Publications

Neural activity resolved in space and time through fusion of large-scale EEG and fMRI datasets.
Ian Charest
Peter Brotherwood
Mathias Salvas-Hébert
Kendrick Kay
Frédéric Gosselin
2025-07-14
Journal of Vision (published)
doi.org
Personalizing brain stimulation: continual learning for sleep spindle detection
Milo Sobral
Hugo R Jourde
S Ehsan M Bajestani
Emily B J Coffey
Giovanni Beltrame
Objective. Personalized stimulation, in which algorithms used to detect neural events adapt to a user’s unique neural characteristics, may… (see more) be crucial to enable optimized and consistent stimulation quality for both fundamental research and clinical applications. Precise stimulation of sleep spindles-transient patterns of brain activity that occur during non rapid eye movement sleep that are involved in memory consolidation-presents an exciting frontier for studying memory functions; however, this endeavour is challenged by the spindles’ fleeting nature, inter-individual variability, and the necessity of real-time detection. Approach. We tackle these challenges using a novel continual learning framework. Using a pre-trained model capable of both online classification of sleep stages and spindle detection, we implement an algorithm that refines spindle detection, tailoring it to the individual throughout one or more nights without manual intervention. Main results. Our methodology achieves accurate, subject-specific targeting of sleep spindles and enables advanced closed-loop stimulation studies. While fine-tuning alone offers minimal benefits for single nights, our approach combining weight averaging demonstrates significant improvement over multiple nights, effectively mitigating catastrophic forgetting. Significance. This work represents an important step towards signal-level personalization of brain stimulation that can be applied to different brain stimulation paradigms including closed-loop brain stimulation, and to different neural events. Applications in fundamental neuroscience may enhance the investigative potential of brain stimulation to understand cognitive processes such as the role of sleep spindles in memory consolidation, and may lead to novel therapeutic applications.
2025-07-14
Journal of Neural Engineering (published)
doi.org
Relative Entropy Pathwise Policy Optimization
Claas Voelcker
Axel Brunnbauer
Marcel Hussing
Michal Nauman
Pieter Abbeel
Eric R. Eaton
Radu Grosu
Amir-massoud Farahmand
Igor Gilitschenski
Score-function policy gradients have delivered strong results in game-playing, robotics and language-model fine-tuning. Yet its high-varianc… (see more)e often undermines training stability. On the other hand, pathwise policy gradients alleviate the training variance, but are reliable only when driven by an accurate action-conditioned value function which is notoriously hard to train without relying on past off-policy data. In this paper, we discuss how to construct a value-gradient driven, on-policy algorithm that allow training Q-value models purely from on-policy data, unlocking the possibility of using pathwise policy updates in the context of on-policy learning. We show how to balance stochastic policies for exploration with constrained policy updates for stable training, and evaluate important architectural components that facilitate accurate value function learning. Building on these insights, we propose Relative Entropy Pathwise Policy Optimization (REPPO), an efficient on-policy algorithm that combines the sample-efficiency of pathwise policy gradients with the simplicity and minimal memory footprint of standard on-policy learning. We demonstrate that REPPO provides strong empirical performance at decreased sample requirements, wall-clock time, memory footprint as well as high hyperparameter robustness in a set of experiments on two standard GPU-parallelized benchmarks.
2025-07-14
ArXiv (preprint)
doi.org
arxiv.org
Scaling Trends in Language Model Robustness
Nikolaus Howe
Ian McKenzie
Oskar Hollinsworth
Michał Zając
Tom Tseng
Aaron Tucker
Pierre-Luc Bacon
Adam Gleave
Increasing model size has unlocked a dazzling array of capabilities in modern language models. At the same time, even frontier models remain… (see more) vulnerable to jailbreaks and prompt injections, despite concerted efforts to make them robust. As both attack and defense gain access to more compute, and as models become larger, what happens to robustness? We argue that to answer this question requires a \emph{scaling} approach, which we employ in an extensive study of language model robustness across several classification tasks, model families, and adversarial attacks. We find that in the absence of explicit safety training, larger models are not consistently more robust; however, scale improves sample efficiency in adversarial training, though it worsens compute efficiency. Further, we find that increasing attack compute smoothly improves attack success rate against both undefended and adversarially trained models. Finally, after exploring robustness transfer across attacks and threat models, we combine attack and defense scaling rates to study the offense-defense balance. We find that while attack scaling outpaces adversarial training across all models studied, larger adversarially trained models might give defense the advantage in the long run. These results underscore the utility of the scaling lens, and provide a paradigm for evaluating future attacks and defenses on frontier models.
2025-07-14
International Conference on Machine Learning (Accept (spotlight poster))
doi.org
proceedings.mlr.press
STAGED: A Multi-Agent Neural Network for Learning Cellular Interaction Dynamics
João Felipe Rocha
Ke Xu
Xingzhi Sun
Ananya Krishna
Dhananjay Bhaskar
Blanche Mongeon
Morgan Craig
Mark B. Gerstein
Smita Krishnaswamy
The advent of single-cell technology has significantly improved our understanding of cellular states and subpopulations in various tissues u… (see more)nder normal and diseased conditions by employing data-driven approaches such as clustering and trajectory inference. However, these methods consider cells as independent data points of population distributions. With spatial transcriptomics, we can represent cellular organization, along with dynamic cell-cell interactions that lead to changes in cell state. Still, key computational advances are necessary to enable the data-driven learning of such complex interactive cellular dynamics. While agent-based modeling (ABM) provides a powerful framework, traditional approaches rely on handcrafted rules derived from domain knowledge rather than data-driven approaches. To address this, we introduce Spatio Temporal Agent-Based Graph Evolution Dynamics(STAGED) integrating ABM with deep learning to model intercellular communication, and its effect on the intracellular gene regulatory network. Using graph ODE networks (GDEs) with shared weights per cell type, our approach represents genes as vertices and interactions as directed edges, dynamically learning their strengths through a designed attention mechanism. Trained to match continuous trajectories of simulated as well as inferred trajectories from spatial transcriptomics data, the model captures both intercellular and intracellular interactions, enabling a more adaptive and accurate representation of cellular dynamics.
2025-07-14
ArXiv (preprint)
doi.org
arxiv.org
UI-Vision: A Desktop-centric GUI Benchmark for Visual Perception and Interaction
Shravan Nayak
Xiangru Jian
Kevin Qinghong Lin
Juan A. Rodriguez
Montek Kalsi
Rabiul Awal
Nicolas Chapados
M. Tamer Özsu
Aishwarya Agrawal
David Vázquez
Christopher Pal
Perouz Taslakian
Spandana Gella
Sai Rajeswar
Human Annotator
Autonomous agents that navigate Graphical User Interfaces (GUIs) to automate tasks like document editing and file management can greatly enh… (see more)ance computer workflows. While existing research focuses on online settings, desktop environments, critical for many professional and everyday tasks, remain underexplored due to data collection challenges and licensing issues. We introduce UI-Vision, the first comprehensive, license-permissive benchmark for offline, fine-grained evaluation of computer use agents in real-world desktop environments. Unlike online benchmarks, UI-Vision provides: (i) dense, high-quality annotations of human demonstrations, including bounding boxes, UI labels, and action trajectories (clicks, drags, and keyboard inputs) across 83 software applications, and (ii) three fine-to-coarse grained tasks—Element Grounding, Layout Grounding, and Action Prediction—with well-defined metrics to rigorously evaluate agents’ performance in desktop environments. Our evaluation reveals critical limitations in state-of-the-art models like UI-TARS-72B, including issues with understanding professional software, spatial reasoning, and complex actions like drag-and-drop. These findings highlight the challenges in developing fully autonomous computer-use agents. With UI-Vision, we aim to advance the development of more capable agents for real-world desktop tasks.
2025-07-14
International Conference on Machine Learning (Accept (poster))
doi.org
proceedings.mlr.press
Effects of a Virtual Reality Hypnosis Intervention on Chronic Pain: A User Experience and Proof-of-concept Study
Alexandra Chevestrier-Lefeuvre
Joséphine Guiné
Jade Véronneau
Julie Lebeau
Floriane Rousseaux
Audrey Laurin
Marie-Fania Simard
Nadia Godin
Karim Jerbi
Philippe Richebé
Mathieu Landry
Pierre Rainville
Valentyn Fournier
David Ogez
Abstract

Chronic pain is a significant public health issue in Canada, with approximately one in four Canadians ove… (see more)r the age of 15 living with this condition. Due to its impact on individuals—both physically and psychologically—and its financial burden on the healthcare system, it is crucial to develop cost-effective and efficient treatment methods. Hypnosis and virtual reality have emerged as promising solutions in this context. This study aims to evaluate the preliminary efficacy and feasibility of an intervention combining virtual reality and hypnosis. The study involved 30 patients with chronic pain who were invited to test a hypnosis application delivered through a virtual reality device. Levels of pain, anxiety, and relaxation were measured before and after the intervention, while satisfaction, cybersickness, and user experience were evaluated post-intervention. At the end of the intervention, participants were invited to participate in a semi-structured interview to provide feedback on their satisfaction with the experience. Participants reported high levels of satisfaction with the intervention, a positive user experience, and minimal symptoms of cybersickness. The intervention was effective in reducing anxiety (W = 173.5, p = .002) and pain (W = 253.5, p< .001) while significantly enhancing relaxation levels (W = 9.00, p< .001). This intervention demonstrated effectiveness in reducing pain and anxiety while improving relaxation levels among individuals with chronic pain, paving the way for further investigations of the involved mechanisms.

2025-07-13
Research Square (preprint)
doi.org
Frequency enrichment of coding variants in a French-Canadian founder population and its implication for inflammatory bowel diseases
Claude Bhérer
Jean-Christophe Grenier
Justin Pelletier
Gabrielle Boucher
Genevieve Gagnon
Philippe Goyette
Dariel Ashton-Beaucage
Christine Stevens
Robert Battat
Alain Bitton
Philippe M Campeau
Catherine Laprise
Quebec IBD Genetics Consortium
Hailiang Huang
Mark Daly
Daniel Taliun
Julie G Hussin
Vincent Mooser
John D Rioux
The genetic features of founder populations with recent bottlenecks, causing some deleterious variants to rise to higher frequencies, can en… (see more)hance the power of rare variant association studies. French Canadians from Quebec represent a recent founder population with a particular disease heritage comprising more than 30 prevalent Mendelian conditions. Here, we characterize coding variation in this founder population using exome sequencing data from 2,820 French-Canadian participants - patients with inflammatory bowel diseases (IBD), parents and controls from the Quebec IBD cohort. We find that 18% of rare coding variants are 10-100 times more frequent than in non-Finnish Europeans (NFE). A total of 4,133 missense and loss-of-function variants were significantly enriched with a median 28-fold enrichment, revealing the potential for genotype-phenotype associations in this population. We describe significantly enriched pathogenic variants, including those known to account for the increased prevalence of rare diseases in FC compared to other European descent populations, such as Agenesis of corpus callosum and peripheral neuropathy (SLC12A6) and Leigh Syndrome French Canadian type (LRPPRC). Finally, we investigate whether rare protein-coding variants, enriched in French Canadians by the founder effect, contribute to the risk of IBD using trio and case/control cohorts. In addition to replicating associations in NOD2 and IL23R, we identified new candidate association signals, including enriched variants in SLC35E3, and ARSA. Our findings show that, even in well-characterized founder populations like the French Canadians, there remains untapped potential for genetic discovery, revealing both rare and complex disease risk factors through enriched coding variation.
2025-07-13
medRxiv (preprint)
doi.org
Integrating equity, diversity, and inclusion throughout the lifecycle of artificial intelligence for healthcare: a scoping review
Ting Wang
Elham Emami
Dana Jafarpour
Raymond Tolentino
Genevieve Gore
S. A. Rahimi
The lack of Equity, Diversity, and Inclusion (EDI) principles in the lifecycle of Artificial Intelligence (AI) technologies in healthcare is… (see more) a growing concern. Despite its importance, there is still a gap in understanding the initiatives undertaken to address this issue. This review aims to explore what and how EDI principles have been integrated into the design, development, and implementation of AI studies in healthcare. We followed the scoping review framework by Levac et al. and the Joanna Briggs Institute. A comprehensive search was conducted until April 29, 2022, across MEDLINE, Embase, PsycInfo, Scopus, and SCI-EXPANDED. Only research studies in which the integration of EDI in AI was the primary focus were included. Non-research articles were excluded. Two independent reviewers screened the abstracts and full texts, resolving disagreements by consensus or by consulting a third reviewer. To synthesize the findings, we conducted a thematic analysis and used a narrative description. We adhered to the PRISMA-ScR checklist for reporting scoping reviews. The search yielded 10,664 records, with 42 studies included. Most studies were conducted on the American population. Previous research has shown that AI models improve when socio-demographic factors such as gender and race are considered. Despite frameworks for EDI integration, no comprehensive approach systematically applies EDI principles in AI model development. Additionally, the integration of EDI into the AI implementation phase remains under-explored, and the representation of EDI within AI teams has been overlooked. This review reports on what and how EDI principles have been integrated into the design, development, and implementation of AI technologies in healthcare. We used a thorough search strategy and rigorous methodology, though we acknowledge limitations such as language and publication bias. A comprehensive framework is needed to ensure that EDI principles are considered throughout the AI lifecycle. Future research could focus on strategies to reduce algorithmic bias, assess the long-term impact of EDI integration, and explore policy implications to ensure that AI technologies are ethical, responsible, and beneficial for all.
2025-07-13
PLOS Digital Health (published)
doi.org
Multi-Armed Sampling Problem and the End of Exploration
Mohammad Pedramfar
Siamak Ravanbakhsh
This paper introduces the framework of multi-armed sampling, as the sampling counterpart to the optimization problem of multi-arm bandits. O… (see more)ur primary motivation is to rigorously examine the exploration-exploitation trade-off in the context of sampling. We systematically define plausible notions of regret for this framework and establish corresponding lower bounds. We then propose a simple algorithm that achieves these optimal regret bounds. Our theoretical results demonstrate that in contrast to optimization, sampling does not require exploration. To further connect our findings with those of multi-armed bandits, we define a continuous family of problems and associated regret measures that smoothly interpolates and unifies multi-armed sampling and multi-armed bandit problems using a temperature parameter. We believe the multi-armed sampling framework, and our findings in this setting can have a foundational role in the study of sampling including recent neural samplers, akin to the role of multi-armed bandits in reinforcement learning. In particular, our work sheds light on the need for exploration and the convergence properties of algorithm for entropy-regularized reinforcement learning, fine-tuning of pretrained models and reinforcement learning with human feedback (RLHF).
2025-07-13
ArXiv (preprint)
doi.org
arxiv.org
Rethinking Prompt Optimization: Reinforcement, Diversification, and Migration in Blackbox LLMs
MohammadReza Davari
Utkarsh Garg
Weixin Cai
Eugene Belilovsky
2025-07-13
ArXiv (preprint)
doi.org
arxiv.org
CADmium: Fine-Tuning Code Language Models for Text-Driven Sequential CAD Design
Prashant Govindarajan
Davide Baldelli
Jay Pathak
Quentin Fournier
A. Chandar
Computer-aided design (CAD) is the digital construction of 2D and 3D objects, and is central to a wide range of engineering and manufacturin… (see more)g applications like automobile and aviation. Despite its importance, CAD modeling remains largely a time-intensive, manual task. Recent works have attempted to automate this process with small transformer-based models and handcrafted CAD sequence representations. However, there has been little effort to leverage the potential of large language models (LLMs) for sequential CAD design. In this work, we introduce a new large-scale dataset of more than 170k CAD models annotated with high-quality, human-like descriptions generated with our pipeline based on GPT-4.1. Using this dataset, we fine-tune powerful code-LLMs to generate CAD sequences represented in a JSON-based format from natural language descriptions, demonstrating the viability and effectiveness of this approach for text-conditioned CAD generation. Because simple metrics often fail to reflect the quality of generated objects, we introduce geometric and topological metrics based on sphericity, mean curvature, and Euler characteristic to provide richer structural insights. Our experiments and ablation studies on both synthetic and human-annotated data demonstrate that CADmium is able to automate CAD design, drastically speeding up the design of new objects. The dataset, code, and fine-tuned models are available online.
2025-07-12
ArXiv (preprint)
doi.org
arxiv.org