Publications

Predicting histopathology markers of endometrial carcinoma with a quantitative image analysis approach based on spherical harmonics in multiparametric MRI.
Thierry L. Lefebvre
Ozan Ciga
Sahir Bhatnagar
Yoshiko Ueno
S. Saif
Eric Winter-Reinhold
Anthony Dohan
P. Soyer
Reza Forghani
Kaleem Siddiqi
Jan Seuntjens
Caroline Reinhold
Peter Savadjiev
2022-10-01
Diagnostic and Interventional Imaging (published)
doi.org
Social isolation and the brain in the pandemic era
Danilo Bzdok
Robin I. M. Dunbar
2022-10-01
Nature Human Behaviour (published)
doi.org
Synthetic data as an enabler for machine learning applications in medicine
Jean-Francois Rajotte
Robert Bergen
David Buckeridge
Khaled El Emam
Raymond Ng
Elissa Strome
2022-10-01
iScience (published)
doi.org
The use of artificial intelligence and virtual reality in doctor-patient risk communication: A scoping review.
Ryan Antel
Samira Abbasgholizadeh-Rahimi
Elena Guadagno
Jason M. Harley
Dan Poenaru
2022-10-01
Patient Education and Counseling (published)
doi.org
Evolution of cell size control is canalized towards adders or sizers by cell cycle structure and selective pressures
Felix Proulx-Giraldeau
Jan M Skotheim
Paul François
Cell size is controlled to be within a specific range to support physiological function. To control their size, cells use diverse mechanisms… (see more) ranging from ‘sizers’, in which differences in cell size are compensated for in a single cell division cycle, to ‘adders’, in which a constant amount of cell growth occurs in each cell cycle. This diversity raises the question why a particular cell would implement one rather than another mechanism? To address this question, we performed a series of simulations evolving cell size control networks. The size control mechanism that evolved was influenced by both cell cycle structure and specific selection pressures. Moreover, evolved networks recapitulated known size control properties of naturally occurring networks. If the mechanism is based on a G1 size control and an S/G2/M timer, as found for budding yeast and some human cells, adders likely evolve. But, if the G1 phase is significantly longer than the S/G2/M phase, as is often the case in mammalian cells in vivo, sizers become more likely. Sizers also evolve when the cell cycle structure is inverted so that G1 is a timer, while S/G2/M performs size control, as is the case for the fission yeast S. pombe. For some size control networks, cell size consistently decreases in each cycle until a burst of cell cycle inhibitor drives an extended G1 phase much like the cell division cycle of the green algae Chlamydomonas. That these size control networks evolved such self-organized criticality shows how the evolution of complex systems can drive the emergence of critical processes.
2022-09-30
eLife (published)
doi.org
SPeCiaL: Self-Supervised Pretraining for Continual Learning
Lucas Caccia
Joelle Pineau
2022-09-28
Continual Semi-Supervised Learning (published)
doi.org
arxiv.org
From analytic to synthetic-organizational pluralisms: A pluralistic enactive psychiatry
Christophe Gauld
Kristopher Nielsen
Manon Job
Hugo Bottemanne
Guillaume Dumas
2022-09-27
Frontiers in Psychiatry (published)
doi.org
Recommendations and guidelines from the ISMRM Diffusion Study Group for preclinical diffusion MRI: Part 2 -- Ex vivo imaging
Kurt G Schilling
Francesco Grussu
Andrada Ianus
Brian Hansen
Manisha Aggarwal
Stijn Michielse
Fatima Nasrallah
Warda Syeda
Nian Wang
Jelle Veraart
Alard Roebroeck
Andrew F. Bagdasarian
Cornelius Eichner
Farshid Sepehrband
Jan Zimmermann
Ben Jeurissen
Lucio Frydman
Yohan van de Looij
David Hike
Jeff F. Dunn … (see 30 more)
Karla Miller
Bennett Landman
Noam Shemesh
Arthur Anderson
Emilie McKinnon
Shawna Farquharson
Flavio Dell’Acqua
Carlo Pierpaoli
Ivana Drobnjak
Alexander Leemans
Kevin D. Harkins
Maxime Descoteaux
Duan Xu
Mathieu D. Santin
Samuel C. Grant
Andre Obenaus
Gene S. Kim
Dan Wu
Denis Le Bihan
Stephen J. Blackband
Luisa Ciobanu
Els Fieremans
Ruiliang Bai
Trygve B. Leergaard
Jiangyang Zhang
Tim B. Dyrby
G. Allan Johnson
Julien Cohen-Adad
Matthew D. Budde
Ileana O. Jelescu
2022-09-27
ArXiv (preprint)
doi.org
arxiv.org
Estimating individual treatment effect on disability progression in multiple sclerosis using deep learning
Jean-Pierre R. Falet
Joshua D. Durso-Finley
Brennan Nichyporuk
Julien Schroeter
Francesca Bovis
Maria-Pia Sormani
Doina Precup
Tal Arbel
Douglas Arnold
2022-09-26
Nature Communications (published)
doi.org
FedShuffle: Recipes for Better Use of Local Work in Federated Learning
Samuel Horváth
Maziar Sanjabi
Lin Xiao
Peter Richtárik
Michael Rabbat
The practice of applying several local updates before aggregation across clients has been empirically shown to be a successful approach to o… (see more)vercoming the communication bottleneck in Federated Learning (FL). Such methods are usually implemented by having clients perform one or more epochs of local training per round while randomly reshuffling their finite dataset in each epoch. Data imbalance, where clients have different numbers of local training samples, is ubiquitous in FL applications, resulting in different clients performing different numbers of local updates in each round. In this work, we propose a general recipe, FedShuffle, that better utilizes the local updates in FL, especially in this regime encompassing random reshuffling and heterogeneity. FedShuffle is the first local update method with theoretical convergence guarantees that incorporates random reshuffling, data imbalance, and client sampling — features that are essential in large-scale cross-device FL. We present a comprehensive theoretical analysis of FedShuffle and show, both theoretically and empirically, that it does not suffer from the objective function mismatch that is present in FL methods that assume homogeneous updates in heterogeneous FL setups, such as FedAvg (McMahan et al., 2017). In addition, by combining the ingredients above, FedShuffle improves upon FedNova (Wang et al., 2020), which was previously proposed to solve this mismatch. Similar to Mime (Karimireddy et al., 2020), we show that FedShuffle with momentum variance reduction (Cutkosky & Orabona, 2019) improves upon non-local methods under a Hessian similarity assumption.
2022-09-26
TMLR (accepted)
doi.org
openreview.net
Recommendations and guidelines from the ISMRM Diffusion Study Group for preclinical diffusion MRI: Part 1 -- In vivo small-animal imaging
Ileana O. Jelescu
Francesco Grussu
Andrada Ianus
Brian Hansen
Manisha Aggarwal
Stijn Michielse
Fatima Nasrallah
Warda Syeda
Nian Wang
Jelle Veraart
Alard Roebroeck
Andrew F. Bagdasarian
Cornelius Eichner
Farshid Sepehrband
Jan Zimmermann
Ben Jeurissen
Lucio Frydman
Yohan van de Looij
David Hike
Jeff F. Dunn … (see 30 more)
Karla Miller
Bennett Landman
Noam Shemesh
Arthur Anderson
Emilie McKinnon
Shawna Farquharson
Flavio Dell’Acqua
Carlo Pierpaoli
Ivana Drobnjak
Alexander Leemans
Kevin D. Harkins
Maxime Descoteaux
Duan Xu
Mathieu D. Santin
Samuel C. Grant
Andre Obenaus
Gene S. Kim
Dan Wu
Denis Le Bihan
Stephen J. Blackband
Luisa Ciobanu
Els Fieremans
Ruiliang Bai
Trygve B. Leergaard
Jiangyang Zhang
Tim B. Dyrby
G. Allan Johnson
Julien Cohen-Adad
Matthew D. Budde
Kurt G Schilling
The value of in vivo preclinical diffusion MRI (dMRI) is substantial. Small-animal dMRI has been used for methodological development and val… (see more)idation, characterizing the biological basis of diffusion phenomena, and comparative anatomy. Many of the influential works in this field were first performed in small animals or ex vivo samples. The steps from animal setup and monitoring, to acquisition, analysis, and interpretation are complex, with many decisions that may ultimately affect what questions can be answered using the data. This work aims to serve as a reference, presenting selected recommendations and guidelines from the diffusion community, on best practices for preclinical dMRI of in vivo animals. In each section, we also highlight areas for which no guidelines exist (and why), and where future work should focus. We first describe the value that small animal imaging adds to the field of dMRI, followed by general considerations and foundational knowledge that must be considered when designing experiments. We briefly describe differences in animal species and disease models and discuss how they are appropriate for different studies. We then give guidelines for in vivo acquisition protocols, including decisions on hardware, animal preparation, imaging sequences and data processing, including pre-processing, model-fitting, and tractography. Finally, we provide an online resource which lists publicly available preclinical dMRI datasets and software packages, to promote responsible and reproducible research. An overarching goal herein is to enhance the rigor and reproducibility of small animal dMRI acquisitions and analyses, and thereby advance biomedical knowledge.
2022-09-26
ArXiv (preprint)
doi.org
arxiv.org
The 5-year longitudinal diagnostic profile and health services utilization of patients treated with electroconvulsive therapy in Quebec: a population-based study
Simon Lafrenière
Fatemeh Gholi-Zadeh-Kharrat
Caroline Sirois
Victoria Massamba
Louis Rochette
Camille Brousseau-Paradis
Simon Patry
Christian Gagné
Morgane Lemasson
Geneviève Gariépy
Chantal Mérette
Elham Rahme
Alain Lesage
2022-09-26
Social Psychiatry and Psychiatric Epidemiology (published)
doi.org