Publications

Pruning Sparse Tensor Neural Networks Enables Deep Learning for 3D Ultrasound Localization Microscopy
Brice Rauby
Paul Xing
Jonathan Porée
Maxime Gasse
Jean Provost
Ultrasound Localization Microscopy (ULM) is a non-invasive technique that allows for the imaging of micro-vessels in vivo, at depth and with… (voir plus) a resolution on the order of ten microns. ULM is based on the sub-resolution localization of individual microbubbles injected in the bloodstream. Mapping the whole angioarchitecture requires the accumulation of microbubbles trajectories from thousands of frames, typically acquired over a few minutes. ULM acquisition times can be reduced by increasing the microbubble concentration, but requires more advanced algorithms to detect them individually. Several deep learning approaches have been proposed for this task, but they remain limited to 2D imaging, in part due to the associated large memory requirements. Herein, we propose to use sparse tensor neural networks to reduce memory usage in 2D and to improve the scaling of the memory requirement for the extension of deep learning architecture to 3D. We study several approaches to efficiently convert ultrasound data into a sparse format and study the impact of the associated loss of information. When applied in 2D, the sparse formulation reduces the memory requirements by a factor 2 at the cost of a small reduction of performance when compared against dense networks. In 3D, the proposed approach reduces memory requirements by two order of magnitude while largely outperforming conventional ULM in high concentration settings. We show that Sparse Tensor Neural Networks in 3D ULM allow for the same benefits as dense deep learning based method in 2D ULM i.e. the use of higher concentration in silico and reduced acquisition time.
2024-12-31
IEEE Transactions on Image Processing (inconnu)
doi.org
arxiv.org
Quantitative Analysis of Miniature Synaptic Calcium Transients Using Positive Unlabeled Deep Learning
Frédéric Beaupré
Anthony Bilodeau
Theresa Wiesner
Gabriel Leclerc
Mado Lemieux
Gabriel Nadeau
Katrine Castonguay
Bolin Fan
Simon Labrecque
Renée Hložek
Paul De Koninck
Christian Gagné
Flavie Lavoie-Cardinal
Ca 2+ imaging methods are widely used for studying cellular activity in the brain, allowing detailed ana… (voir plus)lysis of dynamic processes across various scales. Enhanced by high-contrast optical microscopy and fluorescent Ca 2+ sensors, this technique can be used to reveal localized Ca 2+ fluctuations within neurons, including in sub-cellular compartments, such as the dendritic shaft or spines. Despite advances in Ca 2+ sensors, the analysis of miniature Synaptic Calcium Transients (mSCTs), characterized by variability in morphology and low signal-to-noise ratios, remains challenging. Traditional threshold-based methods struggle with the detection and segmentation of these small, dynamic events. Deep learning (DL) approaches offer promising solutions but are limited by the need for large annotated datasets. Positive Unlabeled (PU) learning addresses this limitation by leveraging unlabeled instances to increase dataset size and enhance performance. This approach is particularly useful in the case of mSCTs that are scarce and small, associated with a very small proportion of the foreground pixels. PU learning significantly increases the effective size of the training dataset, improving model performance. Here, we present a PU learning-based strategy for detecting and segmenting mSCTs. We evaluate the performance of two 3D deep learning models, StarDist-3D and 3D U-Net, which are well established for the segmentation of small volumetric structures in microscopy datasets. By integrating PU learning, we enhance the 3D U-Net’s performance, demonstrating significant gains over traditional methods. This work pioneers the application of PU learning in Ca 2+ imaging analysis, offering a robust framework for mSCT detection and segmentation. We also demonstrate how this quantitative analysis pipeline can be used for subsequent mSCTs feature analysis. We characterize morphological and kinetic changes of mSCTs associated with the application of chemical long-term potentiation (cLTP) stimulation in cultured rat hippocampal neurons. Our data-driven approach shows that a cLTP-inducing stimulus leads to the emergence of new active dendritic regions and differently affects mSCTs subtypes.
2024-12-31
Digital Discovery (publié)
doi.org
R3Design: deep tertiary structure-based RNA sequence design and beyond
Cheng Tan
Yijie Zhang
Zhangyang Gao
Hanqun Cao
Siyuan Li
Siqi Ma
Mathieu Blanchette
Stan Z. Li
The rational design of Ribonucleic acid (RNA) molecules is crucial for advancing therapeutic applications, synthetic biology, and understand… (voir plus)ing the fundamental principles of life. Traditional RNA design methods have predominantly focused on secondary structure-based sequence design, often neglecting the intricate and essential tertiary interactions. We introduce R3Design, a tertiary structure-based RNA sequence design method that shifts the paradigm to prioritize tertiary structure in the RNA sequence design. R3Design significantly enhances sequence design on native RNA backbones, achieving high sequence recovery and Macro-F1 score, and outperforming traditional secondary structure-based approaches by substantial margins. We demonstrate that R3Design can design RNA sequences that fold into the desired tertiary structures by validating these predictions using advanced structure prediction models. This method, which is available through standalone software, provides a comprehensive toolkit for designing, folding, and evaluating RNA at the tertiary level. Our findings demonstrate R3Design’s superior capability in designing RNA sequences, which achieves around \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document}
2024-12-31
Briefings in Bioinformatics (publié)
doi.org
Recovering Dantzig–Wolfe Bounds by Cutting Planes
Ying Chen
Oktay Günlük
Andrea Lodi
Leveraging Dantzig–Wolfe Decomposition in the Original Variable Space for Mixed-Integer Programming Dantzig–Wolfe decomposition has been… (voir plus) extensively applied to solve large-scale mixed-integer programs with decomposable structures, leading to exact solution approaches, such as branch and price. However, these approaches would require solving the problem in an extended variable space and are not readily present in off-the-shelf solvers. In “Recovering Dantzig–Wolfe Bounds by Cutting Planes,” Chen, Günlük, and Lodi propose a computational effective approach for generating cutting planes from Dantzig–Wolfe decomposition to enhance branch and cut in the space of original variables. The proposed approach requires a relatively small number of cutting planes to recover the strength of the Dantzig–Wolfe dual bound and should be easy to implement in general-purpose mixed-integer programming solvers. The authors show that these cutting planes typically lead to a formulation with lower dual degeneracy and hence, a better computational performance than naïve approaches, such as the objective function cut.
2024-12-31
Oper. Res. (publié)
doi.org
arxiv.org
Reinforcement Learning for Versatile, Dynamic, and Robust Bipedal Locomotion Control
Zhongyu Li
Xue Bin Peng
Pieter Abbeel
Sergey Levine
Glen Berseth
Koushil Sreenath
This paper presents a comprehensive study on using deep reinforcement learning (RL) to create dynamic locomotion controllers for bipedal rob… (voir plus)ots. Going beyond focusing on a single locomotion skill, we develop a general control solution that can be used for a range of dynamic bipedal skills, from periodic walking and running to aperiodic jumping and standing. Our RL-based controller incorporates a novel dual-history architecture, utilizing both a long-term and short-term input/output (I/O) history of the robot. This control architecture, when trained through the proposed end-to-end RL approach, consistently outperforms other methods across a diverse range of skills in both simulation and the real world. The study also delves into the adaptivity and robustness introduced by the proposed RL system in developing locomotion controllers. We demonstrate that the proposed architecture can adapt to both time-invariant dynamics shifts and time-variant changes, such as contact events, by effectively using the robot's I/O history. Additionally, we identify task randomization as another key source of robustness, fostering better task generalization and compliance to disturbances. The resulting control policies can be successfully deployed on Cassie, a torque-controlled human-sized bipedal robot. This work pushes the limits of agility for bipedal robots through extensive real-world experiments. We demonstrate a diverse range of locomotion skills, including: robust standing, versatile walking, fast running with a demonstration of a 400-meter dash, and a diverse set of jumping skills, such as standing long jumps and high jumps.
2024-12-31
Int. J. Robotics Res. (publié)
doi.org
arxiv.org
Reputation Gaming in Crowd Technical Knowledge Sharing
Iren Mazloomzadeh
Gias Uddin
Foutse Khomh
Ashkan Sami
Stack Overflow incentive system awards users with reputation scores to ensure quality. The decentralized nature of the forum may make the in… (voir plus)centive system prone to manipulation. This paper offers, for the first time, a comprehensive study of the reported types of reputation manipulation scenarios that might be exercised in Stack Overflow and the prevalence of such reputation gamers by a qualitative study of 1,697 posts from meta Stack Exchange sites. We found four different types of reputation fraud scenarios, such as voting rings where communities form to upvote each other repeatedly on similar posts. We developed algorithms that enable platform managers to automatically identify these suspicious reputation gaming scenarios for review. The first algorithm identifies isolated/semi-isolated communities where probable reputation frauds may occur mostly by collaborating with each other. The second algorithm looks for sudden unusual big jumps in the reputation scores of users. We evaluated the performance of our algorithms by examining the reputation history dashboard of Stack Overflow users from the Stack Overflow website. We observed that around 60-80% of users flagged as suspicious by our algorithms experienced reductions in their reputation scores by Stack Overflow.
2024-12-31
ACM Trans. Softw. Eng. Methodol. (publié)
doi.org
Retreever: Tree-Based Coarse-to-Fine Representations for Retrieval
Shubham Gupta
Zichao Li
Tianyi Chen
Cem Subakan
Siva Reddy
Perouz Taslakian
Valentina Zantedeschi
Document retrieval is a core component of question-answering systems, as it enables conditioning answer generation on new and large-scale co… (voir plus)rpora. While effective, the standard practice of encoding documents into high-dimensional embeddings for similarity search entails large memory and compute footprints, and also makes it hard to inspect the inner workings of the system. In this paper, we propose a tree-based method for organizing and representing reference documents at various granular levels, which offers the flexibility to balance cost and utility, and eases the inspection of the corpus content and retrieval operations. Our method, called ReTreever, jointly learns a routing function per internal node of a binary tree such that query and reference documents are assigned to similar tree branches, hence directly optimizing for retrieval performance. Our evaluations show that ReTreever generally preserves full representation accuracy. Its hierarchical structure further provides strong coarse representations and enhances transparency by indirectly learning meaningful semantic groupings. Among hierarchical retrieval methods, ReTreever achieves the best retrieval accuracy at the lowest latency, proving that this family of techniques can be viable in practical applications.
2024-12-31
arXiv (prépublication)
doi.org
arxiv.org
Do Robot Snakes Dream like Electric Sheep? Investigating the Effects of Architectural Inductive Biases on Hallucination
Jerry Huang
Prasanna Parthasarathi
Mehdi Rezagholizadeh
Boxing Chen
A. Chandar
The growth in prominence of large language models (LLMs) in everyday life can be largely attributed to their generative abilities, yet some … (voir plus)of this is also owed to the risks and costs associated with their use. On one front is their tendency to \textit{hallucinate} false or misleading information, limiting their reliability. On another is the increasing focus on the computational limitations associated with traditional self-attention based LLMs, which has brought about new alternatives, in particular recurrent models, meant to overcome them. Yet it remains uncommon to consider these two concerns simultaneously. Do changes in architecture exacerbate/alleviate existing concerns about hallucinations? Do they affect how and where they occur? Through an extensive evaluation, we study how these architecture-based inductive biases affect the propensity to hallucinate. While hallucination remains a general phenomenon not limited to specific architectures, the situations in which they occur and the ease with which specific types of hallucinations can be induced can significantly differ based on the model architecture. These findings highlight the need for better understanding both these problems in conjunction with each other, as well as consider how to design more universal techniques for handling hallucinations.
2024-12-31
ACL (Findings) (publié)
doi.org
arxiv.org
Robust Fine-Tuning from Non-Robust Pretrained Models: Mitigating Suboptimal Transfer With Adversarial Scheduling
Jonas Ngnawe
Maxime Heuillet
Sabyasachi Sahoo
Yann Pequignot
Ola Ahmad
Audrey Durand
Frédéric Precioso
Christian Gagné
Fine-tuning pretrained models is a standard and effective workflow in modern machine learning. However, robust fine-tuning (RFT), which aims… (voir plus) to simultaneously achieve adaptation to a downstream task and robustness to adversarial examples, remains challenging. Despite the abundance of non-robust pretrained models in open-source repositories, their potential for RFT is less understood. We address this knowledge gap by systematically examining RFT from such non-robust models. Our experiments reveal that fine-tuning non-robust models with a robust objective, even under small perturbations, can lead to poor performance, a phenomenon that we dub \emph{suboptimal transfer}. In challenging scenarios (eg, difficult tasks, high perturbation), the resulting performance can be so low that it may be considered a transfer failure. We find that fine-tuning using a robust objective impedes task adaptation at the beginning of training and eventually prevents optimal transfer. However, we propose a novel heuristic, \emph{Epsilon-Scheduling}, a schedule over perturbation strength used during training that promotes optimal transfer. Additionally, we introduce \emph{expected robustness}, a metric that captures performance across a range of perturbations, providing a more comprehensive evaluation of the accuracy-robustness trade-off for diverse models at test time. Extensive experiments on a wide range of configurations (six pretrained models and five datasets) show that \emph{Epsilon-Scheduling} successfully prevents \emph{suboptimal transfer} and consistently improves expected robustness.
2024-12-31
arXiv (prépublication)
doi.org
arxiv.org
Robust Model Predictive Control for the Optimal Operation of the Indoor Environment of a Cluster of Smart Greenhouses
Ehsan Ghorbani
Ahmed Ouammi
Hanane Dagdougui
Smart greenhouses can be defined as cutting-edge technological systems that efficiently control indoor climate conditions to protect crops f… (voir plus)rom harsh outdoor conditions to increase their productivity. In this article, we developed and implemented a robust model predictive control approach that relies on a recursive state estimation method to cope with the impact of measurement and process signal errors. The aim of this approach is to optimally control the internal environment of intelligent greenhouses. A feedback policy problem is decomposing signals for the accessibility of uncertainties. Then, a robust feasibility set can be defined by determining the ellipsoid set on uncertainty to obtain solvable constrained optimization in the CPLEX solver. In the overall formulation, each greenhouse is considered as an independent element. This method can improve the quality of set-point tracking while reducing the computation time required to arrive at a solution. Extensive numerical simulations involving the application of an innovative and robust algorithm to a cluster of greenhouses were conducted to demonstrate the algorithm’s performance and effectiveness.
2024-12-31
IEEE Transactions on AgriFood Electronics (publié)
doi.org
Rootlets-based registration to the PAM50 spinal cord template
Sandrine Bédard
Jan Valosek
Valeria Oliva
Kenneth A. Weber II
Julien Cohen-Adad
Spinal cord functional MRI studies require precise localization of spinal levels for reliable voxelwise group analyses. Traditional template… (voir plus)-based registration of the spinal cord uses intervertebral discs for alignment. However, substantial anatomical variability across individuals exists between vertebral and spinal levels. This study proposes a novel registration approach that leverages spinal nerve rootlets to improve alignment accuracy and reproducibility across individuals. We developed a registration method leveraging dorsal cervical rootlets segmentation and aligning them non-linearly with the PAM50 spinal cord template. Validation was performed on a multi-subject, multi-site dataset (n=267, 44 sites) and a multi-subject dataset with various neck positions (n=10, 3 sessions). We further validated the method on task-based functional MRI (n=23) to compare group-level activation maps using rootlet-based registration to traditional disc-based methods. Rootlet-based registration showed superior alignment across individuals compared to the traditional disc-based method. Notably, rootlet positions were more stable across neck positions. Group-level analysis of task-based functional MRI using rootlet-based increased Z scores and activation cluster size compared to disc-based registration (number of active voxels from 3292 to 7978). Rootlet-based registration enhances both inter- and intra-subject anatomical alignment and yields better spatial normalization for group-level fMRI analyses. Our findings highlight the potential of rootlet-based registration to improve the precision and reliability of spinal cord neuroimaging group analysis.
2024-12-31
Imaging Neuroscience (publié)
doi.org
arxiv.org
Seeing the world as animals do: How to leverage generative AI for ecological neuroscience
Shahab Bakhtiari
2024-12-31
The Transmitter (publié)
doi.org