Data-driven approaches for genetic characterization of SARS-CoV-2 lineages
Fatima Mostefai
Isabel Gamache
Jessie Huang
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)… (voir plus), 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.
Estimating the lagged effect of price discounting: a time-series study using transaction data of sugar sweetened beverages.
Hiroshi Mamiya
Alexandra M. Schmidt
Erica E. M. Moodie
Guidelines for the Computational Testing of Machine Learning approaches to Vehicle Routing Problems
Luca Accorsi
Andrea Lodi
Daniele Vigo
Population modeling with machine learning can enhance measures of mental health
Kamalaker Dadi
Gael Varoquaux
Josselin Houenou
Bertrand Thirion
Denis-Alexander Engemann
Background Biological aging is revealed by physical measures, e.g., DNA probes or brain scans. Instead, individual differences in mental fun… (voir plus)ction are explained by psychological constructs, e.g., intelligence or neuroticism. These constructs are typically assessed by tailored neuropsychological tests that build on expert judgement and require careful interpretation. Could machine learning on large samples from the general population be used to build proxy measures of these constructs that do not require human intervention? Results Here, we built proxy measures by applying machine learning on multimodal MR images and rich sociodemographic information from the largest biomedical cohort to date: the UK Biobank. Objective model comparisons revealed that all proxies captured the target constructs and were as useful, and sometimes more useful than the original measures for characterizing real-world health behavior (sleep, exercise, tobacco, alcohol consumption). We observed this complementarity of proxy measures and original measures when modeling from brain signals or sociodemographic data, capturing multiple health-related constructs. Conclusions Population modeling with machine learning can derive measures of mental health from brain signals and questionnaire data, which may complement or even substitute for psychometric assessments in clinical populations. Key Points We applied machine learning on more than 10.000 individuals from the general population to define empirical approximations of health-related psychological measures that do not require human judgment. We found that machine-learning enriched the given psychological measures via approximation from brain and sociodemographic data: Resulting proxy measures related as well or better to real-world health behavior than the original measures. Model comparisons showed that sociodemographic information contributed most to characterizing psychological traits beyond aging.
Author Correction: Open-access quantitative MRI data of the spinal cord and reproducibility across participants, sites and manufacturers
Eva Alonso‐Ortiz
Mihael Abramovic
Carina Arneitz
Nicole Atcheson
Laura Barlow
Robert L. Barry
Markus Barth
Marco Battiston
Christian Büchel
Matthew D. Budde
Virginie Callot
Anna J. E. Combes
Benjamin De Leener
Maxime Descoteaux
Paulo Loureiro de Sousa
Marek Dostál
Julien Doyon
Adam Dvorak
Falk Eippert … (voir 71 de plus)
Karla R. Epperson
Kevin S. Epperson
Patrick Freund
Jürgen Finsterbusch
Alexandru Foias
Michela Fratini
Issei Fukunaga
Claudia A. M. Gandini Wheeler-Kingshott
Giancarlo Germani
Guillaume Gilbert
Federico Giove
Charley Gros
Francesco Grussu
Akifumi Hagiwara
Pierre-Gilles Henry
Tomáš Horák
Masaaki Hori
James Joers
Kouhei Kamiya
Haleh Karbasforoushan
Miloš Keřkovský
Ali Khatibi
Joo‐Won Kim
Nawal Kinany
Hagen H. Kitzler
Shannon Kolind
Yazhuo Kong
Petr Kudlička
Paul Kuntke
Nyoman D. Kurniawan
Slawomir Kusmia
René Labounek
Maria Marcella Lagana
Cornelia Laule
Christine S. Law
Christophe Lenglet
Tobias Leutritz
Yaou Liu
Sara Llufriu
Sean Mackey
Eloy Martinez-Heras
Loan Mattera
Igor Nestrašil
Kristin P. O’Grady
Nico Papinutto
Daniel Papp
Deborah Pareto
Todd B. Parrish
Anna Pichiecchio
Ferran Prados
Àlex Rovira
Marc J. Ruitenberg
Rebecca S. Samson
Giovanni Savini
Maryam Seif
Alan C. Seifert
Alex K. Smith
Seth A. Smith
Zachary A. Smith
Elisabeth Solana
Y. Suzuki
George Tackley
Alexandra Tinnermann
Jan Valošek
Dimitri Van De Ville
Marios C. Yiannakas
Kenneth A. Weber
Nikolaus Weiskopf
Richard G. Wise
Patrik O. Wyss
Junqian Xu
Cohort Bias Adaptation in Aggregated Datasets for Lesion Segmentation
Brennan Nichyporuk
Jillian L. Cardinell
Justin Szeto
Raghav Mehta
Sotirios A. Tsaftaris
Douglas Arnold
Stacked Hourglass Network with a Multi-level Attention Mechanism: Where to Look for Intervertebral Disc Labeling
Reza Azad
Lucas Rouhier
Connectivity alterations in autism reflect functional idiosyncrasy
Oualid Benkarim
Casey Paquola
Bo-yong Park
Seok-Jun Hong
Jessica Royer
Reinder Vos de Wael
Sara Lariviere
Sofie Valk
Laurent Mottron
Boris C Bernhardt
Social isolation is linked to classical risk factors of Alzheimer’s disease-related dementias
Kimia Shafighi
Sylvia Villeneuve
P. Rosa-Neto
AmanPreet Badhwar
Judes Poirier
Vaibhav Sharma
Yasser Iturria-Medina
Patricia P. Silveira
Laurette Dubé
David C. Glahn
Alzheimer’s disease and related dementias is a major public health burden – compounding over upcoming years due to longevity. Recently, … (voir plus)clinical evidence hinted at the experience of social isolation in expediting dementia onset. In 502,506 UK Biobank participants and 30,097 participants from the Canadian Longitudinal Study of Aging, we revisited traditional risk factors for developing dementia in the context of loneliness and lacking social support. Across these measures of subjective and objective social deprivation, we have identified strong links between individuals’ social capital and various indicators of Alzheimer’s disease and related dementias risk, which replicated across both population cohorts. The quality and quantity of daily social encounters had deep connections with key aetiopathological factors, which represent 1) personal habits and lifestyle factors, 2) physical health, 3) mental health, and 4) societal and external factors. Our population-scale assessment suggest that social lifestyle determinants are linked to most neurodegeneration risk factors, highlighting them promising targets for preventive clinical action.
Haptics-based Curiosity for Sparse-reward Tasks
Sai Rajeswar
Cyril Ibrahim
Nitin Surya
Florian Golemo
David Vazquez
Pedro O. Pinheiro
Robots in many real-world settings have access to force/torque sensors in their gripper and tactile sensing is often necessary for tasks tha… (voir plus)t involve contact-rich motion. In this work, we leverage surprise from mismatches in haptics feedback to guide exploration in hard sparse-reward reinforcement learning tasks. Our approach, Haptics-based Curiosity (\method{}), learns what visible objects interactions are supposed to ``feel" like. We encourage exploration by rewarding interactions where the expectation and the experience do not match. We test our approach on a range of haptics-intensive robot arm tasks (e.g. pushing objects, opening doors), which we also release as part of this work. Across multiple experiments in a simulated setting, we demonstrate that our method is able to learn these difficult tasks through sparse reward and curiosity alone. We compare our cross-modal approach to single-modality (haptics- or vision-only) approaches as well as other curiosity-based methods and find that our method performs better and is more sample-efficient.
Team NeuroPoly: Description of the Pipelines for the MICCAI 2021 MS New Lesions Segmentation Challenge
Uzay Macar
Enamundram Naga Karthik
Charley Gros
Andreanne Lemay
This paper gives a detailed description of the pipelines used for the 2nd edition of the MICCAI 2021 Challenge on Multiple Sclerosis Lesion … (voir plus)Segmentation. An overview of the data preprocessing steps applied is provided along with a brief description of the pipelines used, in terms of the architecture and the hyperparameters. Our code for this work can be found at: https://github.com/ivadomed/ms-challenge-2021.
Decision Models and Technology Can Help Psychiatry Develop Biomarkers
Daniel S. Barron
Justin T. Baker
Kristin S. Budde
Simon B. Eickhoff
Karl J. Friston
Peter T. Fox
Paul Geha
Stephen Heisig
Avram J. Holmes
Jukka-Pekka Onnela
Albert Powers
David Silbersweig
John H. Krystal