00 a.m. - 9:30 a.m.
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Lacra Bintu - High-throughput discovery and characterization of human transcriptional repressor and activator domains
(
Live Talk, Zoom 1
)
>
link
SlidesLive Video |
Lacramioara Bintu 🔗 |
Tue 9:00 a.m. - 9:30 a.m.
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Jingshu Wang - Model-based trajectory analysis for Single-Cell RNA Sequencing using deep learning with a mixture prior ( Live Talk, Zoom 2 ) > link | 🔗 |
Tue 9:30 a.m. - 10:00 a.m.
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Qingyuan Zhao
(
Live Talk, Zoom 1
)
>
link
SlidesLive Video |
🔗 |
Tue 9:30 a.m. - 10:00 a.m.
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Jackson Loper - Latent representations reveal that stationary covariances are always secretly linear ( Live Talk, Zoom 2 ) > link | 🔗 |
Tue 10:00 a.m. - 10:15 a.m.
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15 min Break - Check out the posters on Gather Town! ( GatherTown ) > link | 🔗 |
Tue 10:15 a.m. - 10:45 a.m.
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Tatyana Sharpee ( Live Talk, Zoom 2 ) > link | 🔗 |
Tue 10:15 a.m. - 10:45 a.m.
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Brian Trippe
(
Live Talk, Zoom 1
)
>
link
SlidesLive Video |
🔗 |
Tue 10:45 a.m. - 11:15 a.m.
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Jian Tang ( Live Talk, Zoom 1 ) > link | 🔗 |
Tue 10:45 a.m. - 11:15 a.m.
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Antonio Moretti
(
Live Talk, Zoom 2
)
>
link
SlidesLive Video |
🔗 |
Tue 11:15 a.m. - 11:45 a.m.
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Mackenzie Mathis ( Live Talk, Zoom 2 ) > link | Mackenzie Mathis 🔗 |
Tue 11:15 a.m. - 11:45 a.m.
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Žiga Avsec
(
Live Talk, Zoom 1
)
>
link
SlidesLive Video |
Ziga Avsec 🔗 |
Tue 11:45 a.m. - 1:15 p.m.
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Poster Session in Gather Town! ( Poster Session ) > link | 🔗 |
Tue 11:45 a.m. - 12:00 p.m.
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15 min Break - Check out the posters on Gather Town! ( GatherTown ) > link | 🔗 |
Tue 11:45 a.m. - 1:05 p.m.
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Panel: How do we define Meaningful Research in ML/Bio?
(
Discussion Panel, Zoom 1
)
>
link
SlidesLive Video |
🔗 |
Tue 12:00 p.m. - 12:30 p.m.
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Bianca Dumitrascu - Beyond multimodality in genomics ( Live Talk, Zoom 2 ) > link | 🔗 |