Publications

Learning and Controlling Silicon Dopant Transitions in Graphene using Scanning Transmission Electron Microscopy
Max Schwarzer
Jesse Farebrother
Joshua Greaves
Ekin Dogus Cubuk
Rishabh Agarwal
Aaron Courville
Bellemare Marc-Emmanuel
Sergei Kalinin
Igor Mordatch
Pablo Samuel Castro
Kevin M Roccapriore
We introduce a machine learning approach to determine the transition dynamics of silicon atoms on a single layer of carbon atoms, when stimu… (see more)lated by the electron beam of a scanning transmission electron microscope (STEM). Our method is data-centric, leveraging data collected on a STEM. The data samples are processed and filtered to produce symbolic representations, which we use to train a neural network to predict transition probabilities. These learned transition dynamics are then leveraged to guide a single silicon atom throughout the lattice to pre-determined target destinations. We present empirical analyses that demonstrate the efficacy and generality of our approach.
2025-05-19
Advanced Materials Interfaces (published)
doi.org
arxiv.org
Multi‐center benchmarking of cervical spinal cord RF coils for 7 T MRI: A traveling spines study
Eva Alonso‐Ortiz
Daniel Papp
Robert L. Barry
Kyota Poëti
Alan C. Seifert
Kyle M. Gilbert
Nibardo Lopez‐Rios
Jan Paska
Falk Eippert
Nikolaus Weiskopf
Laura Beghini
Nadine N. Graedel
Robert Trampel
Martina F. Callaghan
Christoph S. Aigner
Patrick Freund
Maryam Seif
Aurélien Destruel
Virginie Callot
Johanna Vannesjo … (see 1 more)
Julien Cohen‐Adad
The depth within the body, small diameter, long length, and varying tissue surrounding the spinal cord impose specific considerations when d… (see more)esigning RF coils. The optimal coil configuration for 7 T cervical spinal cord MRI is unknown and currently there are very few coil options. The purpose of this work was (1) to establish a quality control protocol for evaluating 7 T cervical spinal cord coils, and (2) to use that protocol to evaluate the performance of four different coil designs. Three healthy volunteers and a custom anthropomorphic phantom (the traveling spines cohort) were scanned at seven 7 T imaging centers using a common protocol and each center's specific cervical spinal cord coil. Four different coil designs were tested (two in‐house, one Rapid Biomedical, and one MRI.TOOLS design). The Rapid Biomedical coil was found to have the highest B1+ efficiency, whereas one of the in‐house designs (NeuroPoly Lab) had the highest SNR and the largest spinal cord coverage. The MRI.TOOLS coil had the most uniform B1+ profile along the cervical spinal cord; however, it was limited in its ability to provide the requested flip angles (especially for larger individuals). The latter was also the case for the second in‐house coil (MSSM). The results of this study serve as a guide for the spinal cord MRI community in selecting the most suitable coil based on specific requirements and offer a standardized protocol for assessing future coils.
2025-05-19
Magnetic Resonance in Medicine (published)
doi.org
SDLog: A Deep Learning Framework for Detecting Sensitive Information in Software Logs
Roozbeh Aghili
Xingfang Wu
Foutse Khomh
Heng Li
2025-05-19
ArXiv (preprint)
doi.org
arxiv.org
Self-Evolving Curriculum for LLM Reasoning
Xiaoyin Chen
Jiarui Lu
Minsu Kim
Dinghuai Zhang
Jian Tang
Alexandre Piché
Nicolas Gontier
Yoshua Bengio
Ehsan Kamalloo
2025-05-19
ArXiv (preprint)
doi.org
arxiv.org
Virtual Cells: Predict, Explain, Discover
Emmanuel Noutahi
Jason Hartford
Prudencio Tossou
Shawn Whitfield
Ali Denton
Cas Wognum
Kristina Ulicna
Michael Craig
Jonathan Hsu
Michael Cuccarese
Emmanuel Bengio
Dominique Beaini
Christopher Gibson
Daniel Cohen
Berton Earnshaw
2025-05-19
ArXiv (preprint)
doi.org
arxiv.org
Building spatial world models from sparse transitional episodic memories
Zizhan He
Maxime Daigle
Pouya Bashivan
Many animals possess a remarkable capacity to rapidly construct flexible mental models of their environments. These world models are crucial… (see more) for ethologically relevant behaviors such as navigation, exploration, and planning. The ability to form episodic memories and make inferences based on these sparse experiences is believed to underpin the efficiency and adaptability of these models in the brain. Here, we ask: Can a neural network learn to construct a spatial model of its surroundings from sparse and disjoint episodic memories? We formulate the problem in a simulated world and propose a novel framework, the Episodic Spatial World Model (ESWM), as a potential answer. We show that ESWM is highly sample-efficient, requiring minimal observations to construct a robust representation of the environment. It is also inherently adaptive, allowing for rapid updates when the environment changes. In addition, we demonstrate that ESWM readily enables near-optimal strategies for exploring novel environments and navigating between arbitrary points, all without the need for additional training.
2025-05-18
ArXiv (preprint)
doi.org
arxiv.org
Generalizable Imitation Learning Through Pre-Trained Representations
Wei-Di Chang
Francois Hogan
David Meger
Scott Fujimoto
Gregory Dudek
In this paper we leverage self-supervised vision transformer models and their emergent semantic abilities to improve the generalization abil… (see more)ities of imitation learning policies. We introduce BC-ViT, an imitation learning algorithm that leverages rich DINO pre-trained Visual Transformer (ViT) patch-level embeddings to obtain better generalization when learning through demonstrations. Our learner sees the world by clustering appearance features into semantic concepts, forming stable keypoints that generalize across a wide range of appearance variations and object types. We show that this representation enables generalized behaviour by evaluating imitation learning across a diverse dataset of object manipulation tasks. Our method, data and evaluation approach are made available to facilitate further study of generalization in Imitation Learners.
2025-05-18
2025 IEEE International Conference on Robotics and Automation (ICRA) (published)
doi.org
arxiv.org
Half Search Space is All You Need
Pavel Rumiantsev
Mark J. Coates
2025-05-18
ArXiv (preprint)
doi.org
arxiv.org
Learning active tactile perception through belief-space control
Jean-François Tremblay
Johanna Hansen
David Meger
Francois Hogan
Gregory Dudek
Robot operating in an open world can encounter novel objects with unknown physical properties, such as mass, friction, or size. It is desira… (see more)ble to be able to sense those property through contact-rich interaction, before performing downstream tasks with the objects. We propose a method for autonomously learning active tactile perception policies, by learning a generative world model leveraging a differentiable bayesian filtering algorithm, and designing an information- gathering model predictive controller. We test the method on three simulated tasks: mass estimation, height estimation and toppling height estimation. Our method is able to discover policies which gather information about the desired property in an intuitive manner.
2025-05-18
2025 IEEE International Conference on Robotics and Automation (ICRA) (published)
doi.org
openreview.net
PedMedQA: Comparing Large Language Model Accuracy in Pediatric and Adult Medicine
Nikhil Jaiswal
Yuanchao Ma
Bertrand Lebouché
Dan Poenaru
Esli Osmanlliu
Large language models (LLMs) have the potential to revolutionize healthcare, including aiding in clinical decision-making. However, recent w… (see more)ork suggests that LLM performance in pediatric cases may be weaker than adult cases. A key limitation in evaluating these differences is the lack of pediatric-specific benchmarks, making it difficult to systematically assess how well LLMs generalize to pediatric scenarios.
2025-05-18
Pediatrics Open Science (published)
doi.org
RobusTAD: reference panel based annotation of nested topologically associating domains
Yanlin Zhang
Rola Dali
Mathieu Blanchette
Topologically associating domains (TADs) are fundamental units of 3D genomes and play essential roles in gene regulation. Hi-C data suggests… (see more) a hierarchical organization of TADs. Accurately annotating nested TADs from Hi-C data remains challenging, both in terms of the precise identification of boundaries and the correct inference of hierarchies. While domain boundary is relatively well conserved across cells, few approaches have taken advantage of this fact. Here, we present RobusTAD to annotate TAD hierarchies. It incorporates additional Hi-C data to refine boundaries annotated from the study sample. RobusTAD outperforms existing tools at boundary and domain annotation across several benchmarking tasks. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-025-03568-9.
2025-05-18
Genome Biology (published)
doi.org
Seeing the Unseen: How EMoE Unveils Bias in Text-to-Image Diffusion Models
Lucas Berry
Axel Brando
Wei-Di Chang
Juan Higuera
David Meger
2025-05-18
ArXiv (preprint)
doi.org
openreview.net