Publications

Adaptive Resolution Residual Networks — Generalizing Across Resolutions Easily and Efficiently
Léa Demeule
Mahtab Sandhu
Glen Berseth
The majority of signal data captured in the real world uses numerous sensors with different resolutions. In practice, most deep learning arc… (voir plus)hitectures are fixed-resolution; they consider a single resolution at training and inference time. This is convenient to implement but fails to fully take advantage of the diverse signal data that exists. In contrast, other deep learning architectures are adaptive-resolution; they directly allow various resolutions to be processed at training and inference time. This provides computational adaptivity but either sacrifices robustness or compatibility with mainstream layers, which hinders their use. In this work, we introduce Adaptive Resolution Residual Networks (ARRNs) to surpass this tradeoff. We construct ARRNs from Laplacian residuals, which serve as generic adaptive-resolution adapters for fixed-resolution layers. We use smoothing filters within Laplacian residuals to linearly separate input signals over a series of resolution steps. We can thereby skip Laplacian residuals to cast high-resolution ARRNs into low-resolution ARRNs that are computationally cheaper yet numerically identical over low-resolution signals. We guarantee this result when Laplacian residuals are implemented with perfect smoothing kernels. We complement this novel component with Laplacian dropout, which randomly omits Laplacian residuals during training. This regularizes for robustness to a distribution of lower resolutions. This also regularizes for numerical errors that may occur when Laplacian residuals are implemented with approximate smoothing kernels. We provide a solid grounding for the advantageous properties of ARRNs through a theoretical analysis based on neural operators, and empirically show that ARRNs embrace the challenge posed by diverse resolutions with computational adaptivity, robustness, and compatibility with mainstream layers.
2025-07-17
TMLR (accepté)
openreview.net
openreview.net
Pixel Perfect MegaMed: A Megapixel-Scale Vision-Language Foundation Model for Generating High Resolution Medical Images
Zahra TehraniNasab
Amar Kumar
Tal Arbel
Medical image synthesis presents unique challenges due to the inherent complexity and high-resolution details required in clinical contexts.… (voir plus) Traditional generative architectures such as Generative Adversarial Networks (GANs) or Variational Auto Encoder (VAEs) have shown great promise for high-resolution image generation but struggle with preserving fine-grained details that are key for accurate diagnosis. To address this issue, we introduce Pixel Perfect MegaMed, the first vision-language foundation model to synthesize images at resolutions of 1024x1024. Our method deploys a multi-scale transformer architecture designed specifically for ultra-high resolution medical image generation, enabling the preservation of both global anatomical context and local image-level details. By leveraging vision-language alignment techniques tailored to medical terminology and imaging modalities, Pixel Perfect MegaMed bridges the gap between textual descriptions and visual representations at unprecedented resolution levels. We apply our model to the CheXpert dataset and demonstrate its ability to generate clinically faithful chest X-rays from text prompts. Beyond visual quality, these high-resolution synthetic images prove valuable for downstream tasks such as classification, showing measurable performance gains when used for data augmentation, particularly in low-data regimes. Our code is accessible through the project website - https://tehraninasab.github.io/pixelperfect-megamed.
2025-07-17
ArXiv (prépublication)
arxiv.org
arxiv.org
Compositional Discrete Latent Code for High Fidelity, Productive Diffusion Models
Samuel Lavoie
Michael Noukhovitch
Aaron Courville
We argue that diffusion models'success in modeling complex distributions is, for the most part, coming from their input conditioning. This p… (voir plus)aper investigates the representation used to condition diffusion models from the perspective that ideal representations should improve sample fidelity, be easy to generate, and be compositional to allow out-of-training samples generation. We introduce Discrete Latent Code (DLC), an image representation derived from Simplicial Embeddings trained with a self-supervised learning objective. DLCs are sequences of discrete tokens, as opposed to the standard continuous image embeddings. They are easy to generate and their compositionality enables sampling of novel images beyond the training distribution. Diffusion models trained with DLCs have improved generation fidelity, establishing a new state-of-the-art for unconditional image generation on ImageNet. Additionally, we show that composing DLCs allows the image generator to produce out-of-distribution samples that coherently combine the semantics of images in diverse ways. Finally, we showcase how DLCs can enable text-to-image generation by leveraging large-scale pretrained language models. We efficiently finetune a text diffusion language model to generate DLCs that produce novel samples outside of the image generator training distribution.
2025-07-16
ArXiv (prépublication)
arxiv.org
arxiv.org
GitChameleon: Evaluating AI Code Generation Against Python Library Version Incompatibilities
Diganta Misra
Nizar Islah
Victor May
Brice Rauby
Zihan Wang
Justine Gehring
Antonio Orvieto
Muawiz Chaudhary
Eilif Benjamin Muller
Irina Rish
Samira Ebrahimi Kahou
Massimo Caccia
The rapid evolution of software libraries poses a considerable hurdle for code generation, necessitating continuous adaptation to frequent v… (voir plus)ersion updates while preserving backward compatibility. While existing code evolution benchmarks provide valuable insights, they typically lack execution-based evaluation for generating code compliant with specific library versions. To address this, we introduce GitChameleon, a novel, meticulously curated dataset comprising 328 Python code completion problems, each conditioned on specific library versions and accompanied by executable unit tests. GitChameleon rigorously evaluates the capacity of contemporary large language models (LLMs), LLM-powered agents, code assistants, and RAG systems to perform version-conditioned code generation that demonstrates functional accuracy through execution. Our extensive evaluations indicate that state-of-the-art systems encounter significant challenges with this task; enterprise models achieving baseline success rates in the 48-51\% range, underscoring the intricacy of the problem. By offering an execution-based benchmark emphasizing the dynamic nature of code libraries, GitChameleon enables a clearer understanding of this challenge and helps guide the development of more adaptable and dependable AI code generation methods. We make the dataset and evaluation code publicly available at https://github.com/mrcabbage972/GitChameleonBenchmark.
2025-07-16
ArXiv (prépublication)
arxiv.org
arxiv.org
GitChameleon: Evaluating AI Code Generation Against Python Library Version Incompatibilities
Diganta Misra
Nizar Islah
Victor May
Brice Rauby
Zihan Wang
Justine Gehring
Antonio Orvieto
Muawiz Chaudhary
Eilif Benjamin Muller
Irina Rish
Samira Ebrahimi Kahou
Massimo Caccia
The rapid evolution of software libraries poses a considerable hurdle for code generation, necessitating continuous adaptation to frequent v… (voir plus)ersion updates while preserving backward compatibility. While existing code evolution benchmarks provide valuable insights, they typically lack execution-based evaluation for generating code compliant with specific library versions. To address this, we introduce GitChameleon, a novel, meticulously curated dataset comprising 328 Python code completion problems, each conditioned on specific library versions and accompanied by executable unit tests. GitChameleon rigorously evaluates the capacity of contemporary large language models (LLMs), LLM-powered agents, code assistants, and RAG systems to perform version-conditioned code generation that demonstrates functional accuracy through execution. Our extensive evaluations indicate that state-of-the-art systems encounter significant challenges with this task; enterprise models achieving baseline success rates in the 48-51\% range, underscoring the intricacy of the problem. By offering an execution-based benchmark emphasizing the dynamic nature of code libraries, GitChameleon enables a clearer understanding of this challenge and helps guide the development of more adaptable and dependable AI code generation methods. We make the dataset and evaluation code publicly available at https://github.com/mrcabbage972/GitChameleonBenchmark.
2025-07-16
ArXiv (prépublication)
arxiv.org
arxiv.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… (voir plus)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.
2025-07-15
ArXiv (prépublication)
doi.org
arxiv.org
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… (voir plus)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.
2025-07-15
ArXiv (prépublication)
doi.org
arxiv.org
Torsional-GFN: a conditional conformation generator for small molecules
Alexandra Volokhova
Lena Nehale Ezzine
Piotr Gai'nski
Luca Scimeca
Emmanuel Bengio
Prudencio Tossou
Yoshua Bengio
Alex Hernandez-Garcia
Generating stable molecular conformations is crucial in several drug discovery applications, such as estimating the binding affinity of a mo… (voir plus)lecule to a target. Recently, generative machine learning methods have emerged as a promising, more efficient method than molecular dynamics for sampling of conformations from the Boltzmann distribution. In this paper, we introduce Torsional-GFN, a conditional GFlowNet specifically designed to sample conformations of molecules proportionally to their Boltzmann distribution, using only a reward function as training signal. Conditioned on a molecular graph and its local structure (bond lengths and angles), Torsional-GFN samples rotations of its torsion angles. Our results demonstrate that Torsional-GFN is able to sample conformations approximately proportional to the Boltzmann distribution for multiple molecules with a single model, and allows for zero-shot generalization to unseen bond lengths and angles coming from the MD simulations for such molecules. Our work presents a promising avenue for scaling the proposed approach to larger molecular systems, achieving zero-shot generalization to unseen molecules, and including the generation of the local structure into the GFlowNet model.
2025-07-15
ArXiv (prépublication)
arxiv.org
arxiv.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 iGenoMed Consortium Hailia NIDDK IBD Genetics Consortium
Hailiang Huang
Mark Daly
Daniel Taliun
Julie Hussin
Vincent Mooser
John D. Rioux
2025-07-14
medRxiv (prépublication)
doi.org
An Artificial Intelligence-Based Model to Predict Pregnancy After Intrauterine Insemination: A Retrospective Analysis of 9501 Cycles
Jaume Minano Masip
Camille Grysole
Penelope Borduas
Isaac-Jacques Kadoch
Simon Phillips
Doina Precup
Daniel Dufort
2025-07-12
Journal of Personalized Medicine (publié)
www.ncbi.nlm.nih.gov
An Artificial Intelligence-Based Model to Predict Pregnancy After Intrauterine Insemination: A Retrospective Analysis of 9501 Cycles.
J. Minano Masip
Camille Grysole
Penelope Borduas
I. Kadoch
Simon Phillips
Doina Precup
Daniel Dufort
Background/Objectives: Intrauterine insemination (IUI) is a common first-line approach in the treatment of numerous infertile couples, espec… (voir plus)ially in cases of unexplained infertility. Its relatively low success rate, however, could benefit from the development of AI-based support tools to predict its outcome, thus helping the clinical management of patients undergoing IUI cycles. Our objective was to develop a robust and accurate machine learning model that predicts pregnancy outcomes following IUI. Methods: A retrospective, observational, and single-center study was conducted. In total, 3535 couples (aged 18-43 years) that underwent IUI between January 2011 and December 2015 were recruited. Twenty-one clinical and laboratory parameters of 9501 IUI cycles were used to train different machine learning algorithms. Accuracy of pregnancy outcome was evaluated by an area under the curve (AUC) analysis. Results: The linear SVM outperformed AdaBoost, Kernel SVM, Random Forest, Extreme Forest, Bagging, and Voting classifiers. Pre-wash sperm concentration, the ovarian stimulation protocol, cycle length, and maternal age were strong predictors of a positive pregnancy test following IUI (AUC = 0.78). Paternal age was found to be the worst predictor. Conclusions: Our Linear SVM model predicts a positive pregnancy outcome following IUI. Although this model shows value for the clinical management of infertile patients and informed decision-making by the patients, further validation using independent datasets is required prior to clinical implementation.
2025-07-12
Journal of Personalized Medicine (publié)
doi.org
An Artificial Intelligence-Based Model to Predict Pregnancy After Intrauterine Insemination: A Retrospective Analysis of 9501 Cycles
Jaume Minano Masip
Camille Grysole
Penelope Borduas
Isaac-Jacques Kadoch
Simon Phillips
Doina Precup
Daniel Dufort
2025-07-12
Journal of Personalized Medicine (publié)
doi.org