Publications

Development of a Framework for Establishing 'Gold Standard' Outbreak Data from Submitted SARS-CoV-2 Genome Samples
Russell Steele
Philip Abdelmalik
David L Buckeridge
Submitted genomic data for respiratory viruses reflect the emergence and spread of new variants. Although delays in submission limit the uti… (voir plus)lity of these data for prospective surveillance, they may be useful for evaluating other surveillance sources. However, few studies have investigated the use of these data for evaluating aberration detection in surveillance systems. Our study used a Bayesian online change point detection algorithm (BOCP) to detect increases in the number of submitted genome samples as a means of establishing 'gold standard' dates of outbreak onset in multiple countries. We compared models using different data transformations and parameter values. BOCP detected change points that were not sensitive to different parameter settings. We also found data transformations were essential prior to change point detection. Our study presents a framework for using global genomic submission data to develop 'gold standard' dates about the onset of outbreaks due to new viral variants.
Learning Valid Dual Bounds in Constraint Programming: Boosted Lagrangian Decomposition with Self-Supervised Learning
Swann Bessa
Darius Dabert
Max Bourgeat
Louis-Martin Rousseau
Non-invasive electroencephalography in awake cats: Feasibility and application to sensory processing in chronic pain
Aliénor Delsart
Aude Castel
Colombe Otis
Mathieu Lachance
Maude Barbeau-Grégoire
Bertrand Lussier
Franck Péron
Marc Hébert
Nicolas Lapointe
Maxim Moreau
Johanne Martel-Pelletier
Jean-Pierre Pelletier
Eric Troncy
scCobra: Contrastive cell embedding learning with domain-adaptation for single-cell data integration and harmonization
Bowen Zhao
Dong-Qing Wei
Yi Xiong
The rapid development of single-cell technologies has underscored the need for more effective methods in the integration and harmonization o… (voir plus)f single-cell sequencing data. The prevalent challenge of batch effects, resulting from technical and biological variations across studies, demands accurate and reliable solutions for data integration. Traditional tools often have limitations, both due to reliance on gene expression distribution assumptions and the common issue of over-correction, particularly in methods based on anchor alignments. Here we introduce scCobra, a deep neural network tool designed specifically to address these challenges. By leveraging a deep generative model that combines a contrastive neural network with domain adaptation, scCobra effectively mitigates batch effects and minimizes over-correction without depending on gene expression distribution assumptions. Additionally, scCobra enables online label transfer across datasets with batch effects, facilitating the continuous integration of new data without retraining, and offers features for batch effect simulation and advanced multi-omic batch integration. These capabilities make scCobra a versatile data integration and harmonization tool for achieving accurate and insightful biological interpretations from complex datasets.
Simultaneous linear connectivity of neural networks modulo permutation
Ekansh Sharma
Tom Denton
Daniel M. Roy
VulEXplaineR: XAI for Vulnerability Detection on Assembly Code
Samaneh Mahdavifar
Mohd Saqib
Benjamin C. M. Fung
Philippe Charland
Andrew Walenstein
Concurrent product layout design optimization and dependency management using a modified NSGA-III approach
Yann-Seing Law-Kam Cio
Aurelian Vadean
Abolfazl Mohebbi
Sofiane Achiche
The complexity of mechatronic systems has increased with the significant advancements of technology in their components which makes their de… (voir plus)sign more challenging. This is due to the need for incorporating expertise from different domains as well as the increased number and complexity of components integrated into the product. To alleviate the burden of designing such products, many industries and researchers are attracted to the concept of modularization which is to identify a subset of system components that can form a module. To achieve this, a novel product-related dependency management approach is proposed in this paper with the support of an augmented design structure matrix. This approach makes it possible to model positive and negative dependencies and to compute the combination potency between components to form modules. This approach is then integrated into a modified non-dominated sorting genetic algorithm III to concurrently optimize the design and identify the modules. The methodology is exemplified through the case study of a layout design of an automatic greenhouse. By applying the proposed methodology to the case study, it was possible to generate concepts that decreased the number of modules from 9 down to 4 while ensuring the optimization of the design performance.
Switching between tasks can cause AI to lose the ability to learn
Clare Lyle
BlueCelluLab: Biologically Detailed Neural NetworkExperimentation API
Anıl Tuncel
Werner Van Geit
Mike Gevaert
Benjamin Torben-Nielsen
Darshan Mandge
İlkan Kılıç
Aurélien T. Jaquier
Lida Kanari
Henry Markram
The NEURON simulator, established in 1984 and continuously developed since, stands as\nthe preeminent tool for neuron simulation within comp… (voir plus)utational neuroscience. Its widespread\nadoption and compatibility with computational clusters and supercomputers underscore its\npivotal role in large-scale neuronal research. However, its integration with the Python pro-\ngramming language has introduced complexities, particularly concerning memory management\nand object lifecycle. To conceal these challenges from the user and seamlessly interface\nwith community standards for neural network representation data formats such as SONATA,\nwe introduce BlueCelluLab. The high-level Python API simplifies the execution of neural\nsimulations, ranging from single neurons to intricate networks, by managing complexities\nrelated to memory management and object lifecycle, thus providing a streamlined experience\nfor users. Today, BlueCelluLab is powering various Python packages, command line interfaces,\nweb applications, and data analysis workflows.
Zero-Shot Object-Centric Representation Learning
Aniket Rajiv Didolkar
Andrii Zadaianchuk
Michael Curtis Mozer
Georg Martius
Maximilian Seitzer
The goal of object-centric representation learning is to decompose visual scenes into a structured representation that isolates the entities… (voir plus). Recent successes have shown that object-centric representation learning can be scaled to real-world scenes by utilizing pre-trained self-supervised features. However, so far, object-centric methods have mostly been applied in-distribution, with models trained and evaluated on the same dataset. This is in contrast to the wider trend in machine learning towards general-purpose models directly applicable to unseen data and tasks. Thus, in this work, we study current object-centric methods through the lens of zero-shot generalization by introducing a benchmark comprising eight different synthetic and real-world datasets. We analyze the factors influencing zero-shot performance and find that training on diverse real-world images improves transferability to unseen scenarios. Furthermore, inspired by the success of task-specific fine-tuning in foundation models, we introduce a novel fine-tuning strategy to adapt pre-trained vision encoders for the task of object discovery. We find that the proposed approach results in state-of-the-art performance for unsupervised object discovery, exhibiting strong zero-shot transfer to unseen datasets.
Multi Teacher Privileged Knowledge Distillation for Multimodal Expression Recognition
Muhammad Haseeb Aslam
Alessandro Lameiras Koerich
Eric Granger
Human emotion is a complex phenomenon conveyed and perceived through facial expressions, vocal tones, body language, and physiological signa… (voir plus)ls. Multimodal emotion recognition systems can perform well because they can learn complementary and redundant semantic information from diverse sensors. In real-world scenarios, only a subset of the modalities employed for training may be available at test time. Learning privileged information allows a model to exploit data from additional modalities that are only available during training. SOTA methods for PKD have been proposed to distill information from a teacher model (with privileged modalities) to a student model (without privileged modalities). However, such PKD methods utilize point-to-point matching and do not explicitly capture the relational information. Recently, methods have been proposed to distill the structural information. However, PKD methods based on structural similarity are primarily confined to learning from a single joint teacher representation, which limits their robustness, accuracy, and ability to learn from diverse multimodal sources. In this paper, a multi-teacher PKD (MT-PKDOT) method with self-distillation is introduced to align diverse teacher representations before distilling them to the student. MT-PKDOT employs a structural similarity KD mechanism based on a regularized optimal transport (OT) for distillation. The proposed MT-PKDOT method was validated on the Affwild2 and Biovid datasets. Results indicate that our proposed method can outperform SOTA PKD methods. It improves the visual-only baseline on Biovid data by 5.5%. On the Affwild2 dataset, the proposed method improves 3% and 5% over the visual-only baseline for valence and arousal respectively. Allowing the student to learn from multiple diverse sources is shown to increase the accuracy and implicitly avoids negative transfer to the student model.
<scp>RF</scp> shimming in the cervical spinal cord at <scp>7 T</scp>
Daniel Papp
Kyle M. Gilbert
Gaspard Cereza
Alexandre D'Astous
Nibardo Lopez‐Rios
Mathieu Boudreau
Marcus J. Couch
Pedram Yazdanbakhsh
Robert L. Barry
Eva Alonso‐Ortiz
Julien Cohen‐Adad
The study's findings highlight the potential of RF shimming to advance 7 T MRI's clinical utility for central nervous system imaging by enab… (voir plus)ling more homogenous and efficient spinal cord imaging. Additionally, the research incorporates a reproducible Jupyter Notebook, enhancing the study's transparency and facilitating peer verification.