Publications

Deep learning reveals that multidimensional social status drives population variation in 11,875 US participant cohort
Justin Marotta
Shambhavi Aggarwal
Nicole Osayande
Karin Saltoun
Jakub Kopal
Avram J. Holmes
Sarah W. Yip
Danilo Bzdok
As an increasing realization, many behavioral relationships are interwoven with inherent variations in human populations. Presently, there i… (see more)s no clarity in the biomedical community on which sources of population variation are most dominant. The recent advent of population-scale cohorts like the Adolescent Brain Cognitive DevelopmentSM Study (ABCD Study®) are now offering unprecedented depth and width of phenotype profiling that potentially explains interfamily differences. Here, we leveraged a deep learning framework (conditional variational autoencoder) on the totality of the ABCD Study® phenome (8,902 candidate phenotypes in 11,875 participants) to identify and characterize major sources of population stratification. 80% of the top 5 sources of explanatory stratifications were driven by distinct combinations of 202 available socioeconomic status (SES) measures; each in conjunction with a unique set of non-overlapping social and environmental factors. Several sources of variation across this cohort flagged geographies marked by material poverty interlocked with mental health and behavioral correlates. Deprivation emerged in another top stratification in relation to urbanicity and its ties to immigrant and racial and ethnic minoritized groups. Conversely, two other major sources of population variation were both driven by indicators of privilege: one highlighted measures of access to educational opportunity and income tied to healthy home environments and good behavior, the other profiled individuals of European ancestry leading advantaged lifestyles in desirable neighborhoods in terms of location and air quality. Overall, the disclosed social stratifications underscore the importance of treating SES as a multidimensional construct and recognizing its ties into social determinants of health.
2025-08-12
PLOS One (published)
doi.org
Pathfinding: a neurodynamical account of intuition
Steven Kotler
Michael Mannino
Karl Friston
Gyorgy Buzsáki
J. A. Scott Kelso
Guillaume Dumas
2025-08-12
Communications Biology (published)
doi.org
WeDesign: Generative AI-Facilitated Community Consultations for Urban Public Space Design
Rashid A. Mushkani
Hugo Berard
Shin Koseki
2025-08-12
ArXiv (preprint)
doi.org
arxiv.org
LIPTER, a cardiomyocyte-enriched long noncoding RNA, controls cardiac cytoskeletal maturation and is regulated by a cardiomyocyte-specific enhancer
Chukwuemeka George Anene-Nzelu
C.J Mick Lee
Svenja Koslowski
Wenhao Zheng
Marouane Benzaki
Michelle Mak
Xiaohua Wang
Lek Wen Tan
Albert Dashi
Yonglin Zhu
Talal Fawaz
Kenneth Ng
Davy Pham
Francis LeBlanc
Guillaume Lettre
Julie Hussin
Roger Foo
2025-08-11
BioRxiv (preprint)
doi.org
LIPTER, a cardiomyocyte-enriched long noncoding RNA, controls cardiac cytoskeletal maturation and is regulated by a cardiomyocyte-specific enhancer.
George Anene Nzelu
Mick Lee
Svenja Koslowski
Wenhao Zheng
Marouane Benzaki
Michelle Mak
Xiaohua Wang
Lek Wen Tan
Albert Dashi
Yonglin Zhu
Talal Fawaz
Kenneth Ng
Davy Pham
Francis LeBlanc
Guillaume Lettre
Julie Hussin
Roger Foo
Cardiac development is characterized by a complex series of molecular, cytoskeletal and electrophysiological changes that guarantee the prop… (see more)er functioning of adult cardiomyocytes (CMs). These changes are defined by cell-type-specific transcriptional rewiring of progenitor cells to form CMs, and are regulated by various epigenetic elements, such as long noncoding RNAs (lncRNAs). LncRNAs are versatile epigenetic regulators as they may act in cis or in trans to orchestrate important gene programs during cardiac development and may concurrently encode micropeptides. LIPTER is one such lncRNA, previously shown to regulate lipid droplet transport in cardiomyocytes and thus an important regulator of cardiomyocyte metabolism. Here we show that LIPTER also plays a role in the cytoskeletal maturation of CMs, as loss of LIPTER leads to persistent expression of fetal genes, changes in chromatin accessibility, disorganized sarcomeres and impaired calcium homeostasis in CMs. Furthermore, we have identified a cardiomyocyte-specific regulatory enhancer that regulates the expression of LIPTER in CMs. CRISPR-mediated inhibition of this enhancer led to reduced LIPTER expression in CMs and increased expression of fetal genes. This CM-specific enhancer could therefore be manipulated to control the expression of LIPTER for therapeutic benefit. In summary, we have unravelled a novel role of LIPTER in CMs cytoskeletal maturation and have identified a CM-specific enhancer for LIPTER.
2025-08-11
bioRxiv (preprint)
doi.org
Multi-Modal Protein Representation Learning with CLASP
Nicolas Bolouri
Joseph Szymborski
Amin Emad
2025-08-11
bioRxiv (preprint)
doi.org
The Impact of a Pediatric Surgery Fundamentals Boot Camp on New Surgical Trainees' Perceived Knowledge and Confidence Levels.
Julia Ferreira
Simon Rahman
Fabio Botelho
Farhan Banji
W. A. Igrine
Gianluca Bertolizio
Sam Daniel
Thomas Engelhardt
Chantal Frigon
Lily H P Nguyen
Catherine Paquet
Dan Poenaru
Pramod Puligandla
Hussein Wissanji
Davinia Withington
Yasmine Yousef
Sherif Emil
2025-08-11
Journal of Pediatric Surgery (published)
doi.org
Adversarial Attack Classification and Robustness Testing for Large Language Models for Code
Yang Liu
Armstrong Foundjem
Foutse Khomh
Heng Li
Large Language Models (LLMs) have become vital tools in software development tasks such as code generation, completion, and analysis. As the… (see more)ir integration into workflows deepens, ensuring robustness against vulnerabilities especially those triggered by diverse or adversarial inputs becomes increasingly important. Such vulnerabilities may lead to incorrect or insecure code generation when models encounter perturbed task descriptions, code, or comments. Prior research often overlooks the role of natural language in guiding code tasks. This study investigates how adversarial perturbations in natural language inputs including prompts, comments, and descriptions affect LLMs for Code (LLM4Code). It examines the effects of perturbations at the character, word, and sentence levels to identify the most impactful vulnerabilities. We analyzed multiple projects (e.g., ReCode, OpenAttack) and datasets (e.g., HumanEval, MBPP), establishing a taxonomy of adversarial attacks. The first dimension classifies the input type code, prompts, or comments while the second dimension focuses on granularity: character, word, or sentence-level changes. We adopted a mixed-methods approach, combining quantitative performance metrics with qualitative vulnerability analysis. LLM4Code models show varying robustness across perturbation types. Sentence-level attacks were least effective, suggesting models are resilient to broader contextual changes. In contrast, word-level perturbations posed serious challenges, exposing semantic vulnerabilities. Character-level effects varied, showing model sensitivity to subtle syntactic deviations.Our study offers a structured framework for testing LLM4Code robustness and emphasizes the critical role of natural language in adversarial evaluation. Improving model resilience to semantic-level disruptions is essential for secure and reliable code-generation systems.
2025-08-10
Empirical Software Engineering (published)
doi.org
arxiv.org
Deep Reinforcement Learning-Based Intrusion Detection System: Defending Edge Gateways Against Mirai and Gafgyt
Saeid Jamshidi
Amin Nikanjam
Kawser Wazed Nafi
Foutse Khomh
The rapid growth of the Internet of Things (IoT) has transformed industries, resulting in unprecedented opportunities alongside significant … (see more)cybersecurity challenges. Malware, for example, Mirai and Gafgyt, exploits IoT vulnerabilities, leading to large-scale attacks. Traditional Intrusion Detection Systems (IDS) struggle to detect these evolving threats due to their reliance on static rule-based or classic Machine Learning (ML) models, which lack adaptability to zero-day attacks and dynamic traffic patterns. This paper presents EdgeShield-DRL, a novel Deep Reinforcement Learning (DRL)-based IDS designed for IoT edge gateways. EdgeShield-DRL dynamically detects and mitigates evolving threats in real-time while ensuring efficient operation on resource-constrained edge devices. We evaluated EdgeShieldDRL on the N-BaIoT dataset, achieving a high detection accuracy of
2025-08-10
2025 12th International Conference on Future Internet of Things and Cloud (FiCloud) (published)
doi.org
Predictive Gene Discovery with EPCY: A Density-Based Alternative to DE analysis
Éric Olivier Audemard
Jean-François Spinella
Vincent-Philippe Lavallee
Josée Hébert
Guy Sauvageau
Sébastien Lemieux
Identifying predictive genes from high-throughput data remains a key challenge in biomedical research. Most current approaches rely on stati… (see more)stical tests to select differentially expressed genes (DEGs), which may not align with the goal of predicting outcomes. We present EPCY, a method that ranks genes based on their predictive power using cross-validated classifiers and density estimation, without relying on null hypothesis testing. Applied to both bulk and single-cell RNA sequencing datasets, EPCY consistently outperforms benchmark DEG-based methods in selecting robust candidate genes. It also demonstrates greater stability across varying cohort sizes, enabling reproducible gene prioritization even in large, heterogeneous datasets. EPCY provides interpretable predictive scores, facilitating candidate selection aligned with downstream validation goals.
2025-08-10
bioRxiv (preprint)
doi.org
Untold stories: A qualitative investigation of patient and family experiences with congenital diaphragmatic hernia.
Alexandra Dimmer
Zanib Nafees
Sabrina Beauseigle
Franco A Carnevale
Elena Guadagno
Dan Poenaru
Pramod Puligandla
2025-08-10
Journal of Pediatric Surgery (published)
doi.org
In Which Areas of Technical AI Safety Could Geopolitical Rivals Cooperate?
BEN BUCKNALL
SAAD SIDDIQUI
Robert Trager
Yoshua Bengio
LARA THURNHERR
CONOR MCGURK
BEN HARACK
International cooperation is common in AI research, including between geopolitical rivals. While many experts advocate for greater internati… (see more)onal cooperation on AI safety to address shared global risks, some view cooperation on AI with suspicion, arguing that it can pose unacceptable risks to national security. However, the extent to which cooperation on AI safety poses such risks, as well as provides benefits, depends on the specific area of cooperation. In this paper, we consider technical factors that impact the risks of international cooperation on AI safety research, focusing on the degree to which such cooperation can advance dangerous capabilities, result in the sharing of sensitive information, or provide opportunities for harm. We begin by why nations historically cooperate on strategic technologies and analyse current US-China cooperation in AI as a case study. We further argue that existing frameworks for managing associated risks can be supplemented with consideration of key risks specific to cooperation on technical AI safety research. Through our analysis, we find that research into AI verification mechanisms and shared protocols may be suitable areas for such cooperation. Through this analysis we aim to help researchers and governments identify and mitigate the risks of international cooperation on AI safety research, so that the benefits of cooperation can be fully realised.
2025-08-10
SuperIntelligence - Robotics - Safety & Alignment (published)
doi.org