Publications

Designing Experimental Setup Emulating Log-Loader Manipulator and Implementing Anti-Sway Trajectory Planner
Iman Jebellat
George Sideris
Rafid Saif
Inna Sharf
Forestry machines are not easily accessible for experimentation or demonstration of research results. These mobile robots are massive, very … (voir plus)expensive, and require a large outdoor space and permits to operate. These factors hinder conducting experiments on real forestry robots. Thus, it is essential to design experimental setups utilizing easily accessible robots in indoor labs that can effectively replicate the behavior of interest of a forestry machine. We design a setup to resemble a log-loader crane and grapple motions using a Kinova Jaco2 arm by manufacturing a specialized end-effector to attach passively to the Jaco2 arm. Passively attached grapple causes undesirable sway, which is problematic and dangerous in forestry. To address the sway problem, we employ dynamic programming to develop an anti-sway motion planner, and validate its performance for different point-to-point maneuvers in our experimental setup. We also repeat each experiment at least 6 times to ensure the repeatability and reliability of the experiments. The experimental results showcase the excellent sway-damping performance of our planner and also the very good repeatability of our experiments.
2024-12-31
IEEE International Conference on Robotics and Automation (publié)
doi.org
A Distributed ADMM-based Deep Learning Approach for Thermal Control in Multi-Zone Buildings
Vincent Taboga
Hanane Dagdougui
The surge in electricity use, coupled with the dependency on intermittent renewable energy sources, poses significant hurdles to effectively… (voir plus) managing power grids, particularly during times of peak demand. Demand Response programs and energy conservation measures are essential to operate energy grids while ensuring a responsible use of our resources This research combines distributed optimization using ADMM with Deep Learning models to plan indoor temperature setpoints effectively. A two-layer hierarchical structure is used, with a central building coordinator at the upper layer and local controllers at the thermal zone layer. The coordinator must limit the building's maximum power by translating the building's total power to local power targets for each zone. Local controllers can modify the temperature setpoints to meet the local power targets. The resulting control algorithm, called Distributed Planning Networks, is designed to be both adaptable and scalable to many types of buildings, tackling two of the main challenges in the development of such systems. The proposed approach is tested on an 18-zone building modeled in EnergyPlus. The algorithm successfully manages Demand Response peak events.
2024-12-31
IEEE Trans Autom. Sci. Eng. (publié)
doi.org
arxiv.org
dyAb: Flow Matching for Flexible Antibody Design with AlphaFold-driven Pre-binding Antigen
Cheng Tan
Yijie Zhang
Zhangyang Gao
Yufei Huang
Haitao Lin
Lirong Wu
Fandi Wu
Mathieu Blanchette
Stan Z. Li
The development of therapeutic antibodies heavily relies on accurate predictions of how antigens will interact with antibodies. Existing com… (voir plus)putational methods in antibody design often overlook crucial conformational changes that antigens undergo during the binding process, significantly impacting the reliability of the resulting antibodies. To bridge this gap, we introduce dyAb, a flexible framework that incorporates AlphaFold2-driven predictions to model pre-binding antigen structures and specifically addresses the dynamic nature of antigen conformation changes. Our dyAb model leverages a unique combination of coarse-grained interface alignment and fine-grained flow matching techniques to simulate the interaction dynamics and structural evolution of the antigen-antibody complex, providing a realistic representation of the binding process. Extensive experiments show that dyAb significantly outperforms existing models in antibody design involving changing antigen conformations. These results highlight dyAb's potential to streamline the design process for therapeutic antibodies, promising more efficient development cycles and improved outcomes in clinical applications.
2024-12-31
AAAI Conference on Artificial Intelligence (publié)
doi.org
arxiv.org
Efficient and Accurate Optimal Transport with Mirror Descent and Conjugate Gradients
Mete Kemertas
Allan Jepson
Amir-massoud Farahmand
2024-12-31
Trans. Mach. Learn. Res. (publié)
doi.org
arxiv.org
Embedding Cultural Diversity in Prototype-based Recommender Systems
Armin Moradi
Nicola Neophytou
Florian Carichon
Golnoosh Farnadi
Popularity bias in recommender systems can increase cultural overrepresentation by favoring norms from dominant cultures and marginalizing u… (voir plus)nderrepresented groups. This issue is critical for platforms offering cultural products, as they influence consumption patterns and human perceptions. In this work, we address popularity bias by identifying demographic biases within prototype-based matrix factorization methods. Using the country of origin as a proxy for cultural identity, we link this demographic attribute to popularity bias by refining the embedding space learning process. First, we propose filtering out irrelevant prototypes to improve representativity. Second, we introduce a regularization technique to enforce a uniform distribution of prototypes within the embedding space. Across four datasets, our results demonstrate a 27\% reduction in the average rank of long-tail items and a 2\% reduction in the average rank of items from underrepresented countries. Additionally, our model achieves a 2\% improvement in HitRatio@10 compared to the state-of-the-art, highlighting that fairness is enhanced without compromising recommendation quality. Moreover, the distribution of prototypes leads to more inclusive explanations by better aligning items with diverse prototypes.
2024-12-31
European Conference on Information Retrieval (publié)
doi.org
arxiv.org
An empirical study of testing machine learning in the wild
Moses Openja
Foutse Khomh
Armstrong Foundjem
Zhen Ming
Mouna Abidi
Ahmed E. Hassan
Recently, machine and deep learning (ML/DL) algorithms have been increasingly adopted in many software systems. Due to their inductive natur… (voir plus)e, ensuring the quality of these systems remains a significant challenge for the research community. Unlike traditional software built deductively by writing explicit rules, ML/DL systems infer rules from training data. Recent research in ML/DL quality assurance has adapted concepts from traditional software testing, such as mutation testing, to improve reliability. However, it is unclear if these proposed testing techniques are adopted in practice, or if new testing strategies have emerged from real-world ML deployments. There is little empirical evidence about the testing strategies. To fill this gap, we perform the first fine-grained empirical study on ML testing in the wild to identify the ML properties being tested, the testing strategies, and their implementation throughout the ML workflow. We conducted a mixed-methods study to understand ML software testing practices. We analyzed test files and cases from 11 open-source ML/DL projects on GitHub. Using open coding, we manually examined the testing strategies, tested ML properties, and implemented testing methods to understand their practical application in building and releasing ML/DL software systems. Our findings reveal several key insights: 1.) The most common testing strategies, accounting for less than 40%, are Grey-box and White-box methods, such as Negative Testing, Oracle Approximation and Statistical Testing. 2.) A wide range of 17 ML properties are tested, out of which only 20% to 30% are frequently tested, including Consistency, Correctness}, and Efficiency. 3.) Bias and Fairness is more tested in Recommendation, while Security & Privacy is tested in Computer Vision (CV) systems, Application Platforms, and Natural Language Processing (NLP) systems.
2024-12-31
ACM Trans. Softw. Eng. Methodol. (publié)
doi.org
arxiv.org
EPISeg: Automated segmentation of the spinal cord on echo planar images using open-access multi-center data
Rohan Banerjee
Merve Kaptan
Alexandra Tinnermann
Ali Khatibi
Alice Dabbagh
Christian Büchel
Christian W. Kündig
Christine Law
Dario Pfyffer
David J. Lythgoe
Dimitra Tsivaka
Dimitri Van De Ville
Falk Eippert
Fauziyya Muhammad
Gary H. Glover
Gergely David
Grace Haynes
Jan Haaker
J.C. Brooks
Jürgen Finsterbusch … (voir 21 de plus)
Katherine T. Martucci
Kimberly J. Hemmerling
Mahdi Mobarak-Abadi
Mark A. Hoggarth
Matthew A. Howard
Molly G. Bright
Nawal Kinany
Olivia S. Kowalczyk
Patrick Freund
Robert Barry
Sean Mackey
Shahabeddin Vahdat
Simon Schading‐Sassenhausen
Stephen B. McMahon
Todd Parish
Véronique Marchand‐Pauvert
Yufen Chen
Zachary A. Smith
Kenneth A. Weber
Benjamin De Leener
Julien Cohen‐Adad
Functional magnetic resonance imaging (fMRI) of the spinal cord is relevant for studying sensation, movement, and autonomic function. Prepro… (voir plus)cessing of spinal cord fMRI data involves segmentation of the spinal cord on gradient-echo echo planar imaging (EPI) images. Current automated segmentation methods do not work well on these data, due to the low spatial resolution, susceptibility artifacts causing distortions and signal drop-out, ghosting, and motion-related artifacts. Consequently, this segmentation task demands a considerable amount of manual effort which takes time and is prone to user bias. In this work, we (i) gathered a multi-center dataset of spinal cord gradient-echo EPI with ground-truth segmentations and shared it on OpenNeuro https://openneuro.org/datasets/ds005143/versions/1.3.1 and (ii) developed a deep learning-based model, EPISeg, for the automatic segmentation of the spinal cord on gradient-echo EPI data. We observe a significant improvement in terms of segmentation quality compared with other available spinal cord segmentation models. Our model is resilient to different acquisition protocols as well as commonly observed artifacts in fMRI data. The training code is available at https://github.com/sct-pipeline/fmri-segmentation/, and the model has been integrated into the Spinal Cord Toolbox as a command-line tool.
2024-12-31
Imaging Neuroscience (publié)
doi.org
Estimating Head Motion in Structural MRI Using a Deep Neural Network Trained on Synthetic Artifacts
C Bricout
S Ebrahimi Kahou
Sylvain Bouix
2024-12-31
arXiv.org (prépublication)
doi.org
On Estimating the Strength of Differentially Private Mechanisms in a Black-Box Setting
Daniele Gorla
Louis Jalouzot
Federica Granese
Catuscia Palamidessi
Pablo Piantanida
We analyze to what extent final users can infer information about the level of protection of their data when the data obfuscation mechanism … (voir plus)is a priori unknown to them (the so-called “black-box” scenario). In particular, we explore four notions of differential privacy, namely local/central
2024-12-31
IEEE Transactions on Dependable and Secure Computing (inconnu)
doi.org
Evaluation of machine learning and deep learning models for the classification of a single extracellular vesicles spectral library
C. del Real Mata
Y. Lu
M. Jalali
A. Bocan
M. Khatami
L. Montermini
J. McCormack-llersich
W. W. Reisner
L. Garzia
J. Rak
D. Bzdok
S. Mahshid
Nanostructure-based sensors study extracellular vesicles; optimization of a single-vesicle resolution spectral library to enhance classifica… (voir plus)tion for future AI-driven diagnostics.
2024-12-31
Sensors and Diagnostics (publié)
doi.org
Exploiting Instruction-Following Retrievers for Malicious Information Retrieval
Parishad BehnamGhader
Nicholas Meade
Siva Reddy
Instruction-following retrievers have been widely adopted alongside LLMs in real-world applications, but little work has investigated the sa… (voir plus)fety risks surrounding their increasing search capabilities. We empirically study the ability of retrievers to satisfy malicious queries, both when used directly and when used in a retrieval augmented generation-based setup. Concretely, we investigate six leading retrievers, including NV-Embed and LLM2Vec, and find that given malicious requests, most retrievers can (for >50% of queries) select relevant harmful passages. For example, LLM2Vec correctly selects passages for 61.35% of our malicious queries. We further uncover an emerging risk with instruction-following retrievers, where highly relevant harmful information can be surfaced by exploiting their instruction-following capabilities. Finally, we show that even safety-aligned LLMs, such as Llama3, can satisfy malicious requests when provided with harmful retrieved passages in-context. In summary, our findings underscore the malicious misuse risks associated with increasing retriever capability.
2024-12-31
ACL (Findings) (publié)
doi.org
arxiv.org
Generalization Limits of Graph Neural Networks in Identity Effects Learning
Giuseppe Alessio D'Inverno
Simone Brugiapaglia
Mirco Ravanelli
Graph Neural Networks (GNNs) have emerged as a powerful tool for data-driven learning on various graph domains. They are usually based on a … (voir plus)message-passing mechanism and have gained increasing popularity for their intuitive formulation, which is closely linked to the Weisfeiler-Lehman (WL) test for graph isomorphism to which they have been proven equivalent in terms of expressive power. In this work, we establish new generalization properties and fundamental limits of GNNs in the context of learning so-called identity effects, i.e., the task of determining whether an object is composed of two identical components or not. Our study is motivated by the need to understand the capabilities of GNNs when performing simple cognitive tasks, with potential applications in computational linguistics and chemistry. We analyze two case studies: (i) two-letters words, for which we show that GNNs trained via stochastic gradient descent are unable to generalize to unseen letters when utilizing orthogonal encodings like one-hot representations; (ii) dicyclic graphs, i.e., graphs composed of two cycles, for which we present positive existence results leveraging the connection between GNNs and the WL test. Our theoretical analysis is supported by an extensive numerical study.
2024-12-31
Neural Networks (publié)
doi.org
arxiv.org