Publications

Two-stage Multiple-Model Compression Approach for Sampled Electrical Signals
Corentin Presvôts
Michel Kieffer
Thibault Prevost
Patrick Panciatici
Zuxing Li
Pablo Piantanida
This paper presents a two-stage Multiple-Model Compression (MMC) approach for sampled electrical waveforms. To limit latency, the processing… (see more) is window-based, with a window length commensurate to the electrical period. For each window, the first stage compares several parametric models to get a coarse representation of the samples. The second stage then compares different residual compression techniques to minimize the norm of the reconstruction error. The allocation of the rate budget among the two stages is optimized. The proposed MMC approach provides better signal-to-noise ratios than state-of-the-art solutions on periodic and transient waveforms.
2024-03-18
Data Compression Conference (published)
doi.org
Reinforcement learning for freight booking control problems
Justin Dumouchelle
Emma Frejinger
Andrea Lodi
2024-03-15
Journal of Revenue and Pricing Management (published)
doi.org
arxiv.org
Normalizing Spinal Cord Compression Morphometric Measures: Application in Degenerative Cervical Myelopathy
Sandrine Bédard
Jan Valosek
Maryam Seif
Armin Curt
Simon Schadings
M.Sc
Nikolai Pfender
Patrick Freund
Markus Hupp
Julien Cohen-Adad
The study introduced an automatic method for computation of normalized MSCC measures of cord compression from MRI scans, which is an importa… (see more)nt step towards better informed therapeutic decisions in DCM patients. The method is open-source and available in the Spinal Cord Toolbox v6.0.
2024-03-14
medRxiv (preprint)
doi.org
Safety Cases: How to Justify the Safety of Advanced AI Systems
Joshua Clymer
Nick Gabrieli
David M. Krueger
T. Larsen
As AI systems become more advanced, companies and regulators will make difficult decisions about whether it is safe to train and deploy them… (see more). To prepare for these decisions, we investigate how developers could make a 'safety case,' which is a structured rationale that AI systems are unlikely to cause a catastrophe. We propose a framework for organizing a safety case and discuss four categories of arguments to justify safety: total inability to cause a catastrophe, sufficiently strong control measures, trustworthiness despite capability to cause harm, and -- if AI systems become much more powerful -- deference to credible AI advisors. We evaluate concrete examples of arguments in each category and outline how arguments could be combined to justify that AI systems are safe to deploy.
2024-03-14
ArXiv (preprint)
doi.org
arxiv.org
Aleatoric and epistemic uncertainty extraction of patient-specific deep learning-based dose predictions in LDR prostate brachytherapy
Francisco Berumen
Samuel Ouellet
S. Enger
Luc Beaulieu
2024-03-13
Physics in Medicine and Biology (published)
doi.org
Analyzing Data Augmentation for Medical Images: A Case Study in Ultrasound Images
Adam Tupper
Christian Gagné
Data augmentation is one of the most effective techniques to improve the generalization performance of deep neural networks. Yet, despite of… (see more)ten facing limited data availability in medical image analysis, it is frequently underutilized. This appears to be due to a gap in our collective understanding of the efficacy of different augmentation techniques across medical imaging tasks and modalities. One domain where this is especially true is breast ultrasound images. This work addresses this issue by analyzing the effectiveness of different augmentation techniques for the classification of breast lesions in ultrasound images. We assess the generalizability of our findings across several datasets, demonstrate that certain augmentations are far more effective than others, and show that their usage leads to significant performance gains.
2024-03-13
ArXiv (preprint)
doi.org
arxiv.org
Bayesian Spectral Graph Denoising with Smoothness Prior
Samuel Leone
Xingzhi Sun
Michael Perlmutter
Smita Krishnaswamy
Here we consider the problem of denoising features associated to complex data, modeled as signals on a graph, via a smoothness prior. This i… (see more)s motivated in part by settings such as single-cell RNA where the data is very high-dimensional, but its structure can be captured via an affinity graph. This allows us to utilize ideas from graph signal processing. In particular, we present algorithms for the cases where the signal is perturbed by Gaussian noise, dropout, and uniformly distributed noise. The signals are assumed to follow a prior distribution defined in the frequency domain which favors signals which are smooth across the edges of the graph. By pairing this prior distribution with our three models of noise generation, we propose Maximum A Posteriori (M.A.P.) estimates of the true signal in the presence of noisy data and provide algorithms for computing the M.A.P. Finally, we demonstrate the algorithms’ ability to effectively restore signals from white noise on image data and from severe dropout in single-cell RNA sequence data.
2024-03-12
Annual Conference on Information Sciences and Systems (published)
doi.org
arxiv.org
Online Bayesian optimization of vagus nerve stimulation
Lorenz Wernisch
Tristan Edwards
Antonin Berthon
Olivier Tessier-Larivière
Elvijs Sarkans
Myrta Stoukidi
Pascal Fortier-Poisson
Max Pinkney
Michael Thornton
Catherine Hanley
Susannah Lee
Joel Jennings
Ben Appleton
Phillip Garsed
Bret Patterson
Will Buttinger
Samuel Gonshaw
Matjaž Jakopec
Sudhakaran Shunmugam
Jorin Mamen … (see 4 more)
Aleksi Tukiainen
Guillaume Lajoie
Oliver Armitage
Emil Hewage
Objective. In bioelectronic medicine, neuromodulation therapies induce neural signals to the brain or organs, modifying their function. Stim… (see more)ulation devices capable of triggering exogenous neural signals using electrical waveforms require a complex and multi-dimensional parameter space to control such waveforms. Determining the best combination of parameters (waveform optimization or dosing) for treating a particular patient’s illness is therefore challenging. Comprehensive parameter searching for an optimal stimulation effect is often infeasible in a clinical setting due to the size of the parameter space. Restricting this space, however, may lead to suboptimal therapeutic results, reduced responder rates, and adverse effects. Approach. As an alternative to a full parameter search, we present a flexible machine learning, data acquisition, and processing framework for optimizing neural stimulation parameters, requiring as few steps as possible using Bayesian optimization. This optimization builds a model of the neural and physiological responses to stimulations, enabling it to optimize stimulation parameters and provide estimates of the accuracy of the response model. The vagus nerve (VN) innervates, among other thoracic and visceral organs, the heart, thus controlling heart rate (HR), making it an ideal candidate for demonstrating the effectiveness of our approach. Main results. The efficacy of our optimization approach was first evaluated on simulated neural responses, then applied to VN stimulation intraoperatively in porcine subjects. Optimization converged quickly on parameters achieving target HRs and optimizing neural B-fiber activations despite high intersubject variability. Significance. An optimized stimulation waveform was achieved in real time with far fewer stimulations than required by alternative optimization strategies, thus minimizing exposure to side effects. Uncertainty estimates helped avoiding stimulations outside a safe range. Our approach shows that a complex set of neural stimulation parameters can be optimized in real-time for a patient to achieve a personalized precision dosing.
2024-03-12
Journal of Neural Engineering (published)
doi.org
Assessing the Security of GitHub Copilot Generated Code - A Targeted Replication Study
Vahid Majdinasab
Michael Joshua Bishop
Shawn Rasheed
Arghavan Moradi Dakhel
Amjed Tahir
Foutse Khomh
2024-03-11
2024 IEEE International Conference on Software Analysis, Evolution and Reengineering (SANER) (published)
doi.org
arxiv.org
Deep Learning Model Reuse in the HuggingFace Community: Challenges, Benefit and Trends
Mina Taraghi
Gianolli Dorcelus
Armstrong Foundjem
Florian Tambon
Foutse Khomh
The ubiquity of large-scale Pre-Trained Models (PTMs) is on the rise, sparking interest in model hubs, and dedicated platforms for hosting P… (see more)TMs. Despite this trend, a comprehensive exploration of the challenges that users encounter and how the community leverages PTMs remains lacking. To address this gap, we conducted an extensive mixed-methods empirical study by focusing on discussion forums and the model hub of HuggingFace, the largest public model hub. Based on our qualitative analysis, we present a taxonomy of the challenges and benefits associated with PTM reuse within this community. We then conduct a quantitative study to track model-type trends and model documentation evolution over time. Our findings highlight prevalent challenges such as limited guidance for beginner users, struggles with model output comprehensibility in training or inference, and a lack of model understanding. We also identified interesting trends among models where some models maintain high upload rates despite a decline in topics related to them. Additionally, we found that despite the introduction of model documentation tools, its quantity has not increased over time, leading to difficulties in model comprehension and selection among users. Our study sheds light on new challenges in reusing PTMs that were not reported before and we provide recommendations for various stakeholders involved in PTM reuse.
2024-03-11
2024 IEEE International Conference on Software Analysis, Evolution and Reengineering (SANER) (published)
doi.org
arxiv.org
GAPS II: Development and Pilot Results of the Global Assessment in Pediatric Surgery, an Evidence-Based Pediatric Surgical Capacity Assessment Tool for Low-Resource Settings
Yasmine Yousef
Sarah Cairo
Etienne St-Louis
Laura F. Goodman
Doulia M. Hamad
Robert Baird
Emily R. Smith
Sherif Emil
Jean-Martin Laberge
Mohamed Abdelmalak
Zipporah Gathuy
Faye Evans
Maryam Ghavami Adel
Ki K. Bertille
Milind Chitnis
Leecarlo Millano
Peter Nthumba
Sergio d'Agostino
Bruno Cigliano
Luis Zea-Salazar … (see 4 more)
Emmanuel Ameh
Doruk Ozgediz
Elena Guadagno
Dan Poenaru
PURPOSE: Pediatric surgical care in low- and middle-income countries is often hindered by systemic gaps in healthcare resources, infrastruc… (see more)ture, training, and organisation. This study aims to develop and validate the Global Assessment of Pediatric Surgery (GAPS) to appraise pediatric surgical capacity and discriminate between levels of care across diverse healthcare settings. METHODS: The GAPS Version 1 was constructed through a synthesis of existing assessment tools and expert panel consultation. The resultant GAPS Version 2 underwent international pilot testing. Construct validation categorized institutions into providing Basic or Advanced Surgical Care. GAPS was further refined to Version 3 to include only questions with a > 75% response rate and those that significantly discriminated between Basic or Advanced Surgical settings. RESULTS: GAPS Version 1 included 139 items, which, after expert panel feedback, was expanded to 168 items in Version 2. Pilot testing, in 65 institutions yielded a high response rate. Of the 168 questions in GAPS Version 2, 64 significantly discriminated between Basic and Advanced Surgical Care. The refined GAPS Version 3 tool comprises 64 questions: Human Resources (9), Material Resources (39), Outcomes (3), Accessibility (3), and Education (10). CONCLUSION: The GAPS Version 3 tool presents a validated instrument for evaluating pediatric surgical capabilities in low-resource settings.
2024-03-11
Research Square (Research Square) (preprint)
doi.org
Refining GPT-3 Embeddings with a Siamese Structure for Technical Post Duplicate Detection
Xingfang Wu
Heng Li
Nobukazu Yoshioka
Hironori Washizaki
Foutse Khomh
2024-03-11
2024 IEEE International Conference on Software Analysis, Evolution and Reengineering (SANER) (published)
doi.org
arxiv.org