Publications

RAMEN Unveils Clinical Variable Networks for COVID-19 Severity and Long COVID Using Absorbing Random Walks and Genetic Algorithms
Yiwei Xiong
Jingtao Wang
Xiaoxiao Shang
Tingting Chen
Douglas D. Fraser
Gregory Fonseca
Simon Rousseau
Jun Ding
The COVID-19 pandemic has significantly altered global socioeconomic structures and individual lives. Understanding the disease mechanisms a… (see more)nd facilitating diagnosis requires comprehending the complex interplay among clinical factors like demographics, symptoms, comorbidities, treatments, lab results, complications, and other metrics, and their relation to outcomes such as disease severity and long term outcomes ( e . g ., post-COVID-19 condition/long COVID). Conventional correlational methods struggle with indirect and directional connections among these factors, while standard graphical methods like Bayesian networks are computationally demanding for extensive clinical variables. In response, we introduced RAMEN, a methodology that integrates Genetic Algorithms with random walks for efficient Bayesian network inference, designed to map the intricate relationships among clinical variables. Applying RAMEN to the Biobanque québécoise de la COVID-19 (BQC19) dataset, we identified critical markers for long COVID and varying disease severity. The Bayesian Network, corroborated by existing literature and supported through multi-omics analyses, highlights significant clinical variables linked to COVID-19 outcomes. RAMEN’s ability to accurately map these connections contributes substantially to developing early and effective diagnostics for severe COVID-19 and long COVID.
2024-02-26
bioRxiv (preprint)
doi.org
Correction to: Recovering the wedge modes lost to 21-cm foregrounds
Samuel Gagnon-Hartman
Yue Cui
Adrian Liu
Siamak Ravanbakhsh
Jacob Kennedy
2024-02-25
Monthly Notices of the Royal Astronomical Society (published)
doi.org
Effective Latent Differential Equation Models via Attention and Multiple Shooting
Germán Abrevaya
Mahta Ramezanian-Panahi
Jean-christophe Gagnon-audet
Irina Rish
Pablo Polosecki
Silvina Ponce Dawson
Guillermo Cecchi
Guillaume Dumas
2024-02-25
Transactions on Machine Learning Research (accepted)
doi.org
openreview.net
Correction to: Multi-agent reinforcement learning for fast-timescale demand response of residential loads
Vincent Mai
Philippe Maisonneuve
Tianyu Zhang
Hadi Nekoei
Liam Paull
Antoine Lesage-Landry
2024-02-22
Machine-Mediated Learning (published)
doi.org
Intra-Host Evolution Analyses in an Immunosuppressed Patient Supports SARS-CoV-2 Viral Reservoir Hypothesis
Dominique Fournelle
Fatima Mostefai
Elsa Brunet-Ratnasingham
Raphaël Poujol
Jean-Christophe Grenier
José Héctor Gálvez
Amélie Pagliuzza
Inès Levade
Sandrine Moreira
Mehdi Benlarbi
Guillaume Beaudoin-Bussières
Gabrielle Gendron-Lepage
Catherine Bourassa
Alexandra Tauzin
Simon Grandjean Lapierre
Nicolas Chomont
Andrés Finzi
Daniel E. Kaufmann
Morgan Craig
Julie G. Hussin
Throughout the SARS-CoV-2 pandemic, several variants of concern (VOCs) have been identified, many of which share recurrent mutations in the … (see more)spike glycoprotein’s receptor-binding domain (RBD). This region coincides with known epitopes and can therefore have an impact on immune escape. Protracted infections in immunosuppressed patients have been hypothesized to lead to an enrichment of such mutations and therefore drive evolution towards VOCs. Here, we present the case of an immunosuppressed patient that developed distinct populations with immune escape mutations throughout the course of their infection. Notably, by investigating the co-occurrence of substitutions on individual sequencing reads in the RBD, we found quasispecies harboring mutations that confer resistance to known monoclonal antibodies (mAbs) such as S:E484K and S:E484A. These mutations were acquired without the patient being treated with mAbs nor convalescent sera and without them developing a detectable immune response to the virus. We also provide additional evidence for a viral reservoir based on intra-host phylogenetics, which led to a viral substrain that evolved elsewhere in the patient’s body, colonizing their upper respiratory tract (URT). The presence of SARS-CoV-2 viral reservoirs can shed light on protracted infections interspersed with periods where the virus is undetectable, and potential explanations for long-COVID cases.
2024-02-22
Viruses (published)
doi.org
Molar Pregnancy in a Quadruplet Conception Following IVF: A Case Report
Madhuri A Mehendale
Meenal Shailesh Sarmalkar
Prerna Kailashchand Gupta
Aishwarya Agrawal
Agraj S Doshi
2024-02-22
Journal of South Asian Federation of Obstetrics and Gynaecology (published)
doi.org
The Sample Average Approximation Method for Solving Two-Stage Stochastic Programs with Endogenous Uncertainty
Maria Bazotte
Margarida Carvalho
Thibaut Vidal
Real-world decision-making problems involve Type 1 decision-dependent uncertainty, where the probability distribution of the stochastic proc… (see more)ess depends on the model decisions. However, few studies focus on two-stage stochastic programs with this type of endogenous uncertainty, and those that do lack general methodologies. We thus propose herein a general method for solving a class of these programs based on the transformation of random variables, a technique widely employed in probability and statistics. The proposed method is tailored to large-scale problems with discrete or continuous endogenous random variables. The random variable transformation allows the use of the sample average approximation (SAA) method, which provides optimality convergence guarantees under certain conditions. We show that, for some classical distributions, the proposed method reduces to solving mixed-integer linear or convex programs. Finally, we validate this method by applying it to a network design and facility-protection problem, considering distinct decision-dependent distributions for the random variables. Whereas most distributions result in a nonlinear nonconvex deterministic equivalent program, the proposed method solves mixed-integer linear programs in all cases. In addition, it produces attractive performance estimators for the SAA method in a reasonable computational time and outperforms the case in which the endogenous distribution defines a mixed-integer deterministic equivalent.
2024-02-22
ArXiv (preprint)
arxiv.org
arxiv.org
Matrix Factorization Recommendation Algorithm Based on Attention Interaction
Chengzhi Mao
Zhifeng Wu
Yingjie Liu
Zhiwei Shi
2024-02-21
Symmetry (published)
doi.org
Posterior inference of Hi-C contact frequency through sampling
Yanlin Zhang
Christopher J. F. Cameron
Mathieu Blanchette
Hi-C is one of the most widely used approaches to study three-dimensional genome conformations. Contacts captured by a Hi-C experiment are r… (see more)epresented in a contact frequency matrix. Due to the limited sequencing depth and other factors, Hi-C contact frequency matrices are only approximations of the true interaction frequencies and are further reported without any quantification of uncertainty. Hence, downstream analyses based on Hi-C contact maps (e.g., TAD and loop annotation) are themselves point estimations. Here, we present the Hi-C interaction frequency sampler (HiCSampler) that reliably infers the posterior distribution of the interaction frequency for a given Hi-C contact map by exploiting dependencies between neighboring loci. Posterior predictive checks demonstrate that HiCSampler can infer highly predictive chromosomal interaction frequency. Summary statistics calculated by HiCSampler provide a measurement of the uncertainty for Hi-C experiments, and samples inferred by HiCSampler are ready for use by most downstream analysis tools off the shelf and permit uncertainty measurements in these analyses without modifications.
2024-02-21
Frontiers in Bioinformatics (published)
doi.org
Reinforcement Learning with Elastic Time Steps
Yong Wang
Giovanni Beltrame
2024-02-21
ArXiv (preprint)
doi.org
arxiv.org
Searching for Strong Gravitational Lenses
Cameron Lemon
Frederic Courbin
Anupreeta More
Paul Schechter
Raoul Cañameras
Ludovic Delchambre
Calvin Leung
Yiping Shu
Chiara Spiniello
Yashar Hezaveh
Jonas Klüter
Richard G. McMahon
2024-02-20
Space Science Reviews (published)
doi.org
arxiv.org
The Past, Present, and Future of the Brain Imaging Data Structure (BIDS)
Russell A. Poldrack
Christopher J. Markiewicz
Stefan Appelhoff
Yoni K. Ashar
Tibor Auer
Sylvain Baillet
Shashank Bansal
Leandro Beltrachini
Christian G. Benar
Giacomo Bertazzoli
Suyash Bhogawar
Ross W. Blair
Marta Bortoletto
Mathieu Boudreau
Teon L. Brooks
Vince D. Calhoun
Filippo Maria Castelli
Patricia Clement
Alexander L Cohen
Julien Cohen-Adad … (see 94 more)
Sasha D'Ambrosio
Gilles de Hollander
María de la iglesia-Vayá
Alejandro de la Vega
Arnaud Delorme
Orrin Devinsky
Dejan Draschkow
Eugene Paul Duff
Elizabeth DuPré
Eric Earl
Oscar Estéban
Franklin W. Feingold
Guillaume Flandin
anthony galassi
Giuseppe Gallitto
Melanie Ganz
Rémi Gau
James Gholam
Satrajit S. Ghosh
Alessio Giacomel
Ashley G Gillman
Padraig Gleeson
Alexandre Gramfort
Samuel Guay
Giacomo Guidali
Yaroslav O. Halchenko
Daniel A. Handwerker
Nell Hardcastle
Peer Herholz
Dora Hermes
Christopher J. Honey
Robert B. Innis
Horea-Ioan Ioanas
Andrew Jahn
Agah Karakuzu
David B. Keator
Gregory Kiar
Balint Kincses
Angela R. Laird
Jonathan C. Lau
Alberto Lazari
Jon Haitz Legarreta
Adam Li
Xiangrui Li
Bradley C. Love
Hanzhang Lu
Camille Maumet
Giacomo Mazzamuto
Steven L. Meisler
Mark Mikkelsen
Henk Mutsaerts
Thomas E. Nichols
Aki Nikolaidis
Gustav Nilsonne
Guiomar Niso
Martin Norgaard
Thomas W Okell
Robert Oostenveld
Eduard Ort
Patrick J. Park
Mateusz Pawlik
Cyril R. Pernet
Franco Pestilli
Jan Petr
Christophe Phillips
Jean-Baptiste Poline
Luca Pollonini
Pradeep Reddy Raamana
Petra Ritter
Gaia Rizzo
Kay A. Robbins
Alexander P. Rockhill
Christine Rogers
Ariel Rokem
Chris Rorden
Alexandre Routier
Jose Manuel Saborit-Torres
Taylor Salo
Michael Schirner
Robert E. Smith
Tamas Spisak
Julia Sprenger
Nicole C. Swann
Martin Szinte
Sylvain Takerkart
Bertrand Thirion
Adam G. Thomas
Sajjad Torabian
Gael Varoquaux
Bradley Voytek
Julius Welzel
Martin Wilson
Tal Yarkoni
Krzysztof J. Gorgolewski
The Brain Imaging Data Structure (BIDS) is a community-driven standard for the organization of data and metadata from a growing range of neu… (see more)roscience modalities. This paper is meant as a history of how the standard has developed and grown over time. We outline the principles behind the project, the mechanisms by which it has been extended, and some of the challenges being addressed as it evolves. We also discuss the lessons learned through the project, with the aim of enabling researchers in other domains to learn from the success of BIDS.
2024-02-19
Imaging Neuroscience (published)
doi.org
arxiv.org