Publications

Species Loss Scenarios Identify Canada's Northern Ecosystems as Disproportionately Vulnerable
Isaac Eckert
Dominique Caron
LLMs Can't Play Hangman: On the Necessity of a Private Working Memory for Language Agents
AfriqueLLM: How Data Mixing and Model Architecture Impact Continued Pre-training for African Languages
Hao Yu
Tianyi Xu
Michael A. Hedderich
Wassim Hamidouche
Syed Waqas Zamir
BayesAdapter: enhanced uncertainty estimation in CLIP few-shot adaptation
Pablo Morales-Álvarez
Stergios Christodoulidis
Maria Vakalopoulou
Jose Dolz
The emergence of large pre-trained vision-language models (VLMs) represents a paradigm shift in machine learning, with unprecedented results… (see more) in a broad span of visual recognition tasks. CLIP, one of the most popular VLMs, has exhibited remarkable zero-shot and transfer learning capabilities in classification. To transfer CLIP to downstream tasks, adapters constitute a parameter-efficient approach that avoids backpropagation through the large model (unlike related prompt learning methods). However, CLIP adapters have been developed to target discriminative performance, and the quality of their uncertainty estimates has been overlooked. In this work we show that the discriminative performance of state-of-the-art CLIP adapters does not always correlate with their uncertainty estimation capabilities, which are essential for a safe deployment in real-world scenarios. We also demonstrate that one of such adapters is obtained through MAP inference from a more general probabilistic framework. Based on this observation we introduce BayesAdapter, which leverages Bayesian inference to estimate a full probability distribution instead of a single point, better capturing the variability inherent in the parameter space. In a comprehensive empirical evaluation we show that our approach obtains high quality uncertainty estimates in the predictions, standing out in calibration and selective classification. Our code will be publicly available upon acceptance of the paper.
Sex Classification Based on the Functional Connectivity Patterns of the Language Network: A Resting State <scp>fMRI</scp> Study
Xanthy Lajoie
C. DeRoy
C. Bedetti
Bérengère Houzé
N. Clarke
Sébastien Hétu
M.‐È. Picard
S. M. Brambati
ABSTRACT Research on sex differences in the brain is essential for a better understanding of how the brain develops and ages, and how neurol… (see more)ogical and psychiatric conditions can impact men and women differently. While numerous studies have focused on sex differences in brain structures, few have examined the characteristics of functional networks, particularly the language network. Although previous research suggests similar overall language performance across sexes, differences may still exist in the brain networks that underlie language processing. In addition, prior studies on sex differences in language have predominantly relied on task‐based fMRI, which may fail to capture subtle differences in underlying functional activity. In this study, we applied a machine learning approach to classify participants' sex based on resting‐state functional connectivity patterns of the language network in healthy young adults (270 men and 288 women; age: 22–36 years), and to identify the most predictive functional connectivity features. The classifier achieved 91.3% accuracy, with key discriminant features anchored to the left opercular part of the inferior frontal gyrus, the left planum temporale, and the left anterior middle temporal gyrus. These regions show distinctive connectivity patterns with heteromodal association cortices, including the occipital poles, angular gyrus, posterior cingulate gyrus, and intraparietal sulcus. Although there was an overlap between men and women, men displayed stronger functional connectivity values in these regions. These findings highlight sex‐related differences in functional connectivity patterns of the language network at rest, underscoring the importance of considering sex as a variable in future research on language and brain function.
Afri-MCQA: Multimodal Cultural Question Answering for African Languages
Atnafu Lambebo Tonja
Srija Anand
Emilio Villa Cueva
Israel Abebe Azime
Jesujoba Oluwadara Alabi
Muhidin A. Mohamed
Debela Desalegn Yadeta
Negasi Haile Abadi
Abigail Oppong
Nnaemeka Casmir Obiefuna
Idris Abdulmumin
Naome Etori
Eric Peter Wairagala
Kanda Patrick Tshinu
Imanigirimbabazi Emmanuel
Gabofetswe Malema
Alham Fikri Aji
Thamar Solorio
Africa is home to over one-third of the world's languages, yet remains underrepresented in AI research. We introduce Afri-MCQA, the first Mu… (see more)ltilingual Cultural Question-Answering benchmark covering 7.5k Q&A pairs across 15 African languages from 12 countries. The benchmark offers parallel English-African language Q&A pairs across text and speech modalities and was entirely created by native speakers. Benchmarking large language models (LLMs) on Afri-MCQA shows that open-weight models perform poorly across evaluated cultures, with near-zero accuracy on open-ended VQA when queried in native language or speech. To evaluate linguistic competence, we include control experiments meant to assess this specific aspect separate from cultural knowledge, and we observe significant performance gaps between native languages and English for both text and speech. These findings underscore the need for speech-first approaches, culturally grounded pretraining, and cross-lingual cultural transfer. To support more inclusive multimodal AI development in African languages, we release our Afri-MCQA under academic license or CC BY-NC 4.0 on HuggingFace (https://huggingface.co/datasets/Atnafu/Afri-MCQA)
Dissecting and steering cell dynamics using spatially-informed RNA velocity with veloAgent
RNA velocity enables inference of cell state transitions from single-cell transcriptomics by modeling transcriptional dynamics from spliced … (see more)and unspliced mRNA. However, existing methods overlook spatial context and struggle to scale to large datasets, limiting insights into tissue organization and dynamic processes. We introduce veloAgent, a deep generative and agent-based framework that estimates gene- and cell-specific transcriptional kinetics while integrating spatial information through agent-based simulations of local microenvironments. By leveraging both molecular and spatial cues, veloAgent improves velocity accuracy and achieves sublinear memory scaling, enabling efficient analysis of large and multi-batch spatial datasets. A distinctive feature of veloAgent is its in silico perturbation module, which allows targeted manipulation of spatial velocity vectors to simulate regulatory interventions and predict their impact on cell fate dynamics. These capabilities position veloAgent as a scalable and versatile framework for dissecting spatially resolved cellular dynamics and guiding cell fate manipulation across diverse biological processes.
Division Asymmetry Drives Cell Size Variability in Budding Yeast
Felix Proulx-Giraldeau
Xin Gao
Yagya Chadha
Jordan Yupeng Xiao
Kurt M. Schmoller
Jan M. Skotheim
Cell size variability within proliferating populations reflects the interdependent regulation of cell growth and division as well as intrins… (see more)ically stochastic effects. In budding yeast, the G1/S transition exerts strong size control in daughter cells, which manifests as the inverse correlation between how big a cell is when it is born and how much it grows in G1. However, mutations affecting this size control checkpoint only modestly influence population-wide size variability, often altering the coefficient of variation (CV) only by ∼10%. To resolve this paradox, we combine computational modeling and live-cell imaging to identify the principal determinants of cell size variability. Using an experimentally validated stochastic model of the yeast cell cycle, we perform parameter sensitivity analysis and find that division asymmetry between mothers and daughters is the dominant driver of CV, outweighing the effects of G1/S size control. Experimental measurements across genetic perturbations and growth conditions confirm a strong correlation between mother-daughter size asymmetry and population CV. These findings reconcile previous observations and show how asymmetric division operates in concert with G1/S size control to govern cell size heterogeneity.
Empirical Characterization of Logging Smells in Machine Learning Code
Patrick Loic Foalem
Leuson Da Silva
Ettore Merlo
Heng Li
\underline{Context:} Logging is a fundamental yet complex practice in software engineering, essential for monitoring, debugging, and auditin… (see more)g software systems. With the increasing integration of machine learning (ML) components into software systems, effective logging has become critical to ensure reproducibility, traceability, and observability throughout model training and deployment. Although various general-purpose and ML-specific logging frameworks exist, little is known about how these tools are actually used in practice or whether ML practitioners adopt consistent and effective logging strategies. To date, no empirical study has systematically characterized recurring bad logging practices--or logging smells--in ML System. \underline{Goal:} This study aims to empirically identify and characterize logging smells in ML systems, providing an evidence-based understanding of how logging is implemented and challenged in practice. \underline{Method:} We propose to conduct a large-scale mining of open-source ML repositories hosted on GitHub to catalogue recurring logging smells. Subsequently, a practitioner survey involving ML engineers will be conducted to assess the perceived relevance, severity, and frequency of the identified smells. \underline{Limitations:} % While The study's limitations include that While our findings may not be generalizable to closed-source industrial projects, we believe our study provides an essential step toward understanding and improving logging practices in ML development.
An Empirical Study of Policy-as-Code Adoption in Open-Source Software Projects
Patrick Loic Foalem
Leuson Da Silva
Ettore Merlo
MILUV: A Multi-UAV Indoor Localization dataset with UWB and Vision
Mohammed Ayman Shalaby
Nicholas Dahdah
Syed Shabbir Ahmed
Charles Champagne Cossette
Jerome Le Ny
This paper introduces MILUV, a Multi-UAV Indoor Localization dataset with UWB and Vision measurements. This dataset comprises 217 minutes of… (see more) flight time over 36 experiments using three quadcopters, collecting ultra-wideband (UWB) ranging data such as the raw timestamps and channel-impulse response data, vision data from a stereo camera and a bottom-facing monocular camera, inertial measurement unit data, height measurements from a laser rangefinder, magnetometer data, and ground-truth poses from a motion-capture system. The UWB data is collected from up to 12 transceivers affixed to mobile robots and static tripods in both line-of-sight and non-line-of-sight conditions. The UAVs fly at a maximum speed of 4.418 m/s in an indoor environment with visual fiducial markers as features. MILUV is versatile and can be used for a wide range of applications beyond localization, but the primary purpose of MILUV is for testing and validating multi-robot UWB- and vision-based localization algorithms. The dataset can be downloaded at https://doi.org/10.25452/figshare.plus.28386041.v1. A development kit is presented alongside the MILUV dataset, which includes benchmarking algorithms such as visual-inertial odometry, UWB-based localization using an extended Kalman filter, and classification of CIR data using machine learning approaches. The development kit can be found at https://github.com/decargroup/miluv, and is supplemented with a website available at https://decargroup.github.io/miluv/.
Multilingual Amnesia: On the Transferability of Unlearning in Multilingual LLMs
As multilingual large language models become more widely used, ensuring their safety and fairness across diverse linguistic contexts present… (see more)s unique challenges. While existing research on machine unlearning has primarily focused on monolingual settings, typically English, multilingual environments introduce additional complexities due to cross-lingual knowledge transfer and biases embedded in both pretraining and fine-tuning data. In this work, we study multilingual unlearning using the Aya-Expanse 8B model under two settings: (1) data unlearning and (2) concept unlearning. We extend benchmarks for factual knowledge and stereotypes to ten languages through translation: English, French, Arabic, Japanese, Russian, Farsi, Korean, Hindi, Hebrew, and Indonesian. These languages span five language families and a wide range of resource levels. Our experiments show that unlearning in high-resource languages is generally more stable, with asymmetric transfer effects observed between typologically related languages. Furthermore, our analysis of linguistic distances indicates that syntactic similarity is the strongest predictor of cross-lingual unlearning behavior.