Publications

Trips and neurotransmitters: Discovering principled patterns across 6850 hallucinogenic experiences
Galen Ballentine
Samuel Freesun Friedman
Danilo Bzdok
Psychedelics probably alter states of consciousness by disrupting how the higher association cortex governs bottom-up sensory signals. Indiv… (see more)idual hallucinogenic drugs are usually studied in participants in controlled laboratory settings. Here, we have explored word usage in 6850 free-form testimonials about 27 drugs through the prism of 40 neurotransmitter receptor subtypes, which were then mapped to three-dimensional coordinates in the brain via their gene transcription levels from invasive tissue probes. Despite high interindividual variability, our pattern-learning approach delineated how drug-induced changes of conscious awareness are linked to cortex-wide anatomical distributions of receptor density proxies. Each discovered receptor-experience factor spanned between a higher-level association pole and a sensory input pole, which may relate to the previously reported collapse of hierarchical order among large-scale networks. Coanalyzing many psychoactive molecules and thousands of natural language descriptions of drug experiences, our analytical framework finds the underlying semantic structure and maps it directly to the brain.
2022-03-15
Science Advances (published)
doi.org
<i>APOE</i> ɛ2 vs <i>APOE</i> ɛ4 dosage shows sex-specific links to hippocampus-default network subregion co-variation
Chloé Savignac
Sylvia Villeneuve
AmanPreet Badhwar
Karin Saltoun
Kimia Shafighi
Chris Zajner
Vaibhav Sharma
Sarah A Gagliano Taliun
Sali Farhan
Judes Poirier
Danilo Bzdok
Alzheimer’s disease and related dementias (ADRD) are marked by intracellular tau aggregates in the medial-temporal lobe (MTL) and extracel… (see more)lular amyloid aggregates in the default network (DN). Here, we sought to clarify ADRD-related co-dependencies between the MTL’s most vulnerable structure, the hippocampus (HC), and the highly associative DN at a subregion resolution. We confronted the effects of APOE ɛ2 and ɛ4, rarely investigated together, with their impact on HC-DN co-variation regimes at the population level. In a two-pronged decomposition of structural brain scans from ∼40,000 UK Biobank participants, we located co-deviating structural patterns in HC and DN subregions as a function of ADRD family risk. Across the disclosed HC-DN signatures, recurrent deviations in the CA1, CA2/3, molecular layer, fornix’s fimbria, and their cortical partners related to ADRD risk. Phenome-wide profiling of HC-DN co- variation expressions from these population signatures revealed male-specific associations with air-pollution, and female-specific associations with cardiovascular traits. We highlighted three main factors associated with brain-APOE associations across the different gene variants: happiness, and satisfaction with friendships, and with family. We further showed that APOE ɛ2/2 interacts preferentially with HC-DN co-variation patterns in estimating social lifestyle in males and physical activity in females. Our findings reinvigorate the often-neglected interplay between APOE ɛ2 dosage and sex, which we have linked to fine-grained structural divergences indicative of ADRD susceptibility.
2022-03-14
bioRxiv (preprint)
doi.org
Medical Image Segmentation on MRI Images with Missing Modalities: A Review
Reza Azad
Nika Khosravi
Mohammad Dehghanmanshadi
Julien Cohen-Adad
Dorit Merhof
2022-03-10
ArXiv (preprint)
doi.org
arxiv.org
A New Era: Intelligent Tutoring Systems Will Transform Online Learning for Millions
Francois St-Hilaire
Dung D. Vu
Antoine Frau
Nathan J. Burns
Farid Faraji
Joseph Potochny
Stephane Robert
Arnaud Roussel
Selene Zheng
Taylor Glazier
Junfel Vincent Romano
Robert Belfer
Muhammad Shayan
Ariella Smofsky
Tommy Delarosbil
Seulmin Ahn
Simon Eden-Walker
Kritika Sony
Ansona Onyi Ching
Sabina Elkins … (see 11 more)
A. Stepanyan
Adela Matajova
Victor Chen
Hossein Sahraei
Robert Larson
N. Markova
Andrew Barkett
Laurent Charlin
Yoshua Bengio
Iulian V. Serban
Ekaterina Kochmar
2022-03-02
ArXiv (preprint)
doi.org
arxiv.org
On Lyapunov Exponents for RNNs: Understanding Information Propagation Using Dynamical Systems Tools
Ryan Vogt
Maximilian Puelma Touzel
Eli Shlizerman
Guillaume Lajoie
Recurrent neural networks (RNNs) have been successfully applied to a variety of problems involving sequential data, but their optimization i… (see more)s sensitive to parameter initialization, architecture, and optimizer hyperparameters. Considering RNNs as dynamical systems, a natural way to capture stability, i.e., the growth and decay over long iterates, are the Lyapunov Exponents (LEs), which form the Lyapunov spectrum. The LEs have a bearing on stability of RNN training dynamics because forward propagation of information is related to the backward propagation of error gradients. LEs measure the asymptotic rates of expansion and contraction of nonlinear system trajectories, and generalize stability analysis to the time-varying attractors structuring the non-autonomous dynamics of data-driven RNNs. As a tool to understand and exploit stability of training dynamics, the Lyapunov spectrum fills an existing gap between prescriptive mathematical approaches of limited scope and computationally-expensive empirical approaches. To leverage this tool, we implement an efficient way to compute LEs for RNNs during training, discuss the aspects specific to standard RNN architectures driven by typical sequential datasets, and show that the Lyapunov spectrum can serve as a robust readout of training stability across hyperparameters. With this exposition-oriented contribution, we hope to draw attention to this understudied, but theoretically grounded tool for understanding training stability in RNNs.
2022-03-01
Frontiers in Applied Mathematics and Statistics (published)
doi.org
arxiv.org
Cross-ethnicity/race generalization failure of behavioral prediction from resting-state functional connectivity
Jingwei Li
Danilo Bzdok
Jianzhong Chen
Angela Tam
Leon Qi Rong Ooi
Avram J. Holmes
Tian Ge
Kaustubh R. Patil
Mbemba Jabbi
Simon B. Eickhoff
B.T. Thomas Yeo
Sarah Genon
Algorithmic biases that favor majority populations pose a key challenge to the application of machine learning for precision medicine. Here,… (see more) we assessed such bias in prediction models of behavioral phenotypes from brain functional magnetic resonance imaging. We examined the prediction bias using two independent datasets (preadolescent versus adult) of mixed ethnic/racial composition. When predictive models were trained on data dominated by white Americans (WA), out-of-sample prediction errors were generally higher for African Americans (AA) than for WA. This bias toward WA corresponds to more WA-like brain-behavior association patterns learned by the models. When models were trained on AA only, compared to training only on WA or an equal number of AA and WA participants, AA prediction accuracy improved but stayed below that for WA. Overall, the results point to the need for caution and further research regarding the application of current brain-behavior prediction models in minority populations.
2022-02-28
Science Advances (published)
doi.org
Enjeux éthiques de l’IA en santé - Fiche 4
Joé T. Martineau
Frédérique Romy Godin
Janine Badr
Alexandre Castonguay
Martin Cousineau
Philippe Després
Aude Motulsky
Jean Noel Nikiema
Cecile Petitgand
Catherine Régis
La présente fiche propose une revue des différents enjeux éthiques liés au développement et à l’utilisation des technologies d’int… (see more)elligence artificielle dans le milieu de la santé, en trois parties. D’abord, nous aborderons les enjeux éthiques liés à l’exploitation de données massives nécessaires à l’entrainement des algorithmes de l’IA. Ensuite, nous présenterons les principaux enjeux éthiques liés au développement et à l’utilisation des SIA en santé, en abordant la façon dont ces systèmes impactent nos vies ainsi que l’environnement physique et social dans lequel nous vivons. Nous présenterons finalement les principales initiatives nationales et internationales en matière d’éthique de l’IA et de la gestion des données, fruits et reflets d’une réflexion globale sur ces sujets. Ces initiatives ont notamment proposé des lignes directrices et principes normatifs servant de guides pour le développement de technologies de l’IA éthiques et responsables Il s'agit de la quatrième fiche d'une série de 4 développée dans le cadre d'un mandat réalisé pour le Ministère de la Santé et des Services sociaux du Québec (MSSS).
2022-02-28
(published)
doi.org
Guidelines for the Computational Testing of Machine Learning approaches to Vehicle Routing Problems
Luca Accorsi
Andrea Lodi
Daniele Vigo
2022-02-28
Operations Research Letters (published)
doi.org
arxiv.org
Interindividual Differences in Cortical Thickness and Their Genomic Underpinnings in Autism Spectrum Disorder.
Christine Ecker
Charlotte M. Pretzsch
Anke Bletsch
Caroline Mann
Tim Schaefer
Sara Ambrosino
Julian Tillmann
Afsheen Yousaf
Andreas Chiocchetti
Michael V. Lombardo
Varun Warrier
Nico Bast
Carolin Moessnang
Sarah Baumeister
Flavio Dell’Acqua
Dorothea L. Floris
Mariam Zabihi
Andre Marquand
Freddy Cliquet
Claire Leblond … (see 19 more)
Clara A. Moreau
Nick Puts
Tobias Banaschewski
Emily J. H. Jones
Luke Mason
Sven Bölte
Andreas Meyer-Lindenberg
Antonio Persico
Sarah Durston
Simon Baron-Cohen
Will Spooren
Eva Loth
Christine M. Freitag
Tony Charman
Guillaume Dumas
Thomas Bourgeron
Christian Beckmann
Jan K. Buitelaar
Declan Murphy
2022-02-28
American Journal of Psychiatry (published)
doi.org
JANOS: An Integrated Predictive and Prescriptive Modeling Framework
David Bergman
Teng Huang
Philip Brooks
Andrea Lodi
Arvind U. Raghunathan
Business research practice is witnessing a surge in the integration of predictive modeling and prescriptive analysis. We describe a modeling… (see more) framework JANOS that seamlessly integrates the two streams of analytics, allowing researchers and practitioners to embed machine learning models in an end-to-end optimization framework. JANOS allows for specifying a prescriptive model using standard optimization modeling elements such as constraints and variables. The key novelty lies in providing modeling constructs that enable the specification of commonly used predictive models within an optimization model, have the features of the predictive model as variables in the optimization model, and incorporate the output of the predictive models as part of the objective. The framework considers two sets of decision variables: regular and predicted. The relationship between the regular and the predicted variables is specified by the user as pretrained predictive models. JANOS currently supports linear regression, logistic regression, and neural network with rectified linear activation functions. In this paper, we demonstrate the flexibility of the framework through an example on scholarship allocation in a student enrollment problem and provide a numeric performance evaluation. Summary of Contribution. This paper describes a new software tool, JANOS, that integrates predictive modeling and discrete optimization to assist decision making. Specifically, the proposed solver takes as input user-specified pretrained predictive models and formulates optimization models directly over those predictive models by embedding them within an optimization model through linear transformations.
2022-02-28
INFORMS Journal on Computing (published)
doi.org
arxiv.org
Multistep networks for roll force prediction in hot strip rolling mill
Shuhong Shen
Denzel Guye
Xiaoping Ma
Stephen Yue
Narges Armanfard
2022-02-28
Machine Learning with Applications (published)
doi.org
Software-Engineering Design Patterns for Machine Learning Applications
Hironori Washizaki
Foutse Khomh
Yann‐Gaël Guéhéneuc
Hironori Takeuchi
Naotake Natori
Takuo Doi
Satoshi Okuda
In this study, a multivocal literature review identified 15 software-engineering design patterns for machine learning applications. Findings… (see more) suggest that there are opportunities to increase the patterns’ adoption in practice by raising awareness of such patterns within the community.
2022-02-28
Computer (published)
doi.org