Christian Gagné

Biography

Christian Gagné has been a professor in the Department of Electrical and Computer Engineering at Université Laval since 2008.

He is the director of the Institute Intelligence and Data (IID), holds a Canada CIFAR AI Chair, and is an associate member of Mila – Quebec Artificial Intelligence Institute.

Gagné is also a member of Université Laval’s Computer Vision and Systems Laboratory (LVSN), as well as its Robotics, Vision and Machine Intelligence Research Centre (CeRVIM) and its Big Data Research Centre (CRDM). He is a member of the REPARTI and UNIQUE strategic clusters of the FRQNT, the VITAM centre of the FRQS, and the International Observatory on the Societal Impacts of AI and Digital Technologies (OBVIA).

Gagné’s research focuses on the development of methods for machine learning and stochastic optimization. In particular, he is interested in deep neural networks, representation learning and transfer, meta-learning and multitasking. He is also interested in optimization approaches based on probabilistic models and evolutionary algorithms, including black-box optimization and automatic programming. An important part of his work is the practical application of these techniques in fields like computer vision, microscopy, healthcare, energy and transportation.

Current Students

Frédéric Beaupré

PhD - Université Laval

Catherine Bouchard

PhD - Université Laval

Olivier Bussière

Master's Research - Université Laval

Sara Karami

PhD - Université Laval

Rose Nayoung Kwon

PhD - Université Laval

Benjamin Léger

PhD - Université Laval

Samy Mammeri

Undergraduate - Université Laval

Jonas Ngnawe

PhD - Université Laval

PhD - Université Laval

Website

Adam Tupper

PhD - Université Laval

Website

Publications

Multi-Modal Learning meets Genetic Programming: Analyzing Alignment in Latent Space Optimization

Benjamin Léger

Kazem Meidani

Symbolic regression (SR) aims to discover mathematical expressions from data, a task traditionally tackled using Genetic Programming (GP) th… (see more)rough combinatorial search over symbolic structures. Latent Space Optimization (LSO) methods use neural encoders to map symbolic expressions into continuous spaces, transforming the combinatorial search into continuous optimization. SNIP (Meidani et al., 2024), a contrastive pre-training model inspired by CLIP, advances LSO by introducing a multi-modal approach: aligning symbolic and numeric encoders in a shared latent space to learn the phenotype-genotype mapping, enabling optimization in the numeric space to implicitly guide symbolic search. However, this relies on fine-grained cross-modal alignment, whereas literature on similar models like CLIP reveals that such an alignment is typically coarse-grained. In this paper, we investigate whether SNIP delivers on its promise of effective bi-modal optimization for SR. Our experiments show that: (1) cross-modal alignment does not improve during optimization, even as fitness increases, and (2) the alignment learned by SNIP is too coarse to efficiently conduct principled search in the symbolic space. These findings reveal that while multi-modal LSO holds significant potential for SR, effective alignment-guided optimization remains unrealized in practice, highlighting fine-grained alignment as a critical direction for future work.

2026-04-08

arXiv (preprint)

arxiv.org

Ca2+ transient detection and segmentation with the Astronomically motivated algorithm for Background Estimation And Transient Segmentation (Astro-BEATS)

Bi Fan

Anthony Bilodeau

Frédéric Beaupré

Theresa Wiesner

Flavie Lavoie-Cardinal

Renée Hložek

Fluorescence-based Ca…

2026-03-18

arXiv (preprint)

Robust Fine-Tuning from Non-Robust Pretrained Models: Mitigating Suboptimal Transfer With Epsilon-Scheduling

Ola Ahmad

Frédéric Precioso

Fine-tuning pretrained models is a standard and effective workflow in modern machine learning. However, robust fine-tuning (RFT), which aims… (see more) to simultaneously achieve adaptation to a downstream task and robustness to adversarial examples, remains challenging. Despite the abundance of non-robust pretrained models in open-source repositories, their potential for RFT is less understood. We address this knowledge gap by systematically examining RFT from such non-robust models. Our experiments reveal that fine-tuning non-robust models with a robust objective, even under small perturbations, can lead to poor performance, a phenomenon that we dub _suboptimal transfer_. In challenging scenarios (eg, difficult tasks, high perturbation), the resulting performance can be so low that it may be considered a transfer failure. We find that fine-tuning using a robust objective impedes task adaptation at the beginning of training and eventually prevents optimal transfer. However, we propose a novel heuristic, _Epsilon-Scheduling_, a schedule over perturbation strength used during training that promotes optimal transfer. Additionally, we introduce _expected robustness_, a metric that captures performance across a range of perturbations, providing a more comprehensive evaluation of the accuracy-robustness trade-off of diverse models at test-time. Extensive experiments on wide range of configurations (six pretrained models and five datasets) show that _Epsilon-Scheduling_ successfully prevents _suboptimal transfer_ and consistently improves expected robustness.

2025-12-31

International Conference on Learning Representations (Accept (Poster))

Personalized Federated Fine-Tuning of Vision Foundation Models for Healthcare

Adam Tupper

2025-09-30

arXiv (published)

arxiv.org

A Guide to Robust Generalization: The Impact of Architecture, Pre-training, and Optimization Strategy

Ola Ahmad

Deep learning models operating in the image domain are vulnerable to small input perturbations. For years, robustness to such perturbations … (see more)was pursued by training models from scratch (i.e., with random initializations) using specialized loss objectives. Recently, robust fine-tuning has emerged as a more efficient alternative: instead of training from scratch, pretrained models are adapted to maximize predictive performance and robustness. To conduct robust fine-tuning, practitioners design an optimization strategy that includes the model update protocol (e.g., full or partial) and the specialized loss objective. Additional design choices include the architecture type and size, and the pretrained representation. These design choices affect robust generalization, which is the model's ability to maintain performance when exposed to new and unseen perturbations at test time. Understanding how these design choices influence generalization remains an open question with significant practical implications. In response, we present an empirical study spanning 6 datasets, 40 pretrained architectures, 2 specialized losses, and 3 adaptation protocols, yielding 1,440 training configurations and 7,200 robustness measurements across five perturbation types. To our knowledge, this is the most diverse and comprehensive benchmark of robust fine-tuning to date. While attention-based architectures and robust pretrained representations are increasingly popular, we find that convolutional neural networks pretrained in a supervised manner on large datasets often perform best. Our analysis both confirms and challenges prior design assumptions, highlighting promising research directions and offering practical guidance.

2025-09-28

NeurIPS.cc/2025/Workshop/Reliable_ML (published)

High-order Component Attribution via Kolmogorov-Arnold Networks

Samy Mammeri

Component attribution methods provide insight into how parts of deep learning models, such as convolutional filters and attention heads, inf… (see more)luence model predictions. Despite their successes, existing attribution approaches typically assume component effects are additive and independent, neglecting complex interactions among components. Capturing these relations between components is crucial for a better mechanistic understanding of these models. In this work, we improve component attribution (COAR) by replacing the linear counterfactual estimator with a Kolmogorov–Arnold Network (KAN) surrogate fitted to example‑wise perturbation–response data. Then, a symbolic approximation of the learned KAN lets us compute mixed partial derivatives that captures and makes explicit high‑order component interactions that linear methods are missing. These symbolic expressions facilitate future integration with formal verification methods, enabling richer counterfactual analyses of internal model behavior. Preliminary results on standard image classification models demonstrate that our approach improves the accuracy of predicted counterfactuals and enable extraction of higher-order component interactions compared to linear attribution methods.

2025-09-28

NeurIPS.cc/2025/Workshop/MechInterp (poster)

Robust Fine-Tuning from Non-Robust Pretrained Models: Mitigating Suboptimal Transfer With Epsilon-Scheduling

Jonas Ngnawe

Maxime Heuillet

Sabyasachi Sahoo

Yann Batiste Pequignot

Frédéric Precioso

Fine-tuning pretrained models is the standard approach in current machine learning practice, but simultaneously achieving adversarial robust… (see more)ness to adversarial examples remains a challenge. Despite the abundance of non-robust pretrained models in open-source repositories, their use for Robust Fine-Tuning (RFT) remains understudied. This work aims to bridge this knowledge gap by systematically examining RFT from such models. Our experiments reveal that fine-tuning non-robust models with a robust objective, even under small perturbations, can lead to poor performance, a phenomenon that we dub \emph{suboptimal transfer}. In fact, we find that fine-tuning using a robust objective impedes task alignment at the beginning of training and eventually prevents optimal transfer. To promote optimal transfer, we propose \emph{Epsilon-Scheduling}, a simple heuristic scheduling over perturbation strength. Additionally, we introduce \emph{expected robustness}, a metric that measures performance across a range of perturbations. Experiments on six pretrained models and five datasets show that \emph{Epsilon-Scheduling} prevents \emph{suboptimal transfer} and consistently improves the expected robustness.

2025-09-28

NeurIPS.cc/2025/Workshop/Reliable_ML (published)

Conditional Adversarial Random Forest for Synthetic Electronic Health Record Generation

Cynthia García Ybarra

2025-09-21

NeurIPS.cc/2025/Workshop/WiML (published)

Enhancing STED Microscopy via Fluorescence Lifetime Unmixing and Filtering in Two-Species SPLIT-STED

Andréanne Deschênes

Antoine Ollier

Marie Lafontaine

Albert Michaud-Gagnon

Jeffrey-Gabriel Steavan Santiague

Anthony Bilodeau

Paul De Koninck

Flavie Lavoie-Cardinal

2025-07-17

bioRxiv (preprint)

A Self-Supervised Foundation Model for Robust and Generalizable Representation Learning in STED Microscopy

Anthony Bilodeau

Frédéric Beaupré

Julia Chabbert

Kamylle Thériault

Andréanne Deschênes

Jean-Michel Bellavance

Koraly Lessard

Renaud Bernatchez

Paul De Koninck

Flavie Lavoie-Cardinal

Foundation Models (FMs) have dramatically increased the potential and power of deep learning algorithms through general capacities over a va… (see more)riety of tasks. The performance increase they offer is obtained without elaborated specific trainings for domains such as natural language processing and computer vision. However, their application in specialized fields like biomedical imaging and fluorescence microscopy remains difficult due to distribution shifts and the scarcity of high-quality annotated datasets. The high cost of data acquisition and the requirement for in-domain expertise further exacerbate this challenge in microscopy. To address this we introduce STED-FM, a foundation model specifically designed for super-resolution STimulated Emission Depletion (STED) microscopy. STED-FM leverages a Vision Transformer architecture trained at scale with Masked Autoencoding on a new dataset of nearly one million STED images. STED-FM learns expressive latent representations without requiring extensive annotations, yielding robust performance across diverse downstream microscopy image analysis tasks. Unsupervised experiments demonstrate the discriminative structure of its learned latent space. These representations can be leveraged for multiple downstream applications, including fully supervised classification and segmentation with reduced annotation requirements. Moreover, STED-FM representations enhance the performance of deep learning–based image denoising and improve the quality of images generated by diffusion models, enabling latent attribute manipulation for the data-driven discovery of subtle nanostructures and phenotypes, as well as algorithmic super-resolution. Moreover, its powerful structure retrieval capabilities are integrated into automated STED microscopy acquisition pipelines, paving the way for smart microscopy. In sum, we demonstrate that STED-FM lays a robust foundation for state-of-the-art algorithms across a wide array of tasks, establishing it as a highly valuable and scalable resource for researchers in super-resolution microscopy.

2025-06-05

bioRxiv (preprint)

Fatemeh Nourilenjan Nokabadi

TrackPGD: Efficient Adversarial Attack using Object Binary Masks against Robust Transformer Trackers

Yann Batiste Pequignot

Jean-François Lalonde

Adversarial perturbations can deceive neural networks by adding small, imperceptible noise to the input. Recent object trackers with transfo… (see more)rmer backbones have shown strong performance on tracking datasets, but their adversarial robustness has not been thoroughly evaluated. While transformer trackers are resilient to black-box attacks, existing white-box adversarial attacks are not universally applicable against these new transformer trackers due to differences in backbone architecture. In this work, we introduce TrackPGD, a novel white-box attack that utilizes predicted object binary masks to target robust transformer trackers. Built upon the powerful segmentation attack SegPGD, our proposed TrackPGD effectively influences the decisions of transformer-based trackers. Our method addresses two primary challenges in adapting a segmentation attack for trackers: limited class numbers and extreme pixel class imbalance. TrackPGD uses the same number of iterations as other attack methods for tracker networks and produces competitive adversarial examples that mislead transformer and non-transformer trackers such as MixFormerM, OSTrackSTS, TransT-SEG, and RTS on datasets including VOT2022STS, DAVIS2016, UAV123, and GOT-10k.

2025-05-26

Proceedings of the Conference on Robots and Vision (published)

A Layer Selection Approach to Test Time Adaptation

Sabyasachi Sahoo

Mostafa Elaraby

Jonas Ngnawe

Yann Batiste Pequignot

Frédéric Precioso

Test Time Adaptation (TTA) addresses the problem of distribution shift by adapting a pretrained model to a new domain during inference. When… (see more) faced with challenging shifts, most methods collapse and perform worse than the original pretrained model. In this paper, we find that not all layers are equally receptive to the adaptation, and the layers with the most misaligned gradients often cause performance degradation. To address this, we propose GALA, a novel layer selection criterion to identify the most beneficial updates to perform during test time adaptation. This criterion can also filter out unreliable samples with noisy gradients. Its simplicity allows seamless integration with existing TTA loss functions, thereby preventing degradation and focusing adaptation on the most trainable layers. This approach also helps to regularize adaptation to preserve the pretrained features, which are crucial for handling unseen domains. Through extensive experiments, we demonstrate that the proposed layer selection framework improves the performance of existing TTA approaches across multiple datasets, domain shifts, model architectures, and TTA losses.

2025-04-10

Proceedings of the AAAI Conference on Artificial Intelligence (published)