Publications

Predictive Performance Precision Analysis in Medicine: Identification of low-confidence predictions at patient and profile levels (MED3pa I)
Olivier Lefebvre
Félix Camirand Lemyre
Jean-François Ethier
Lyna Hiba Chikouche
Ludmila Amriou
Dan Poenaru
Martin Vallières
Artificial Intelligence models are increasingly used in healthcare, yet global performance metrics can mask variations in reliability across… (see more) individual patients or subgroups with shared attributes, called patient profiles . This study introduces MED3pa, a method that identifies when models are less reliable, allowing clinicians to better assess model limitations. We propose a framework that estimates predictive confidence using three combined approaches: Individualized (IPC), Aggregated (APC), and Mixed Predictive Confidence (MPC). IPC estimates confidence for each patient, APC assesses it across profiles, and MPC combines both. We evaluate our method on four datasets: one simulated, two public, and one private clinical dataset. Metrics by Declaration Rate (MDR) curves show how performance changes when retaining only the most confident predictions, while interpretable decision trees reveal profiles with higher or lower model confidence. We demonstrate our method in internal, temporal, and external validation settings, as well as through a clinical example. In internal validation, limiting predictions to the 93% most confident cases improved sensitivity by 14.3% and the AUC by 5.1%. In the clinical example, MED3pa identified a patient profile with high misclassification risk, demonstrating its potential for safer deployment. By identifying low-confidence predictions, our framework improves model reliability in clinical settings. It can be integrated into decision support systems to help clinicians make more informed decisions. Confidence thresholds help balance model performance with the proportion of patients for whom predictions are considered reliable. Better leveraging confidence in model predictions could improve reliability and trustworthiness, supporting safer and more effective use in healthcare.
2025-08-25
medRxiv (preprint)
doi.org
Source-free Domain Adaptation Requires Penalized Diversity
Laya Rafiee Sevyeri
Ivaxi Sheth
Farhood Farahnak
Alexandre See
Samira Ebrahimi Kahou
Thomas Fevens
Mohammad Havaei
While neural networks are capable of achieving human-like performance in many tasks such as image classification, the impressive performance… (see more) of each model is limited to its own dataset. Source-free domain adaptation (SFDA) was introduced to address knowledge transfer between different domains in the absence of source data, thus, increasing data privacy. Diversity in representation space can be vital to a model`s adaptability in varied and difficult domains. In unsupervised SFDA, the diversity is limited to learning a single hypothesis on the source or learning multiple hypotheses with a shared feature extractor. Motivated by the improved predictive performance of ensembles, we propose a novel unsupervised SFDA algorithm that promotes representational diversity through the use of separate feature extractors with Distinct Backbone Architectures (DBA). Although diversity in feature space is increased, the unconstrained mutual information (MI) maximization may potentially introduce amplification of weak hypotheses. Thus we introduce the Weak Hypothesis Penalization (WHP) regularizer as a mitigation strategy. Our work proposes Penalized Diversity (PD) where the synergy of DBA and WHP is applied to unsupervised source-free domain adaptation for covariate shift. In addition, PD is augmented with a weighted MI maximization objective for label distribution shift. Empirical results on natural, synthetic, and medical domains demonstrate the effectiveness of PD under different distributional shifts.
2025-08-25
Machine Learning (published)
doi.org
arxiv.org
Posttraumatic Growth in Intensive Care Unit Health Care Professionals After COVID-19
Elie Azoulay
Laurent Argaud
Vincent Labbé
Guillaume Dumas
Fabrice Bruneel
Mercé Jourdain
Christophe Guitton
Amelie Seguin
Samir Jaber
David Schnell
Isabelle Vinatier
Fanny Ardisson
Michel Ramakers
Antoine Herault
Olivier Lesieur
Alain Cariou
Antoine Vieillard-Baron
Olivier Guisset
Frédéric Pochard
Michael Darmon … (see 1 more)
Nancy Kentish-Barnes
2025-08-24
JAMA Network Open (published)
doi.org
Uncovering executive function profiles within interindividual variability: A data driven clustering exploration of design fluency in school-aged children
Myriam Sahraoui
Karim Jerbi CoCo Lab
Vanessa Hadid
Bruno Gauthier
2025-08-23
bioRxiv (preprint)
doi.org
Low-dimensional embeddings of high-dimensional data
Cyril de Bodt
Alex Diaz-Papkovich
Michael Bleher
Kerstin Bunte
Corinna Coupette
Sebastian Damrich
Enrique Fita Sanmartin
Fred Hamprecht
EmHoke-'Agnes Horv'at
Dhruv Kohli
Smita Krishnaswamy
John A. Lee 0001
Boudewijn P. F. Lelieveldt
Leland McInnes
Ian T. Nabney
Maximilian Noichl
Pavlin G. Polivcar
Bastian Rieck
Guy Wolf
Gal Mishne … (see 1 more)
Dmitry Kobak
Large collections of high-dimensional data have become nearly ubiquitous across many academic fields and application domains, ranging from b… (see more)iology to the humanities. Since working directly with high-dimensional data poses challenges, the demand for algorithms that create low-dimensional representations, or embeddings, for data visualization, exploration, and analysis is now greater than ever. In recent years, numerous embedding algorithms have been developed, and their usage has become widespread in research and industry. This surge of interest has resulted in a large and fragmented research field that faces technical challenges alongside fundamental debates, and it has left practitioners without clear guidance on how to effectively employ existing methods. Aiming to increase coherence and facilitate future work, in this review we provide a detailed and critical overview of recent developments, derive a list of best practices for creating and using low-dimensional embeddings, evaluate popular approaches on a variety of datasets, and discuss the remaining challenges and open problems in the field.
2025-08-20
ArXiv (preprint)
doi.org
arxiv.org
On the Challenges and Opportunities in Generative AI
Laura Manduchi
Clara Meister
Kushagra Pandey
Robert Bamler
Ryan Cotterell
Sina Däubener
Sophie Fellenz
Asja Fischer
Thomas Gärtner
Matthias Kirchler
Marius Kloft
Yingzhen Li
Christoph Lippert
Gerard de Melo
Eric Nalisnick
Björn Ommer
Rajesh Ranganath
Maja Rudolph
Karen Ullrich
Guy Van den Broeck … (see 6 more)
Julia E Vogt
Yixin Wang
Florian Wenzel
Frank N. Wood
Stephan Mandt
Vincent Fortuin
2025-08-20
TMLR (accepted)
doi.org
openreview.net
Robustness of Neural Ratio and Posterior Estimators to Distributional Shifts for Population-Level Dark Matter Analysis in Strong Gravitational Lensing
Andreas Filipp
Yashar Hezaveh
Laurence Perreault-Levasseur
We investigate the robustness of Neural Ratio Estimators (NREs) and Neural Posterior Estimators (NPEs) to distributional shifts in the conte… (see more)xt of measuring the abundance of dark matter subhalos using strong gravitational lensing data. While these data-driven inference frameworks can be accurate on test data from the same distribution as the training sets, in real applications, it is expected that simulated training data and true observational data will differ in their distributions. We explore the behavior of a trained NRE and trained sequential NPEs to estimate the population-level parameters of dark matter subhalos from a large sample of images of strongly lensed galaxies with test data presenting distributional shifts within and beyond the bounds of the training distribution in the nuisance parameters (e.g., the background source morphology). While our results show that NREs and NPEs perform well when tested perfectly in distribution, they exhibit significant biases when confronted with slight deviations from the examples seen in the training distribution. This indicates the necessity for caution when applying NREs and NPEs to real astrophysical data, where high-dimensional underlying distributions are not perfectly known.
2025-08-19
The Astrophysical Journal (published)
doi.org
arxiv.org
Causal single-cell RNA-seq simulation, in silico perturbation, and GRN inference benchmarking using GRouNdGAN-Toolkit
Yazdan Zinati
Amin Emad
2025-08-18
bioRxiv (preprint)
doi.org
RadiSeq: a single- and bulk-cell whole-genome DNA sequencing simulator for radiation-damaged cell models
Felix Mathew
Luc Galarneau
J. Kildea
Objective To build and validate a simulation framework to perform single-cell and bulk-cell whole genome sequencing simulation of radiation-… (see more)exposed Monte Carlo cell models to assist radiation genomics studies. Approach Sequencing the genomes of radiation-damaged cells can provide useful insight into radiation action for radiobiology research. However, carrying out post-irradiation sequencing experiments can often be challenging, expensive, and time-consuming. Although computational simulations have the potential to provide solutions to these experimental challenges, and aid in designing optimal experiments, the absence of tools currently limits such application. Monte Carlo toolkits exist to simulate radiation exposures of cell models but there are no tools to simulate single- and bulk-cell sequencing of cell models containing radiation-damaged DNA. Therefore, we aimed to develop a Monte Carlo simulation framework to address this gap by designing a tool capable of simulating sequencing processes for radiation-damaged cells. Main Results We developed RadiSeq – a multi-threaded whole-genome DNA sequencing simulator written in C++. RadiSeq can be used to simulate Illumina sequencing of radiation-damaged cell models produced by Monte Carlo simulations. RadiSeq has been validated through comparative analysis, where simulated data were matched against experimentally obtained data, demonstrating reasonable agreement between the two. Additionally, it comes with numerous features designed to closely resemble actual whole-genome sequencing. RadiSeq is also highly customizable with a single input parameter file. Significance RadiSeq enables the research community to perform complex simulations of radiation-exposed DNA sequencing, supporting the optimization, planning, and validation of costly and time-intensive radiation biology experiments. This framework provides a powerful tool for advancing radiation genomics research.
2025-08-18
Physics in Medicine & Biology (published)
doi.org
Field-Level Comparison and Robustness Analysis of Cosmological N-Body Simulations
Adrian E. Bayer
Francisco Villaescusa-navarro
Sammy Nasser Sharief
Romain Teyssier
Lehman H. Garrison
Laurence Perreault-Levasseur
Greg L. Bryan
Marco Gatti
E. Visbal
2025-08-17
The Astrophysical Journal (published)
doi.org
arxiv.org
Pharmaco-nutraceutical improvement of the response to obeticholic acid with omega-3 polyunsaturated fatty acids
Audrey-Anne Lavoie
Ariane Thérien
Anisia Silva
Emanuel Paré
Anna Ciešlak
William Gagnon
Clémence Desjardins
Mélanie Verreault
Jocelyn Trottier
Marie-Claude Vohl
Jean-Philippe Drouin-Chartier
J. Corbeil
Alexandre Caron
Olivier Barbier
2025-08-17
Biochemical Journal (published)
doi.org
Proceedings of the OHBM Open Science Room 2024
Selma Lugtmeijer
Ju-Chi Yu
Xiangzhen Kong
Lune P Bellec
Janine D. Bijsterbosch
Elizabeth DuPré
Oscar Estéban
Ibrahim Faye
Seok-Jun Hong
Chuan-Peng Hu
Shella Keilholz
Chun-Chia Kung
Hyeong Hun Lee
Daniel Margulies
Cyril Pernet
Franco Pestilli
Jean-Baptiste Poline
Pradeep R. Raamana
Francesco Santini
Won Mok Shim … (see 30 more)
Paul M. Thompson
Chao-Gan Yan
Niall W. Duncan
Nikhil Bhagwat
Peter Fox
Ana Van Gulick
David N. Kennedy
Gorana Pobric
Neda Sadeghi
Nick Souter
Sandeep Panta
Isabelle van der Velpen
Tonya White
Sina Mansour L.
Qing Wang
Povilas Karvelis
Anibal S. Heinsfeld
Yu-Fang Yang
Hong Ji Kim
Nur Shahidatul Nabila Binti Ibrahim
Stefano Moia
Wei Zhang
Jessica Haigh
Rose-Marie Kouwenhoven
Terra Hyun Lee
Hurshitha Vasudevan
Yuping Yang
Subapriya Suppiah
Yi-Ju Lee
Nils Muhlert
2025-08-17
Aperture Neuro (published)
doi.org