Jessie Huang

Je-chun Huang

Guillaume Huguet

Janhavi Narain

Kisung You

George Mourgkos … (see 6 more)

Rahul M. Dhodapkar

Matthew Hirn

Bastian Rieck

Brian P. Hafler

2023-05-05

Nature Communications (published)

Learning Shared Neural Manifolds from Multi-Subject FMRI Data

Je-chun Huang

Erica Lindsey Busch

Tom Wallenstein

Michal Gerasimiuk

Andrew Benz

Guillaume Lajoie

Nicholas Turk-Browne

Functional magnetic resonance imaging (fMRI) data is collected in millions of noisy, redundant dimensions. To understand how different brain… (see more)s process the same stimulus, we aim to denoise the fMRI signal via a meaningful embedding space that captures the data's intrinsic structure as shared across brains. We assume that stimulus-driven responses share latent features common across subjects that are jointly discoverable. Previous approaches to this problem have relied on linear methods like principal component analysis and shared response modeling. We propose a neural network called MRMD-AE (manifold-regularized multiple- decoder, autoencoder) that learns a common embedding from multi-subject fMRI data while retaining the ability to decode individual responses. Our latent common space represents an extensible manifold (where untrained data can be mapped) and improves classification accuracy of stimulus features of unseen timepoints, as well as cross-subject translation of fMRI signals.

2022-08-22

2022 IEEE 32nd International Workshop on Machine Learning for Signal Processing (MLSP) (published)

openreview.net

Population Genomics Approaches for Genetic Characterization of SARS-CoV-2 Lineages

Fatima Mostefai

Isabel Gamache

Arnaud N’Guessan

Justin Pelletier

Carmen Lia Murall

Ahmad Pesaranghader

Vanda Gaonac'h-Lovejoy

David J. Hamelin

Raphael Poujol

Jean-Christophe Grenier

Martin Smith

Etienne Caron

Morgan Craig

B. Jesse Shapiro

2022-02-21

Frontiers in Medicine (published)

Population Genomics Approaches for Genetic Characterization of SARS-CoV-2 Lineages

Fatima Mostefai

I. Gamache

Arnaud N’Guessan

Justin Pelletier

Carmen Lia Murall

Ahmad Pesaranghader

Vanda Gaonac'h-Lovejoy

David J. Hamelin

Raphael Poujol

Jean-Christophe Grenier

Martin W. Smith

Étienne Caron

Morgan Craig

B. Jesse Shapiro

The genome of the Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), the pathogen that causes coronavirus disease 2019 (COVID-19)… (see more), has been sequenced at an unprecedented scale leading to a tremendous amount of viral genome sequencing data. To assist in tracing infection pathways and design preventive strategies, a deep understanding of the viral genetic diversity landscape is needed. We present here a set of genomic surveillance tools from population genetics which can be used to better understand the evolution of this virus in humans. To illustrate the utility of this toolbox, we detail an in depth analysis of the genetic diversity of SARS-CoV-2 in first year of the COVID-19 pandemic. We analyzed 329,854 high-quality consensus sequences published in the GISAID database during the pre-vaccination phase. We demonstrate that, compared to standard phylogenetic approaches, haplotype networks can be computed efficiently on much larger datasets. This approach enables real-time lineage identification, a clear description of the relationship between variants of concern, and efficient detection of recurrent mutations. Furthermore, time series change of Tajima's D by haplotype provides a powerful metric of lineage expansion. Finally, principal component analysis (PCA) highlights key steps in variant emergence and facilitates the visualization of genomic variation in the context of SARS-CoV-2 diversity. The computational framework presented here is simple to implement and insightful for real-time genomic surveillance of SARS-CoV-2 and could be applied to any pathogen that threatens the health of populations of humans and other organisms.

2022-02-21

Frontiers in Medicine (published)

Data-driven approaches for genetic characterization of SARS-CoV-2 lineages

Fatima Mostefai

Isabel Gamache

Arnaud N’Guessan

Justin Pelletier

Ahmad Pesaranghader

David J. Hamelin

Carmen Lia Murall

Raphael Poujol

Jean-Christophe Grenier

Martin Smith

Etienne Caron

Morgan Craig

Jesse Shapiro

The genome of the Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), the pathogen that causes coronavirus disease 2019 (COVID-19)… (see more), has been sequenced at an unprecedented scale, leading to a tremendous amount of viral genome sequencing data. To understand the evolution of this virus in humans, and to assist in tracing infection pathways and designing preventive strategies, we present a set of computational tools that span phylogenomics, population genetics and machine learning approaches. To illustrate the utility of this toolbox, we detail an in depth analysis of the genetic diversity of SARS-CoV-2 in first year of the COVID-19 pandemic, using 329,854 high-quality consensus sequences published in the GISAID database during the pre-vaccination phase. We demonstrate that, compared to standard phylogenetic approaches, haplotype networks can be computed efficiently on much larger datasets, enabling real-time analyses. Furthermore, time series change of Tajima’s D provides a powerful metric of population expansion. Unsupervised learning techniques further highlight key steps in variant detection and facilitate the study of the role of this genomic variation in the context of SARS-CoV-2 infection, with Multiscale PHATE methodology identifying fine-scale structure in the SARS-CoV-2 genetic data that underlies the emergence of key lineages. The computational framework presented here is useful for real-time genomic surveillance of SARS-CoV-2 and could be applied to any pathogen that threatens the health of worldwide populations of humans and other organisms.

2021-09-29

bioRxiv (preprint)

Multiscale PHATE Exploration of SARS-CoV-2 Data Reveals Multimodal Signatures of Disease

Manik Kuchroo

Patrick Wong

Jean-Christophe Grenier

Dennis Shung

Alexander Tong

Carolina Lucas

Jon Klein

Daniel B. Burkhardt

Scott Gigante

Abhinav Godavarthi

Benjamin Israelow

Tianyang Mao

Ji Eun Oh

Julio Silva

Takehiro Takahashi

Camila D. Odio

Arnau Casanovas-Massana

John Fournier

Shelli Farhadian … (see 7 more)

Charles S. Dela Cruz

Albert I. Ko

F. Perry Wilson

Akiko Iwasaki

2020-11-17

bioRxiv (preprint)