Publications

Monitoring non-pharmaceutical public health interventions during the COVID-19 pandemic
Yannan Shen
Guido Powell
Iris Ganser
Qulu Zheng
Chris Grundy
Anya Okhmatovskaia
David L. Buckeridge
Measuring and monitoring non-pharmaceutical interventions is important yet challenging due to the need to clearly define and encode non-phar… (see more)maceutical interventions, to collect geographically and socially representative data, and to accurately document the timing at which interventions are initiated and changed. These challenges highlight the importance of integrating and triangulating across multiple databases and the need to expand and fund the mandate for public health organizations to track interventions systematically.
2021-08-23
Scientific Data (published)
doi.org
Generating community measures of food purchasing activities using store-level electronic grocery transaction records: an ecological study in Montreal, Canada
Hiroshi Mamiya
Alexandra M. Schmidt
Erica E.M. Moodie
Yu Ma
David L Buckeridge
2021-08-22
Public Health Nutrition (published)
doi.org
Deep Learning for Detecting Extreme Weather Patterns
Mayur Mudigonda
Mayur Mudigonda, Prabhat Ram
Prabhat Ram
Karthik Kashinath
Evan Racah
Ankur Mahesh
Yunjie Liu
Christopher Beckham
Jim Biard
Thorsten Kurth
Sookyung Kim
S Ebrahimi Kahou
Tegan Maharaj
Burlen Loring
Christopher Pal
Travis O'Brien
K. Kunkel
Kenneth E. Kunkel
M. Wehner
Michael F. Wehner … (see 2 more)
W. Collins
William D. Collins
2021-08-19
Deep Learning for the Earth Sciences (published)
doi.org
Loneliness is linked to specific subregional alterations in hippocampus-default network co-variation
Chris Zajner
R. Nathan Spreng
Danilo Bzdok
Social interaction complexity makes humans unique. But in times of social deprivation this strength risks to expose important vulnerabilitie… (see more)s. Human social neuroscience studies have placed a premium on the default network (DN). In contrast, hippocampus (HC) subfields have been intensely studied in rodents and monkeys. To bridge these two literatures, we here quantified how DN subregions systematically co-vary with specific HC subfields in the context of subjective social isolation (i.e., loneliness). By co-decomposition using structural brain scans of ∼40,000 UK Biobank participants, loneliness was specially linked to midline subregions in the uncovered DN patterns. These association cortex signatures coincided with concomitant HC patterns implicating especially CA1 and molecular layer. These patterns also showed a strong affiliation with the fornix white-matter tract and the nucleus accumbens. In addition, separable signatures of structural HC-DN co-variation had distinct associations with the genetic predisposition for loneliness at the population level.
2021-08-18
bioRxiv (preprint)
doi.org
Toward Optimal Solution for the Context-Attentive Bandit Problem
Djallel Bouneffouf
Raphael Feraud
Sohini Upadhyay
Irina Rish
Yasaman Khazaeni
2021-08-18
Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence (published)
doi.org
A Two-step Heuristic for the Periodic Demand Estimation Problem
Greta Laage
Emma Frejinger
Gilles Savard
Freight carriers rely on tactical plans to satisfy demand in a cost-effective way. For computational tractability in real large-scale settin… (see more)gs, such plans are typically computed by solving deterministic and cyclic formulations. An important input is the periodic demand, i.e., the demand that is expected to repeat in each period of the planning horizon. Motivated by the discrepancy between time series forecasts of demand in each period and the periodic demand, Laage et al. (2021) recently introduced the Periodic Demand Estimation (PDE) problem and showed that it has a high value. However, they made strong assumptions on the solution space so that the problem could be solved by enumeration. In this paper we significantly extend their work. We propose a new PDE formulation that relaxes the strong assumptions on the solution space. We solve large instances of this formulation with a two-step heuristic. The first step reduces the dimension of the feasible space by performing clustering of commodities based on instance-specific information about demand and supply interactions. The formulation along with the first step allow to solve the problem in a second step by either metaheuristics or the state-of-the-art black-box optimization solver NOMAD. In an extensive empirical study using real data from the Canadian National Railway Company, we show that our methodology produces high quality solutions and outperforms existing ones.
2021-08-17
ArXiv (preprint)
arxiv.org
arxiv.org
Generic acquisition protocol for quantitative MRI of the spinal cord
Julien Cohen-Adad
Eva Alonso-Ortiz
Mihael Abramovic
Carina Arneitz
Nicole Atcheson
Laura Barlow
Robert L. Barry
Markus Barth
Marco Battiston
Christian Büchel
Matthew Budde
Virginie Callot
Anna J. E. Combes
Benjamin De Leener
Maxime Descoteaux
Paulo Loureiro de Sousa
Marek Dostál
Julien Cohen-Adad
Adam Dvorak
Falk Eippert … (see 71 more)
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 Kitzler
Shannon Kolind
Yazhuo Kong
Petr Kudlička
Paul Kuntke
Nyoman D. Kurniawan
Slawomir Kusmia
René Labounek
Maria Marcella Laganà
Cornelia Laule
Christine S. Law
Christophe Lenglet
Tobias Leutritz
Yaou Liu
Sara Llufriu
Sean Mackey
Eloy Martinez-Heras
Loan Mattera
Igor Nestrasil
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
Yuichi Suzuki
George Tackley
Alexandra Tinnermann
Jan Valosek
Dimitri Van De Ville
Marios C. Yiannakas
Kenneth A. Weber
Nikolaus Weiskopf
Richard G. Wise
Patrik O. Wyss
Junqian Xu
Optimized and standardized MRI acquisition protocols for the spinal cord, compatible with Siemens, GE and Philips scanners.
2021-08-15
Nature Protocols (published)
doi.org
Open-access quantitative MRI data of the spinal cord and reproducibility across participants, sites and manufacturers
Julien Cohen-Adad
Eva Alonso-Ortiz
Mihael Abramovic
Carina Arneitz
Nicole Atcheson
Laura Barlow
Robert L. Barry
Markus Barth
Marco Battiston
Christian Büchel
Matthew Budde
Virginie Callot
Anna J. E. Combes
Benjamin De Leener
Maxime Descoteaux
Paulo Loureiro de Sousa
Marek Dostál
Julien Doyon
Adam Dvorak
Falk Eippert … (see 71 more)
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 Laganà
Cornelia Laule
Christine S. Law
Christophe Lenglet
Tobias Leutritz
Yaou Liu
Sara Llufriu
Sean Mackey
Eloy Martinez-Heras
Loan Mattera
Igor Nestrasil
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 Valosek
Dimitri Van De Ville
Marios C. Yiannakas
Kenneth A. Weber II
Nikolaus Weiskopf
Richard G. Wise
Patrik O. Wyss
Junqian Xu
In a companion paper by Cohen-Adad et al. we introduce the spine generic quantitative MRI protocol that provides valuable metrics for assess… (see more)ing spinal cord macrostructural and microstructural integrity. This protocol was used to acquire a single subject dataset across 19 centers and a multi-subject dataset across 42 centers (for a total of 260 participants), spanning the three main MRI manufacturers: GE, Philips and Siemens. Both datasets are publicly available via git-annex. Data were analysed using the Spinal Cord Toolbox to produce normative values as well as inter/intra-site and inter/intra-manufacturer statistics. Reproducibility for the spine generic protocol was high across sites and manufacturers, with an average inter-site coefficient of variation of less than 5% for all the metrics. Full documentation and results can be found at https://spine-generic.rtfd.io/. The datasets and analysis pipeline will help pave the way towards accessible and reproducible quantitative MRI in the spinal cord.
2021-08-15
Scientific Data (published)
doi.org
Hybrid Harmony: A Multi-Person Neurofeedback Application for Interpersonal Synchrony
Phoebe Chen
Sophie Hendrikse
Kaia Sargent
Michele Romani
Matthias Oostrik
Tom F. Wilderjans
Sander Koole
Guillaume Dumas
David Medine
Suzanne Dikker
Recent years have seen a dramatic increase in studies measuring brain activity, physiological responses, and/or movement data from multiple … (see more)individuals during social interaction. For example, so-called “hyperscanning” research has demonstrated that brain activity may become synchronized across people as a function of a range of factors. Such findings not only underscore the potential of hyperscanning techniques to capture meaningful aspects of naturalistic interactions, but also raise the possibility that hyperscanning can be leveraged as a tool to help improve such naturalistic interactions. Building on our previous work showing that exposing dyads to real-time inter-brain synchrony neurofeedback may help boost their interpersonal connectedness, we describe the biofeedback application Hybrid Harmony, a Brain-Computer Interface (BCI) that supports the simultaneous recording of multiple neurophysiological datastreams and the real-time visualization and sonification of inter-subject synchrony. We report results from 236 dyads experiencing synchrony neurofeedback during naturalistic face-to-face interactions, and show that pairs' social closeness and affective personality traits can be reliably captured with the inter-brain synchrony neurofeedback protocol, which incorporates several different online inter-subject connectivity analyses that can be applied interchangeably. Hybrid Harmony can be used by researchers who wish to study the effects of synchrony biofeedback, and by biofeedback artists and serious game developers who wish to incorporate multiplayer situations into their practice.
2021-08-11
Frontiers in Neuroergonomics (published)
doi.org
Evaluation of distortion correction methods in diffusion MRI of the spinal cord
Haykel Snoussi
Emmanuel Caruyer
Julien Cohen-Adad
Olivier Commowick
Benoit Combes
Elise Bannier
Anne Kerbrat
Christian Barillot
2021-08-08
ArXiv (preprint)
arxiv.org
arxiv.org
Learning function from structure in neuromorphic networks
Laura E. Suárez
Blake A. Richards
Guillaume Lajoie
Bratislav Misic
The connection patterns of neural circuits in the brain form a complex network. Collective signaling within the network manifests as pattern… (see more)ed neural activity, and is thought to support human cognition and adaptive behavior. Recent technological advances permit macro-scale reconstructions of biological brain networks. These maps, termed connectomes, display multiple non-random architectural features, including heavy-tailed degree distributions, segregated communities and a densely interconnected core. Yet, how computation and functional specialization emerge from network architecture remains unknown. Here we reconstruct human brain connectomes using in vivo diffusion-weighted imaging, and use reservoir computing to implement these connectomes as artificial neural networks. We then train these neuromorphic networks to learn a cognitive task. We show that biologically realistic neural architectures perform optimally when they display critical dynamics. We find that performance is driven by network topology, and that the modular organization of large-scale functional systems is computationally relevant. Throughout, we observe a prominent interaction between network structure and dynamics, such that the same underlying architecture can support a wide range of learning capacities across dynamical regimes. This work opens new opportunities to discover how the network organization of the brain optimizes cognitive capacity, conceptually bridging neuroscience and artificial intelligence.
2021-08-08
Nature Machine Intelligence (unknown)
doi.org
Neocortical inhibitory interneuron subtypes are differentially attuned to synchrony- and rate-coded information
Luke Y. Prince
Matthew M. Tran
Dorian Grey
Lydia Saad
Helen Chasiotis
Jeehyun Kwag
Michael M. Kohl
Blake A. Richards
Neurons can carry information with both the synchrony and rate of their spikes. However, it is unknown whether distinct subtypes of neurons … (see more)are more sensitive to information carried by synchrony versus rate, or vice versa. Here, we address this question using patterned optical stimulation in slices of somatosensory cortex from mouse lines labelling fast-spiking (FS) and regular-spiking (RS) interneurons. We used optical stimulation in layer 2/3 to encode a 1-bit signal using either the synchrony or rate of activity. We then examined the mutual information between this signal and the interneuron responses. We found that for a synchrony encoding, FS interneurons carried more information in the first five milliseconds, while both interneuron subtypes carried more information than excitatory neurons in later responses. For a rate encoding, we found that RS interneurons carried more information after several milliseconds. These data demonstrate that distinct interneuron subtypes in the neocortex have distinct sensitivities to synchrony versus rate codes.
2021-08-04
Communications Biology (published)
doi.org