Publications

Pepid: a Highly Modifiable, Bioinformatics-Oriented Peptide Search Engine
Jeremie Zumer
SatBird: Bird Species Distribution Modeling with Remote Sensing and Citizen Science Data
Mélisande Teng
Amna Elmustafa
Benjamin Akera
Hager Radi
Biodiversity is declining at an unprecedented rate, impacting ecosystem services necessary to ensure food, water, and human health and well-… (see more)being. Understanding the distribution of species and their habitats is crucial for conservation policy planning. However, traditional methods in ecology for species distribution models (SDMs) generally focus either on narrow sets of species or narrow geographical areas and there remain significant knowledge gaps about the distribution of species. A major reason for this is the limited availability of data traditionally used, due to the prohibitive amount of effort and expertise required for traditional field monitoring. The wide availability of remote sensing data and the growing adoption of citizen science tools to collect species observations data at low cost offer an opportunity for improving biodiversity monitoring and enabling the modelling of complex ecosystems. We introduce a novel task for mapping bird species to their habitats by predicting species encounter rates from satellite images, and present SatBird, a satellite dataset of locations in the USA with labels derived from presence-absence observation data from the citizen science database eBird, considering summer (breeding) and winter seasons. We also provide a dataset in Kenya representing low-data regimes. We additionally provide environmental data and species range maps for each location. We benchmark a set of baselines on our dataset, including SOTA models for remote sensing tasks. SatBird opens up possibilities for scalably modelling properties of ecosystems worldwide.
What Mechanisms Does Knowledge Distillation Distill?
Cindy Wu
Ekdeep Singh Lubana
Bruno Mlodozeniec
Robert Kirk
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
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.
Electric Power Fuse Identification With Deep Learning
Simon Giard-Leroux
Guillaume Cléroux
Shreyas Sunil Kulkarni
François Bouffard
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.
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
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.
Integrating Equity, Diversity, and Inclusion Throughout the Lifecycle of Artificial Intelligence for Better Health and Oral Health Care: A Workshop Summary.
Elham Emami
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.
Integrating Equity, Diversity, and Inclusion Throughout the Lifecycle of Artificial Intelligence for Better Health and Oral Health Care: A Workshop Summary.
Elham Emami
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.
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
Vladimir Adrien
Karl J. Friston
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
Alexander G. Weil
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
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
Yuriy Nevmyvaka
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.