Publications

What Mechanisms Does Knowledge Distillation Distill?
Cindy Wu
Ekdeep Singh Lubana
Bruno Mlodozeniec
Robert Kirk
David Scott Krueger
2023-11-02
NeurIPS.cc/2023/Workshop/UniReps (poster)
openreview.net
openreview.net
Behavioral Imitation with Artificial Neural Networks Leads to Personalized Models of Brain Dynamics During Videogame Play
Anirudha Kemtur
Fraçois Paugam
Basile Pinsard
Pravish Sainath
Maximilien Le Clei
Julie Boyle
Karim Jerbi
Pierre (Louis) Bellec
Artificial Neural networks (ANN) trained on complex tasks are increasingly used in neuroscience to model brain dynamics, a process called br… (see more)ain encoding. Videogames have been extensively studied in the field of artificial intelligence, but have hardly been used yet for brain encoding. Videogames provide a promising framework to understand brain activity in a rich, engaging, and active environment. A major challenge raised by complex videogames is that individual behavior is highly variable across subjects, and we hypothesized that ANNs need to account for subject-specific behavior in order to properly capture brain dynamics. In this study, we used ANNs to model functional magnetic resonance imaging (fMRI) and behavioral gameplay data, both collected while subjects played the Shinobi III videogame. Using imitation learning, we trained an ANN to play the game while closely replicating the unique gameplay style of individual participants. We found that hidden layers of our imitation learning model successfully encoded task-relevant neural representations, and predicted individual brain dynamics with higher accuracy than models trained on other subjects’ gameplay or control models. The highest correlations between layer activations and brain signals were observed in biologically plausible brain areas, i.e. somatosensory, attention, and visual networks. Our results demonstrate that combining imitation learning, brain imaging, and videogames can allow us to model complex individual brain patterns derived from decision making in a rich, complex environment.
2023-11-01
bioRxiv (preprint)
doi.org
Electric Power Fuse Identification With Deep Learning
Simon Giard-Leroux
Guillaume Cléroux
Shreyas Sunil Kulkarni
François Bouffard
Martin Vallières
As part of arc flash studies, survey pictures of electrical installations need to be manually analyzed. A challenging task is to identify fu… (see more)se types, which can be determined from physical characteristics, such as shape, color, and size. To automate this process using deep learning techniques, a new dataset of fuse pictures from past arc flash projects and data from the web was created. Multiple experiments were performed to train a final model, reaching an average precision of 91.06% on the holdout set, which confirms its potential for identification of fuse types in new photos. By identifying fuse types using physical characteristics only, the need to take clear pictures of the label text is eliminated, allowing pictures to be taken away from danger, thereby improving the safety of workers. All the resources needed to repeat the experiments are openly accessible, including the code and datasets.
2023-11-01
IEEE Transactions on Industrial Informatics (published)
doi.org
Gene-metabolite annotation with shortest reactional distance enhances metabolite genome-wide association studies results
Cantin Baron
Sarah Cherkaoui
Sandra Therrien-Laperriere
Yann Ilboudo
Raphael Poujol
Pamela Mehanna
Melanie E. Garrett
Marilyn J. Telen
Allison E. Ashley-Koch
Pablo Bartolucci
John D. Rioux
Guillaume Lettre
Christine Des Rosiers
Matthieu Ruiz
Julie Hussin
Studies combining metabolomics and genetics, known as metabolite genome-wide association studies (mGWAS), have provided valuable insights in… (see more)to our understanding of the genetic control of metabolite levels. However, the biological interpretation of these associations remains challenging due to a lack of existing tools to annotate mGWAS gene-metabolite pairs beyond the use of conservative statistical significance threshold. Here, we computed the shortest reactional distance (SRD) based on the curated knowledge of the KEGG database to explore its utility in enhancing the biological interpretation of results from three independent mGWAS, including a case study on sickle cell disease patients. Results show that, in reported mGWAS pairs, there is an excess of small SRD values and that SRD values and p-values significantly correlate, even beyond the standard conservative thresholds. The added-value of SRD annotation is shown for identification of potential false negative hits, exemplified by the finding of gene-metabolite associations with SRD ≤1 that did not reach standard genome-wide significance cut-off. The wider use of this statistic as an mGWAS annotation would prevent the exclusion of biologically relevant associations and can also identify errors or gaps in current metabolic pathway databases. Our findings highlight the SRD metric as an objective, quantitative and easy-to-compute annotation for gene-metabolite pairs that can be used to integrate statistical evidence to biological networks.
2023-11-01
iScience (published)
doi.org
Integrating Equity, Diversity, and Inclusion Throughout the Lifecycle of Artificial Intelligence for Better Health and Oral Health Care: A Workshop Summary.
Elham Emami
Samira Abbasgholizadeh-Rahimi
Milka Nyariro
Professors Elham Emami and Samira Rahimi organized and co-led an international interdisciplinary workshop in June 2023 at McGill University,… (see more) built upon an intersectoral approach addressing equity, diversity and inclusion within the field of AI.
2023-11-01
Journal (published)
pubmed.ncbi.nlm.nih.gov
Integrating Equity, Diversity, and Inclusion Throughout the Lifecycle of Artificial Intelligence for Better Health and Oral Health Care: A Workshop Summary.
Elham Emami
Samira Abbasgholizadeh-Rahimi
Milka Nyariro
Professors Elham Emami and Samira Rahimi organized and co-led an international interdisciplinary workshop in June 2023 at McGill University,… (see more) built upon an intersectoral approach addressing equity, diversity and inclusion within the field of AI.
2023-11-01
Journal (published)
pubmed.ncbi.nlm.nih.gov
Interoceptive technologies for psychiatric interventions: From diagnosis to clinical applications
Felix Schoeller
Adam Haar Horowitz
Abhinandan Jain
Pattie Maes
Nicco Reggente
Leonardo Christov-Moore
Giovanni Pezzulo
Laura Barca
Micah Allen
Roy Salomon
Mark Miller
Daniele Di Lernia
Giuseppe Riva
Manos Tsakiris
Moussa A. Chalah
Arno Klein
Ben Zhang
Teresa Garcia
Ursula Pollack
Marion Trousselard … (see 4 more)
Charles Verdonk
Guillaume Dumas
Vladimir Adrien
Karl J. Friston
2023-11-01
Neuroscience and Biobehavioral Reviews (published)
doi.org
Invasive Brain Computer Interface for Motor Restoration in Spinal Cord Injury: A Systematic Review.
Jordan J. Levett
Lior M. Elkaim
Farbod Niazi
Michael H. Weber
Christian Iorio-Morin
Marco Bonizzato
Alexander G. Weil
2023-11-01
Neuromodulation: Technology at the Neural Interface (published)
doi.org
Investigation of the Dosimetry Characteristics of the GAFCHROMIC® EBT3 Film Response to Alpha Particle Irradiation
Mélodie Cyr
Victor D. Martinez
S. Devic
Nada Tomic
David F. Lewis
Shirin A. Enger
2023-11-01
Journal of Physics: Conference Series (published)
doi.org
Lag-Llama: Towards Foundation Models for Time Series Forecasting
Kashif Rasul
Arjun Ashok
Andrew Robert Williams
Arian Khorasani
George Adamopoulos
Rishika Bhagwatkar
Marin Biloš
Hena Ghonia
Nadhir Hassen
Anderson Schneider
Sahil Garg
Alexandre Drouin
Nicolas Chapados
Yuriy Nevmyvaka
Irina Rish
Aiming to build foundation models for time-series forecasting and study their scaling behavior, we present here our work-in-progress on Lag-… (see more)Llama, a general-purpose univariate probabilistic time-series forecasting model trained on a large collection of time-series data. The model shows good zero-shot prediction capabilities on unseen "out-of-distribution" time-series datasets, outperforming supervised baselines. We use smoothly broken power-laws to fit and predict model scaling behavior. The open source code is made available at https://github.com/kashif/pytorch-transformer-ts.
2023-11-01
NeurIPS.cc/2023/Workshop/R0-FoMo (poster)
doi.org
openreview.net
Mining Mass Spectra for Peptide Facts
Jeremie Zumer
Sébastien Lemieux
The current mainstream software for peptide-centric tandem mass spectrometry data analysis can be categorized as either database-driven, whi… (see more)ch rely on a library of mass spectra to identify the peptide associated with novel query spectra, or de novo sequencing-based, which aim to find the entire peptide sequence by relying only on the query mass spectrum. While the first paradigm currently produces state-of-the-art results in peptide identification tasks, it does not inherently make use of information present in the query mass spectrum itself to refine identifications. Meanwhile, de novo approaches attempt to solve a complex problem in one go, without any search space constraints in the general case, leading to comparatively poor results. In this paper, we decompose the de novo problem into putatively easier subproblems, and we show that peptide identification rates of database-driven methods may be improved in terms of peptide identification rate by solving one such subsproblem without requiring a solution for the complete de novo task. We demonstrate this using a de novo peptide length prediction task as the chosen subproblem. As a first prototype, we show that a deep learning-based length prediction model increases peptide identification rates in the ProteomeTools dataset as part of an Pepid-based identification pipeline. Using the predicted information to better rank the candidates, we show that combining ideas from the two paradigms produces clear benefits in this setting. We propose that the next generation of peptide-centric tandem mass spectrometry identification methods should combine elements of these paradigms by mining facts “de novo; about the peptide represented in a spectrum, while simultaneously limiting the search space with a peptide candidates database.
2023-11-01
bioRxiv (preprint)
doi.org
Open design of a reproducible videogame controller for MRI and MEG
Yann Harel
André Cyr
Julie Boyle
Basile Pinsard
Jeremy Bernard
Marie-France Fourcade
Himanshu Aggarwal
Ana Fernanda Ponce
Bertrand Thirion
Karim Jerbi
Pierre (Louis) Bellec
2023-11-01
PLOS ONE (published)
doi.org