Publications

Harnessing agent-based frameworks in CellAgentChat to unravel cell–cell interactions from single-cell and spatial transcriptomics
Vishvak Raghavan
Yumin Zheng
Yue Li
Jun Ding
Understanding cell–cell interactions (CCIs) is essential yet challenging owing to the inherent intricacy and diversity of cellular dynamic… (see more)s. Existing approaches often analyze global patterns of CCIs using statistical frameworks, missing the nuances of individual cell behavior owing to their focus on aggregate data. This makes them insensitive in complex environments where the detailed dynamics of cell interactions matter. We introduce CellAgentChat, an agent-based model (ABM) designed to decipher CCIs from single-cell RNA sequencing and spatial transcriptomics data. This approach models biological systems as collections of autonomous agents governed by biologically inspired principles and rules. Validated across eight diverse single-cell data sets, CellAgentChat demonstrates its effectiveness in detecting intricate signaling events across different cell populations. Moreover, CellAgentChat offers the ability to generate animated visualizations of single-cell interactions and provides flexibility in modifying agent behavior rules, facilitating thorough exploration of both close and distant cellular communications. Furthermore, CellAgentChat leverages ABM features to enable intuitive in silico perturbations via agent rule modifications, facilitating the development of novel intervention strategies. This ABM method unlocks an in-depth understanding of cellular signaling interactions across various biological contexts, thereby enhancing in silico studies for cellular communication–based therapies.
2025-06-30
Genome Research (published)
doi.org
Health data issues in Africa: time for digitization, standardization and harmonization
Abdoelnaser Degoot
Ismaël Koné
Shakuntala Baichoo
Mercy Ngungu
Nzisa Liku
Judit Kumuthini
Joyce Nakatumba‐Nabende
Foutse Khomh
Bubacarr Bah
This commentary discusses health data challenges in Africa, focusing on digitization, standardization, and harmonization as key solutions. I… (see more)t highlights how addressing these foundational issues can enable AI and data science to transform healthcare systems across the continent.
2025-06-30
Nature Communications (published)
doi.org
HVAC-GRACE: Transferable Building Control via Heterogeneous Graph Neural Network Policies
Anaïs Berkes
Donna Vakalis
David Rolnick
Yoshua Bengio
Buildings consume 40% of global energy, with HVAC systems responsible for up to half of that demand. As energy use grows, optimizing HVAC ef… (see more)ficiency is critical to meeting climate goals. While reinforcement learning (RL) offers a promising alternative to rule-based control, real-world adoption is limited by poor sample efficiency and generalisation. We introduce HVAC-GRACE, a graph-based RL framework that models buildings as heterogeneous graphs and integrates spatial message passing directly into temporal GRU gates. This enables each zone to learn control actions informed by both its own history and its structural context. Our architecture supports zero-shot transfer by learning topology-agnostic functions—but initial experiments reveal that this benefit depends on sufficient conditioned zone connectivity to maintain gradient flow. These findings highlight both the promise and the architectural requirements of scalable, transferable RL for building control
2025-06-30
ICML.cc/2025/Workshop/CO-BUILD (poster)
openreview.net
openreview.net
Longitudinal changes in brain asymmetry track lifestyle and disease
Karin Saltoun
B. T. Thomas Yeo
Lynn Paul
Jörn Diedrichsen
Danilo Bzdok
Human beings may have evolved the largest asymmetries of brain organization in the animal kingdom. Hemispheric left-vs-right specialization … (see more)is especially pronounced in species-unique capacities, including emotional processing such as facial judgments, language-based feats such as reading books, and creativity such as musical performances. We hence chart the largest longitudinal brain-imaging resource, and provide evidence that brain asymmetry changes continuously in a manner suggestive of neural plasticity throughout adulthood. In the UK Biobank population cohort, we demonstrate that whole-brain patterns of asymmetry changes show robust phenome-wide associations across 959 distinct variables spanning 11 categories. We also find that changes in brain asymmetry over years co-occur with changes among specific lifestyle markers. We uncover specific brain asymmetry changes which systematically co-occur with entering a new phase of life, namely retirement. Finally, we reveal relevance of evolving brain asymmetry within subjects to major disease categories across ~4500 total medical diagnoses. Our findings speak against the idea that asymmetrical neural systems are conserved throughout adulthood.
2025-06-30
Nature Communications (published)
doi.org
Model approximation in MDPs with unbounded per-step cost
Berk Bozkurt
Aditya Mahajan
Ashutosh Nayyar
Yi Ouyang
We consider the problem of designing a control policy for an infinite-horizon discounted cost Markov decision process …
2025-06-30
IEEE Transactions on Automatic Control (published)
doi.org
arxiv.org
A Modular Approach for Clinical SLMs Driven by Synthetic Data with Pre-Instruction Tuning, Model Merging, and Clinical-Tasks Alignment
Jean-Philippe Corbeil
Amin Dada
Jean-Michel Attendu
Asma Ben Abacha
Alessandro Sordoni
Lucas Caccia
Franccois Beaulieu
Thomas Lin
Jens Kleesiek
Paul Vozila
High computation costs and latency of large language models such as GPT-4 have limited their deployment in clinical settings. Small language… (see more) models (SLMs) offer a cost-effective alternative, but their limited capacity requires biomedical domain adaptation, which remains challenging. An additional bottleneck is the unavailability and high sensitivity of clinical data. To address these challenges, we propose a novel framework for adapting SLMs into high-performing clinical models. We introduce the MediPhi collection of 3.8B-parameter SLMs developed with our novel framework: pre-instruction tuning of experts on relevant medical and clinical corpora (PMC, Medical Guideline, MedWiki, etc.), model merging, and clinical-tasks alignment. To cover most clinical tasks, we extended the CLUE benchmark to CLUE+, doubling its size. Our expert models deliver relative improvements on this benchmark over the base model without any task-specific fine-tuning: 64.3% on medical entities, 49.5% on radiology reports, and 44% on ICD-10 coding (outperforming GPT-4-0125 by 14%). We unify the expert models into MediPhi via model merging, preserving gains across benchmarks. Furthermore, we built the MediFlow collection, a synthetic dataset of 2.5 million high-quality instructions on 14 medical NLP tasks, 98 fine-grained document types, and JSON format support. Alignment of MediPhi using supervised fine-tuning and direct preference optimization achieves further gains of 18.9% on average.
2025-06-30
Proceedings of the 63rd Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) (published)
doi.org
arxiv.org
Modulation of leg trajectory by transcranial magnetic stimulation during walking
Héloïse Bourgeois
Rose Guay-Hottin
El-Mehdi Meftah
Marina Martinez
Marco Bonizzato
Dorothy Barthélemy
The primary motor cortex is involved in initiation and adaptive control of locomotion. However, the role of the motor cortex in controlling … (see more)gait trajectories remains unclear. In animals, cortical neuromodulation allows for precise control of step height. We hypothesized that a similar control framework applies to humans, whereby cortical stimulation would primarily increase foot elevation. Transcranial magnetic stimulation (TMS) was applied over the motor cortex to assess the involvement of the corticospinal tract over the limb trajectory during human walking. Ten healthy adults (aged 20–32 years) participated in treadmill walking at 1.5 km/h. TMS was applied over the left motor cortex at an intensity of 120% of the threshold to elicit a dorsiflexion of the right ankle during the swing phase of gait. Electromyographic (EMG) measurements and three-dimensional (3D) lower limb kinematics were collected. When delivered during the early swing phase, TMS led to a significant increase in the maximum height of the right toe by a mean of 34.9% ± 9.6% (21.4 mm ± 7.9 mm, p = 0.032) and knee height by 52.8% ± 14.1% (28.8 mm ± 7.7 mm, p = 0.0021) across participants. These findings indicate that TMS can influence limb trajectory during walking, highlighting its potential as a tool for studying cortical control of locomotion.
2025-06-30
Scientific Reports (published)
doi.org
MSR37 Improve Analyst Accuracy in Systematic Literature Reviews Using Reliant Tabular and LLM-Based Relevance Scoring
Christoph R. Schlegel
Sam Work
Bellemare Marc-Emmanuel
2025-06-30
Value in Health (published)
doi.org
Parsing Autism Heterogeneity: Transcriptomic Subgrouping of Imaging-Derived Phenotypes in Autism.
Johanna Leyhausen
Caroline Gurr
Lisa M. Berg
Hanna Seelemeyer
Bassem Hermila
Tim Schäfer
Andreas Chiocchetti
Charlotte M. Pretzsch
Eva Loth
Beth Oakley
Jan K. Buitelaar
Christian Beckmann
Tony Charman
Thomas Bourgeron
Eli Barthome
Tobias Banaschewski
Jumana Ahmad
Sara Ambrosino
Bonnie Auyeung
Simon Baron-Cohen … (see 56 more)
Sarah Baumeister
Sven Bölte
Carsten Bours
Michael Brammer
Daniel Brandeis
Claudia Brogna
Yvette de Bruijn
Bhismadev Chakrabarti
Ineke Cornelissen
Daisy Crawley
Flavio Dell’Acqua
Guillaume Dumas
Sarah Durston
Christine Ecker
Jessica Faulkner
Vincent Frouin
Pilar Garcés
David Goyard
Lindsay Ham
Hannah Hayward
Joerg F. Hipp
Rosemary Holt
Mark Johnson
Emily J. H. Jones
Prantik Kundu
Meng-Chuan Lai
Xavier Liogier D’ardhuy
Michael V. Lombardo
David J. Lythgoe
René Mandl
Andre Marquand
Luke Mason
Maarten Mennes
Andreas Meyer-Lindenberg
Carolin Moessnang
Nico Bast
Larry O’Dwyer
Marianne Oldehinkel
Bob Oranje
Gahan Pandina
Antonio Persico
Barbara Ruggeri
Amber N. V. Ruigrok
Jessica Sabet
Roberto Sacco
Antonia San José Cáceres
Emily Simonoff
Will Spooren
Julian Tillmann
Roberto Toro
Heike Tost
Jack Waldman
Steve C. R. Williams
Caroline Wooldridge
Marcel P. Zwiers
Declan Murphy
2025-06-30
Biological Psychiatry: Cognitive Neuroscience and Neuroimaging (published)
doi.org
Public perceptions of Montréal's streets: Implications for inclusive public space making and management
Rashid Mushkani
Hugo Berard
Toumadher Ammar
Shin Koseki
2025-06-30
Journal of Urban Management (published)
doi.org
Self-Predictive Representations for Combinatorial Generalization in Behavioral Cloning
Daniel Lawson
Adriana Hugessen
Charlotte Cloutier
Glen Berseth
Khimya Khetarpal
Behavioral cloning (BC) methods trained with supervised learning (SL) are an effective way to learn policies from human demonstrations in do… (see more)mains like robotics. Goal-conditioning these policies enables a single generalist policy to capture diverse behaviors contained within an offline dataset. While goal-conditioned behavior cloning (GCBC) methods can perform well on in-distribution training tasks, they do not necessarily generalize zero-shot to tasks that require conditioning on novel state-goal pairs, i.e. combinatorial generalization. In part, this limitation can be attributed to a lack of temporal consistency in the state representation learned by BC; if temporally related states are encoded to similar latent representations, then the out-of-distribution gap for novel state-goal pairs would be reduced. Hence, encouraging this temporal consistency in the representation space should facilitate combinatorial generalization. Successor representations, which encode the distribution of future states visited from the current state, nicely encapsulate this property. However, previous methods for learning successor representations have relied on contrastive samples, temporal-difference (TD) learning, or both. In this work, we propose a simple yet effective representation learning objective,
2025-06-30
rl-conference.cc/RLC/2025/Workshop/RLBrew (published)
doi.org
openreview.net
Speciation of coral-associated barnacles: generalists versus specialists in the Indo-West Pacific
Hsiu-Chin Lin
Lorenzo C. Halasan
Yoko Nozawa
Benny Kwok Kan Chan
2025-06-30
Coral Reefs (published)
doi.org