Publications

Task-optimized neural networks reveal distinct contributions of specialized and broader visual learning to neural representations of face familiarity
How neural activity across the ventral visual hierarchy supports face recognition is an open question. A long-standing debate asks whether f… (see more)ace processing, particularly in fusiform cortex, relies on face-specific computations or representations shared with broader visual recognition. Here we combine source-resolved magnetoencephalography (MEG) with task-optimized neural networks as controlled computational models of visual experience. Rather than manipulating long-term expertise in human observers, we systematically vary learning objective on the model side—what the networks are trained to recognize—while holding architecture and loss function constant within model comparisons. We then ask which learned representational geometries best align with neural responses, where and when. We measured millisecond-resolved brain–model alignment across V1, lateral occipital cortex (LOC) and fusiform cortex while participants viewed familiar, unfamiliar and scrambled faces. The same stimuli were presented to seven CNN architectures trained for face-identity recognition (FR), object-category recognition (OR) or object categorization including a face category (Dual), alongside untrained controls. Familiarity produced a stage-dependent dissociation: in LOC, familiar faces showed earlier brain–model alignment than unfamiliar faces in the M170 range, an effect most consistent in models trained for face-recognition, whereas broader objectives produced more variable, architecture-dependent peak alignment latencies. In fusiform cortex they showed stronger alignment around the M200 range. This fusiform advantage was not uniquely associated with face-recognition training: dual- and object-trained models showed greater fusiform correspondence than face-trained models. Together, these findings support stage-dependent specialization, with training for face-identity recognition constraining intermediate-stage timing while later fusiform representations remain compatible with representational structure acquired through broader visual computations. Significance Statement Recognizing a familiar face feels immediate, yet it remains unclear which stages of visual processing are specifically shaped by learning individual identities. We combine millisecond-resolved MEG with task-optimized neural networks used as controllable models of visual experience, manipulating learning objective on the model side—that is, what the networks are trained to recognize and tracking when and where the resulting representations align with human brain activity. Familiarity advances representational alignment in lateral occipital cortex but strengthens later alignment in fusiform cortex. The earlier LOC effect was most consistent across architectures after face-identity recognition training, whereas the later fusiform effect also emerged under broader visual learning objectives. These findings support a stage-dependent account of face recognition that moves beyond a simple face-specific versus broader-visual-processing dichotomy.
From Connectivity to Rewards: Dense Reward Learning with Directed State Graphs
The integration of graphs with Goal-Conditioned Hierarchical Reinforcement Learning (GCHRL) has received increasing attention, as graphs nat… (see more)urally encode task hierarchies for effective subgoal sampling. However, existing methods often overlook intrinsic connectivity information, failing to fully leverage the underlying topology for efficient learning. Most graph-based GCHRL methods use the graph as a stochastic sampling tool rather than as an environmental model that encodes connectivity and state-accessibility information. This limitation is particularly acute in quasimetric environments, where the inherent asymmetry of state transitions poses a fundamental challenge to stable policy learning and robust path planning. In this paper, we address these problems by introducing a state connectivity model designed to predict pairwise state connectivity strength in asymmetric environments. We transform these connectivity strengths into scalar auxiliary dense rewards, providing continuous guidance across multiple hierarchical levels. We demonstrate that our proposed framework, Graph-Guided Quasimetric Dense Reward (G2QDR), can theoretically be integrated into any existing GCHRL architecture, and the state connectivity model is efficiently implemented via a neural network trained on a directed state graph generated during exploration. Empirical results across a wide range of sparse reward environments indicate that, in general, G2QDR can enhance the performance of baseline GCHRL approaches with acceptable computational overhead.
Gaussian Process–Based Bayesian Optimization of Lower-Limb PNS–TMS Interstimulus Intervals in Adults and Children: A Proof-of-Concept Toward a Personalized Framework
Mohammad Reza Effatparvar
Mathilde Tardif
Mickaël Begon
Yosra Cherni
Heterogeneity of brain dynamics in genetic and psychiatric conditions
Adrien E. E. Dubois
Sarah Lippé
Charles-Olivier Martin
Inga Sophia Knoth
Valerie Fontaine
Anne-Marie Bélanger
Pascale Abadie
Melissa T. Carter
Mélanie Couture
Mayada Elsabbagh
Alan Evans
Carl Ernst
Baudouin Forgeot d’Arc
Ridha Joober
Guy Rouleau
Julie Scorah
Christine Tardif
Ma'n H Zawati
Grace Westerkamp
Ernest V. Pedapati … (see 11 more)
Craig Erickson
Borja Rodríguez‐Herreros
Nadia Chabane
Kenza Latreche
Marie Schaer
Aline Lefebvre
Richard Delorme
Sara Jane Webb
James C. McPartland
Sébastien Jacquemont
Abstract Whether the heterogeneity of psychiatric conditions converges on shared neurophysiological alterations or translates into distinct … (see more)signatures remains unclear. We assembled high-density electroencephalogram (hd-EEG) resting-state recordings from 4,812 individuals aged 5 months to 66 years across 11 psychiatric conditions, a broad spectrum of rare genetic variants, and typically developing (TD) individuals. We established normative developmental trajectories of source-space EEG across spectral organization, connectivity, and signal complexity. Psychiatric conditions showed small deviations, revealing a shared transdiagnostic profile. In contrast, single rare variants showed substantially larger, distinct and sometimes mirror-opposite signatures that collapsed toward the psychiatric profile when pooled. Autism Spectrum Disorder showed some of the smallest group-level effects yet the largest individual deviations, indicating substantial but directionally inconsistent alterations. EEG deviations followed a cortical gradient, with larger effects in sensorimotor regions. We demonstrate that sample sizes in the hundreds are required for robust associations with psychiatric diagnoses. This interactive open resource provides normative scores to benchmark future results.
Impact of dimensionality reduction on machine learning-based crop health prediction
Zahia Aouabed
Stéphane Samson
Elyes Lounissi
Ousmane Assani Amate
Étienne Lord
Abstract Accurately predicting fungal disease dynamics poses a major challenge for data-driven sustainable agriculture. This study evaluates… (see more) the impact of dimensionality reduction (DR) on the predictive performance of classical machine learning (ML) and deep learning (DL) models for classification (fungal disease occurrence) and regression (fungal disease severity) tasks using multidimensional meteorological and phytosanitary data collected from carrot, lettuce, and onion farms in southern Quebec (Canada). We systematically benchmark traditional ML models - Decision Tree (DT), Random Forest (RF), and k-Nearest Neighbours (k-NN), a basic non-temporal deep learner - Multilayer Perceptron (MLP), recurrent DL models - Long Short-Term Memory (LSTM) and Gated Recurrent Unit (GRU), as well as state-of-the-art Mamba state-space model (SSM) and pretrained tabular foundation model TabPFN, each of them combined with linear (PCA and MDS), nonlinear (KernelPCA and Isomap), and domain-informed (BOTCAST) DR methods. TabPFN provides the best overall performance in classification and RF in regression, while LSTM and GRU networks rank among top-performing models for both tasks. In classification, DR methods combine well with TabPFN and the recurrent approaches, with the BOTCAST + TabPFN, PCA + TabPFN, and Isomap + GRU pairings, yielding the best overall classification results for carrot, lettuce, and onion data, respectively. In regression, nonlinear DR methods perform best when coupled with ensemble learners (i.e. the best overall results were obtained by the KernelPCA + RF pairing for both lettuce and onion data), while the domain-informed BOTCAST embedding yields excellent results when combined with TabPFN (i.e. the best overall result was obtained by the BOTCAST + TabPFN pairing for carrot data). Overall, the success of predictions largely depends on a good alignment of the selected dimensionality reduction strategy with the downstream machine learning or deep learning model. Our results provide practical guidance for decision-support systems aiming at forecasting fungal disease occurrence and severity in agricultural plants.
A Joint 2D-3D Statistical Shape Model for Orthopedic Reconstruction
Florence Dell’Aniello Picard
Frédéric Lavoie
Three-dimensional femoral reconstruction from radiographs supports surgical planning, implant sizing, and post-operative follow-up, but rema… (see more)ins ill-posed as X-ray projections discard depth information. Existing methods often incorporate a 3D statistical shape model (SSM) as a shape prior to guide reconstructions toward anatomically plausible shapes, relying on iterative 3D-to-2D projection matching. Yet, these approaches are computationally expensive and constrain their SSM to a single dimensionality, leaving the statistical relationship between 2D observations and 3D geometry largely unexploited and unexplored. We instead propose a joint 2D-3D SSM that explicitly captures the co-variation between 2D and 3D segmentations in a shared latent space. During training, 2D and 3D segmentations are registered to a common 3D template and its corresponding 2D projections, and the resulting stationary velocity fields are jointly decomposed using principal component analysis (PCA). This joint modeling allows the 2D-to-3D mapping to be learned directly from data rather than computing correspondences at inference time. For unseen subjects, the 3D shape is recovered directly by lifting the 2D latent coordinates to the 3D PCA subspace, thereby eliminating the need for iterative 3D-to-2D projection. Experiments on NMDID demonstrate that the proposed joint 2D-3D SSM outperforms a widely-used 3D-only SSM baseline while achieving inference approximately 4 times faster, at under 3 seconds per subject. The code is available at: https://github.com/florence-dellaniello-picard/joint2d3d-ssm.
Longitudinal tracking of multiple sclerosis lesions in the spinal cord: A validation study
Pierre-Louis Benveniste
Julian McGinnis
Shannon Kolind
Larry D. Lynd
Sarah A. Morrow
Jiwon Oh
Alexandre Prat
Alice Schabas
Penelope Smyth
Roger Tam
Anthony Traboulsee
Mark Mühlau
Longitudinal characterization of multiple sclerosis (MS) lesions remains constrained by the lack of frameworks capable of establishing consi… (see more)stent instance-level correspondences across time. Conventional segmentation approaches produce semantic lesion masks at each visit and therefore fail to capture the complex instance temporal patterns associated with lesion appearance, disappearance, splitting, or merging. This study presents a comparative evaluation of five strategies for automated tracking of spinal cord MS lesions in longitudinal MRI data from a multi-site cohort. The investigated strategies rely either on deformable registration or on a spinal anatomical reference system, and encompass overlap-based matching, coordinate-based Hungarian algorithm, gradient-boosted classification, and Siamese model classification. Tracking accuracy is quantified using instance-level true positives, false positives, and false negatives, allowing to assess the presence of one-to-many and many-to-one associations. Results show best performance for the registration-based overlap method. This study provides the first systematic analysis of lesion-instance correspondence in the spinal cord and outlines the strengths and limitations of registration-based and registration-free paradigms for longitudinal MS assessment. The code is available at http://github.com/ivadomed/longitudinal-sc-ms-lesion-tracking .
A Profit-Driven Simulation framework for real-time evaluation of toxicity detection models in social media
Arezo Bodaghi
Benjamin C. M. Fung
Jonathan Shahen
Ketra A. Schmitt
SnowGalileo: A Pre-trained Earth Observation Transformer for Daily, 100 m Fractional Snow Cover Mapping
Donovan J. M. Allum
Sebastian Roessler
Samip Shrestha
Zhibang Lv
J Truckenbrodt
Gabriele Schwaizer
Thomas Nägler
John W. Pomeroy
Christopher B. Marsh
Benoît Montpetit
Tobias Jonas
A.J. Dietz
Celia A. Baumhoer
Abstract. Mountain snow is an important component of the cryosphere that directly affects downstream livelihoods. Accurate monitoring of mou… (see more)ntain snow is crucial, yet remains challenging due to complex topography and frequent cloud cover. Although combining data from multiple Earth Observation (EO) satellites can improve spatial and temporal coverage, extracting Fractional Snow Cover (FSC) from sensors with different spatial and temporal resolutions remains difficult. AI-based Earth foundation models can process diverse sensor inputs and have been successfully applied to various remote sensing tasks; however, they often lack snow-specific design considerations. This paper presents SnowGalileo, a pre-trained transformer model designed to integrate EO data to map snow-covered areas. We evaluated SnowGalileo's potential for generating daily, gap-free FSC maps at 100m resolution in mountainous regions. SnowGalileo combines one week of satellite time-series data from multiple sensors, including Sentinel-1, Sentinel-2, Landsat, Sentinel-3, MODIS, and VIIRS, with topographic, land cover, and meteorological information to predict FSC for a given day. The model was pre-trained using masked autoencoding and fine-tuned using labeled data from various mountain ranges across the Northern Hemisphere. In addition to clear-sky conditions, SnowGalileo is evaluated under a wider variety of conditions than was previously possible, including cloud cover and lack of high-resolution (~10–30 m) satellite imagery. For the Canadian Rockies and the Swiss Alps, respectively, SnowGalileo achieves RMSEs of 0.099 and 0.124 on clear days, 0.144 and 0.209 on cloudy days, 0.185 and 0.262 on days without high-resolution imagery, and 0.200 and 0.299 on cloudy days without high-resolution imagery. SnowGalileo also consistently outperforms random forests, support vector regressors, and multi-layer perceptrons. While the current product is a proof of concept that has undergone limited validation across geographic regions, operates on 1km × 1km tiles rather than full maps, and has restricted capabilities in challenging conditions, this approach could ultimately enable the continuous, gap-free operational generation of FSC time series for mountain regions worldwide.
Evaluating the Performance of Traditional Pharmacoepidemiologic and Machine Learning Models to Predict Pregnancies at Risk of Major Congenital Malformations
Gabra Nohmie
Marc J. Lanovaz
Odile Sheehy
Cristina Longo
Robert W. Platt
Christine Damase‐Michel
Anick Bérard
BACKGROUND: With approximately 50% of pregnancies being unplanned, there is an unintended exposure to potential feto-toxic drugs that may ca… (see more)use major congenital malformations (MCM). This study aims to compare the predictive performance between traditional pharmacoepidemiologic (PE) and machine learning (ML) models. METHODS: We conducted a cohort study within the Quebec Pregnancy Cohort, including all pregnancies covered by Quebec's prescription drug insurance program and their children from 01/1998 to 12/2015. Medication exposures, comorbidities, and women's characteristics 12 months before pregnancy and during the first trimester were considered. Robust Poisson models were used to obtain adjusted risk ratios (aRR) and 95% confidence intervals (CI) of predictors. Logistic regression, robust Poisson, K-Nearest Neighbors, Random Forest, XGBoost, Naïve bayes, Multilayer Perceptron, and Support Vector Machine were developed to predict pregnancies at risk of MCM. Sensitivity, specificity, PPV, NPV, accuracy, ROC-AUCs, PR-AUCs, and F1-score were used to evaluate the performance of predictive models. RESULTS: We analyzed 213,744 pregnancies, finding a 9.7% prevalence of MCM. Logistic regression had the highest discriminative power across models at predicting MCM, with a ROC-AUC of 53.3% and the highest sensitivity (41.5%) and F1-score (46.6%). KNN had the highest specificity (97.9%) but the lowest sensitivity (2.3%). Robust Poisson performed similarly to logistic regression, with the highest accuracy (52.3%). Robust Poisson performed slightly better than logistic regression at classifying organ-specific malformations. All models showed poor overall predictive performance. Results were robust across sensitivity analyses. CONCLUSION: There is insufficient evidence for the superiority of ML over traditional pharmacoepidemiologic modeling in predicting MCM.
FrogNano: Training a 4B Coding Agent via Online Task Synthesis
Minseon Kim
Zhengyan Shi
Christopher Cui
Roger Creus Castanyer
Isadora White
Jonathan Light
Jeonghye Kim
Matheus Pereira
Darya Moldavskaya
Chinmay Singh
Fabio Vera
Baolin Peng
Xingdi Yuan
We present FrogNano, a 4B coding agent designed to tackle software engineering (SWE) tasks efficiently and effectively, even under resource-… (see more)constrained environments. It is post-trained exclusively via RL on around 1,500 SWE environments with synthetic tasks. A key ingredient for improving performance is an online task synthesis pipeline that creates tasks calibrated to the frontier of learnability for the current checkpoint. This report provides evidence that competitive small coding agents can be trained with synthetic tasks alone, without traditional distillation from larger models, and that generating tasks at the learnability frontier of the current agent is important. We report details on the training methodology, evaluations across diverse environments, and in-depth analyses, serving as a foundation for our ongoing exploration of lightweight yet capable coding agents that can run on minimal hardware.
ATAD2 is a novel regulator of myogenesis and autophagy in skeletal muscles
Sami Sedraoui
Alaa Moamer
Tomer Jordi Chaffer
Jean-Philippe Leduc-Gaudet
Dominique Mayaki
Hanfen Shi
Ryann Lang
Minna Woo
Yumin Zheng
Marco Sandri
Gilles Gouspillou
Sabah N.A. Hussain
The nuclear protein ATAD2 (ATPase family AAA domain containing 2) is a known positive regulator of cell proliferation in various cancer type… (see more)s. The expression and functional roles of ATAD2 in skeletal muscle cells are unknown. In this study, we used transient and stable knockdown approaches using siRNA and shRNA oligos to evaluate how ATAD2 regulates proliferation, migration, differentiation, and autophagy in C2C12 myoblasts. Atad2 knockdown (KD) significantly increased myoblast proliferation rate, S-phase entry, overall cell viability, and early differentiation into myotubes. However, Atad2 KD also elicited myotube atrophy and upregulation of ubiquitin E3 ligases Atrogin-1 and MuRF1. Basal autophagy was inhibited in Atad2 KD cells as a result of downregulation of autophagy-related genes ( Lc3b , Gabarapl1 , Atg5 , and Atg7 ). Immunoblotting and immunostaining revealed significant decrease in LC3B protein levels and the number of LC3B punctae per cell with Atad2 KD, respectively. LAMP1 staining confirmed the presence of enlarged lysosomes in Atad2 KD cells. Additionally, genes involved in lysosome function and integrity including Rab7 , Rab29 , Rab32 , Nrbf2 , and Cathepsin L were downregulated in Atad2 KD cells. Collectively, these results indicate that ATAD2 is a critical regulator of muscle cell proliferation, differentiation, autophagy and lysosomal integrity.