Gabriel Misrachi's guest appearances

Gabriel Misrachi

the bioinformatics chat

David Kelley

Irineo Cabreros

Romain Lopez

Hassan Samee

Kristina Grigaityte

Jacob Schreiber

Simeon Carstens

Trevor Pesout

HoJoon Lee

Seung Woo Cho

Kaushik Panda

Keith Slotkin

Fernando Portela

Chang Xu

Andrey Ziyatdinov

OwlTail

In this episode, we hear from Romain Lopez and Gabriel Misrachi aboutscVI—Single-cell Variational Inference.scVI is a probabilistic model for single-cell gene expression data thatcombines a hierarchical Bayesian model with deep neural networks encoding theconditional distributions. scVI scales to over one million cells and can beused for scRNA-seq normalization and batch effect removal, dimensionalityreduction, visualization, and differential expression. We alsodiscuss the recently implemented in scVI automatic hyperparameter selectionvia Bayesian optimization. Links:  Deep generative modeling for single-cell transcriptomics (Romain Lopez, Jeffrey Regier, Michael Cole, Michael I. Jordan, Nir Yosef) scVI on GitHub Should we zero-inflate scVI? Hyperparameter search for scVI Droplet scRNA-seq is not zero inflated (Valentine Svensson)  If you enjoyed this episode, please consider supporting the podcast on Patreon!

In this episode, we hear from <a href="https://people.eecs.berkeley.edu/~romain_lopez/" rel="nofollow" target="_blank">Romain Lopez</a> and <a href="https://www.linkedin.com/in/gabriel-misrachi/" rel="nofollow" target="_blank">Gabriel Misrachi</a> about scVI—Single-cell Variational Inference. scVI is a probabilistic model for single-cell gene expression data that combines a hierarchical Bayesian model with deep neural networks encoding the conditional distributions. scVI scales to over one million cells and can be used for scRNA-seq normalization and batch effect removal, dimensionality reduction, visualization, and differential expression. We also discuss the recently implemented in scVI automatic hyperparameter selection via Bayesian optimization. Links: <ul> <li><a href="https://rdcu.be/bdHYQ" rel="nofollow" target="_blank">Deep generative modeling for single-cell transcriptomics</a> (Romain Lopez, Jeffrey Regier, Michael Cole, Michael I. Jordan, Nir Yosef)</li> <li><a href="https://github.com/YosefLab/scVI" rel="nofollow" target="_blank">scVI on GitHub</a></li> <li><a href="https://yoseflab.github.io/2019/06/25/ZeroInflation/" rel="nofollow" target="_blank">Should we zero-inflate scVI?</a></li> <li><a href="https://yoseflab.github.io/2019/07/05/Hyperoptimization/" rel="nofollow" target="_blank">Hyperparameter search for scVI</a></li> <li><a href="http://www.nxn.se/valent/2017/11/16/droplet-scrna-seq-is-not-zero-inflated" rel="nofollow" target="_blank">Droplet scRNA-seq is not zero inflated (Valentine Svensson)</a></li> </ul> If you enjoyed this episode, please consider supporting the podcast on <a href="https://www.patreon.com/bioinfochat" rel="nofollow" target="_blank">Patreon</a>!

#36 scVI with Romain Lopez and Gabriel Misrachi