Publications

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… (voir plus)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.
2024-03-14
ArXiv (prépublication)
doi.org
arxiv.org
Bugs in Large Language Models Generated Code: An Empirical Study
Florian Tambon
Arghavan Moradi Dakhel
Amin Nikanjam
Foutse Khomh
Michel C. Desmarais
Giuliano Antoniol
2024-03-13
ArXiv (prépublication)
doi.org
arxiv.org
Online Bayesian optimization of vagus nerve stimulation.
Lorenz Wernisch
Tristan Edwards
Antonin Berthon
Olivier Tessier-Lariviere
Elvijs Sarkans
Myrta Stoukidi
Pascal Fortier-Poisson
Max Pinkney
Michael Thornton
Catherine Hanley
Susannah Lee
Joel Jennings
Ben Appleton
Philip Garsed
Bret Patterson
Buttinger Will
Samuel Gonshaw
Matjaž Jakopec
Sudhakaran Shunmugam
Jorin Mamen … (voir 4 de plus)
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. Stimu… (voir plus)lation 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 innervates, among other thoracic and visceral organs, the heart, thus controlling heart rate, 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 vagus nerve stimulation intraoperatively in porcine subjects. Optimization converged quickly on parameters achieving target heart rates 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. .
2024-03-13
Journal of Neural Engineering (publié)
doi.org
Scattered Mixture-of-Experts Implementation
Shawn Tan
Yikang Shen
Rameswar Panda
Aaron Courville
We present ScatterMoE, an implementation of Sparse Mixture-of-Experts (SMoE) on GPUs. ScatterMoE builds upon existing implementations, and o… (voir plus)vercoming some of the limitations to improve inference and training speed, and memory footprint. This implementation achieves this by avoiding padding and making excessive copies of the input. We introduce ParallelLinear, the main component we use to build our implementation and the various kernels used to speed up the operation. We benchmark our implementation against Megablocks, and show that it enables a higher throughput and lower memory footprint. We also show how ParallelLinear enables extension of the Mixture-of-Experts concept by demonstrating with an implementation of Mixture of Attention.
2024-03-13
ArXiv (prépublication)
doi.org
arxiv.org
Simple and Scalable Strategies to Continually Pre-train Large Language Models
Adam Ibrahim
Benjamin Thérien
Kshitij Gupta
Mats Leon Richter
Quentin Anthony
Timothee LESORT
Eugene Belilovsky
Irina Rish
Large language models (LLMs) are routinely pre-trained on billions of tokens, only to start the process over again once new data becomes ava… (voir plus)ilable. A much more efficient solution is to continually pre-train these models, saving significant compute compared to re-training. However, the distribution shift induced by new data typically results in degraded performance on previous data or poor adaptation to the new data. In this work, we show that a simple and scalable combination of learning rate (LR) re-warming, LR re-decaying, and replay of previous data is sufficient to match the performance of fully re-training from scratch on all available data, as measured by the final loss and the average score on several language model (LM) evaluation benchmarks. Specifically, we show this for a weak but realistic distribution shift between two commonly used LLM pre-training datasets (English
2024-03-13
ArXiv (prépublication)
doi.org
arxiv.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
2024-03-12
2024 IEEE International Conference on Software Analysis, Evolution and Reengineering (SANER) (publié)
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… (voir plus)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.
2024-03-12
2024 IEEE International Conference on Software Analysis, Evolution and Reengineering (SANER) (publié)
doi.org
arxiv.org
Maxwell's Demon at Work: Efficient Pruning by Leveraging Saturation of Neurons
Simon Dufort-Labbé
Pierluca D'Oro
Evgenii Nikishin
Razvan Pascanu
Pierre-Luc Bacon
Aristide Baratin
2024-03-12
ArXiv (prépublication)
doi.org
arxiv.org
Refining GPT-3 Embeddings with a Siamese Structure for Technical Post Duplicate Detection
Xingfang Wu
Heng Li
Nobukazu Yoshioka
Hironori Washizaki
Foutse Khomh
2024-03-12
2024 IEEE International Conference on Software Analysis, Evolution and Reengineering (SANER) (publié)
doi.org
arxiv.org
Rethinking Machine Learning Benchmarks in the Context of Professional Codes of Conduct
Peter Henderson
Jieru Hu
Mona Diab
Joelle Pineau
2024-03-12
Proceedings of the Symposium on Computer Science and Law (publié)
doi.org
Simulating Weighted Automata over Sequences and Trees with Transformers
Michael Rizvi
Maude Lizaire
Clara Lacroce
Guillaume Rabusseau
2024-03-12
ArXiv (prépublication)
doi.org
arxiv.org
WorkArena: How Capable Are Web Agents at Solving Common Knowledge Work Tasks?
Alexandre Drouin
Maxime Gasse
Massimo Caccia
Issam Hadj Laradji
Manuel Del Verme
Tom Marty
Léo Boisvert
Megh Thakkar
Quentin Cappart
David Vazquez
Nicolas Chapados
Alexandre Lacoste
We study the use of large language model-based agents for interacting with software via web browsers. Unlike prior work, we focus on measuri… (voir plus)ng the agents' ability to perform tasks that span the typical daily work of knowledge workers utilizing enterprise software systems. To this end, we propose WorkArena, a remote-hosted benchmark of 29 tasks based on the widely-used ServiceNow platform. We also introduce BrowserGym, an environment for the design and evaluation of such agents, offering a rich set of actions as well as multimodal observations. Our empirical evaluation reveals that while current agents show promise on WorkArena, there remains a considerable gap towards achieving full task automation. Notably, our analysis uncovers a significant performance disparity between open and closed-source LLMs, highlighting a critical area for future exploration and development in the field.
2024-03-12
ArXiv (prépublication)
doi.org
arxiv.org