Publications

FairFLRep: Fairness aware fault localization and repair of Deep Neural Networks
Moses Openja
Paolo Arcaini
Foutse Khomh
Fuyuki Ishikawa
2025-08-11
ArXiv (preprint)
arxiv.org
arxiv.org
Untold stories: A qualitative investigation of patient and family experiences with congenital diaphragmatic hernia.
Alexandra Dimmer
Zanib Nafees
Sabrina Beauseigle
Franco A Carnevale
Elena Guadagno
Dan Poenaru
Pramod Puligandla
2025-08-11
Journal of Pediatric Surgery (published)
doi.org
Parity Requires Unified Input Dependence and Negative Eigenvalues in SSMs
Behnoush Khavari
Mehran Shakerinava
Jayesh Khullar
Jerry Huang
Franccois Rivest
Siamak Ravanbakhsh
Sarath Chandar
Recent work has shown that LRNN models such as S4D, Mamba, and DeltaNet lack state-tracking capability due to either time-invariant transiti… (see more)on matrices or restricted eigenvalue ranges. To address this, input-dependent transition matrices, particularly those that are complex or non-triangular, have been proposed to enhance SSM performance on such tasks. While existing theorems demonstrate that both input-independent and non-negative SSMs are incapable of solving simple state-tracking tasks, such as parity, regardless of depth, they do not explore whether combining these two types in a multilayer SSM could help. We investigate this question for efficient SSMs with diagonal transition matrices and show that such combinations still fail to solve parity. This implies that a recurrence layer must both be input-dependent and include negative eigenvalues. Our experiments support this conclusion by analyzing an SSM model that combines S4D and Mamba layers.
2025-08-10
ArXiv (preprint)
arxiv.org
arxiv.org
An Empirical Study on Method-Level Performance Evolution in Open-Source Java Projects
Kaveh Shahedi
Nana Gyambrah
Heng Li
Maxime Lamothe
Foutse Khomh
Performance is a critical quality attribute in software development, yet the impact of method-level code changes on performance evolution re… (see more)mains poorly understood. While developers often make intuitive assumptions about which types of modifications are likely to cause performance regressions or improvements, these beliefs lack empirical validation at a fine-grained level. We conducted a large-scale empirical study analyzing performance evolution in 15 mature open-source Java projects hosted on GitHub. Our analysis encompassed 739 commits containing 1,499 method-level code changes, using Java Microbenchmark Harness (JMH) for precise performance measurement and rigorous statistical analysis to quantify both the significance and magnitude of performance variations. We employed bytecode instrumentation to capture method-specific execution metrics and systematically analyzed four key aspects: temporal performance patterns, code change type correlations, developer and complexity factors, and domain-size interactions. Our findings reveal that 32.7% of method-level changes result in measurable performance impacts, with regressions occurring 1.3 times more frequently than improvements. Contrary to conventional wisdom, we found no significant differences in performance impact distributions across code change categories, challenging risk-stratified development strategies. Algorithmic changes demonstrate the highest improvement potential but carry substantial regression risk. Senior developers produce more stable changes with fewer extreme variations, while code complexity correlates with increased regression likelihood. Domain-size interactions reveal significant patterns, with web server + small projects exhibiting the highest performance instability. Our study provides empirical evidence for integrating automated performance testing into continuous integration pipelines.
2025-08-09
ArXiv (preprint)
arxiv.org
arxiv.org
An Empirical Study on Method-Level Performance Evolution in Open-Source Java Projects
Kaveh Shahedi
Nana Gyambrah
Heng Li
Maxime Lamothe
Foutse Khomh
Performance is a critical quality attribute in software development, yet the impact of method-level code changes on performance evolution re… (see more)mains poorly understood. While developers often make intuitive assumptions about which types of modifications are likely to cause performance regressions or improvements, these beliefs lack empirical validation at a fine-grained level. We conducted a large-scale empirical study analyzing performance evolution in 15 mature open-source Java projects hosted on GitHub. Our analysis encompassed 739 commits containing 1,499 method-level code changes, using Java Microbenchmark Harness (JMH) for precise performance measurement and rigorous statistical analysis to quantify both the significance and magnitude of performance variations. We employed bytecode instrumentation to capture method-specific execution metrics and systematically analyzed four key aspects: temporal performance patterns, code change type correlations, developer and complexity factors, and domain-size interactions. Our findings reveal that 32.7% of method-level changes result in measurable performance impacts, with regressions occurring 1.3 times more frequently than improvements. Contrary to conventional wisdom, we found no significant differences in performance impact distributions across code change categories, challenging risk-stratified development strategies. Algorithmic changes demonstrate the highest improvement potential but carry substantial regression risk. Senior developers produce more stable changes with fewer extreme variations, while code complexity correlates with increased regression likelihood. Domain-size interactions reveal significant patterns, with web server + small projects exhibiting the highest performance instability. Our study provides empirical evidence for integrating automated performance testing into continuous integration pipelines.
2025-08-09
ArXiv (preprint)
arxiv.org
arxiv.org
Low-Rank Expert Merging for Multi-Source Domain Adaptation in Person Re-Identification
Taha Mustapha Nehdi
Nairouz Mrabah
Atif Belal
Marco Pedersoli
Eric Granger
Adapting person re-identification (reID) models to new target environments remains a challenging problem that is typically addressed using u… (see more)nsupervised domain adaptation (UDA) methods. Recent works show that when labeled data originates from several distinct sources (e.g., datasets and cameras), considering each source separately and applying multi-source domain adaptation (MSDA) typically yields higher accuracy and robustness compared to blending the sources and performing conventional UDA. However, state-of-the-art MSDA methods learn domain-specific backbone models or require access to source domain data during adaptation, resulting in significant growth in training parameters and computational cost. In this paper, a Source-free Adaptive Gated Experts (SAGE-reID) method is introduced for person reID. Our SAGE-reID is a cost-effective, source-free MSDA method that first trains individual source-specific low-rank adapters (LoRA) through source-free UDA. Next, a lightweight gating network is introduced and trained to dynamically assign optimal merging weights for fusion of LoRA experts, enabling effective cross-domain knowledge transfer. While the number of backbone parameters remains constant across source domains, LoRA experts scale linearly but remain negligible in size (= 2% of the backbone), reducing both the memory consumption and risk of overfitting. Extensive experiments conducted on three challenging b
2025-08-09
ArXiv (preprint)
arxiv.org
arxiv.org
Low-Rank Expert Merging for Multi-Source Domain Adaptation in Person Re-Identification
Taha Mustapha Nehdi
Nairouz Mrabah
Atif Belal
Marco Pedersoli
Eric Granger
2025-08-09
ArXiv (preprint)
arxiv.org
arxiv.org
Spatio-Temporal Conditional Diffusion Models for Forecasting Future Multiple Sclerosis Lesion Masks Conditioned on Treatments
Gian Mario Favero
Ge Ya Luo
Nima Fathi
Justin Szeto
Douglas Arnold
Brennan Nichyporuk
Chris Pal
Tal Arbel
Image-based personalized medicine has the potential to transform healthcare, particularly for diseases that exhibit heterogeneous progressio… (see more)n such as Multiple Sclerosis (MS). In this work, we introduce the first treatment-aware spatio-temporal diffusion model that is able to generate future masks demonstrating lesion evolution in MS. Our voxel-space approach incorporates multi-modal patient data, including MRI and treatment information, to forecast new and enlarging T2 (NET2) lesion masks at a future time point. Extensive experiments on a multi-centre dataset of 2131 patient 3D MRIs from randomized clinical trials for relapsing-remitting MS demonstrate that our generative model is able to accurately predict NET2 lesion masks for patients across six different treatments. Moreover, we demonstrate our model has the potential for real-world clinical applications through downstream tasks such as future lesion count and location estimation, binary lesion activity classification, and generating counterfactual future NET2 masks for several treatments with different efficacies. This work highlights the potential of causal, image-based generative models as powerful tools for advancing data-driven prognostics in MS.
2025-08-09
ArXiv (preprint)
arxiv.org
arxiv.org
Spatio-Temporal Conditional Diffusion Models for Forecasting Future Multiple Sclerosis Lesion Masks Conditioned on Treatments
Gian Mario Favero
Ge Ya Luo
Nima Fathi
Justin Szeto
Douglas Arnold
Brennan Nichyporuk
Chris Pal
Tal Arbel
2025-08-09
ArXiv (preprint)
arxiv.org
arxiv.org
CISO: Species Distribution Modeling Conditioned on Incomplete Species Observations
Hager Radi
Mélisande Teng
Robin Zbinden
Laura Pollock
Hugo Larochelle
Devis Tuia
David Rolnick
Species distribution models (SDMs) are widely used to predict species'geographic distributions, serving as critical tools for ecological res… (see more)earch and conservation planning. Typically, SDMs relate species occurrences to environmental variables representing abiotic factors, such as temperature, precipitation, and soil properties. However, species distributions are also strongly influenced by biotic interactions with other species, which are often overlooked. While some methods partially address this limitation by incorporating biotic interactions, they often assume symmetrical pairwise relationships between species and require consistent co-occurrence data. In practice, species observations are sparse, and the availability of information about the presence or absence of other species varies significantly across locations. To address these challenges, we propose CISO, a deep learning-based method for species distribution modeling Conditioned on Incomplete Species Observations. CISO enables predictions to be conditioned on a flexible number of species observations alongside environmental variables, accommodating the variability and incompleteness of available biotic data. We demonstrate our approach using three datasets representing different species groups: sPlotOpen for plants, SatBird for birds, and a new dataset, SatButterfly, for butterflies. Our results show that including partial biotic information improves predictive performance on spatially separate test sets. When conditioned on a subset of species within the same dataset, CISO outperforms alternative methods in predicting the distribution of the remaining species. Furthermore, we show that combining observations from multiple datasets can improve performance. CISO is a promising ecological tool, capable of incorporating incomplete biotic information and identifying potential interactions between species from disparate taxa.
2025-08-08
ArXiv (preprint)
arxiv.org
arxiv.org
CISO: Species Distribution Modeling Conditioned on Incomplete Species Observations
Hager Radi
Mélisande Teng
Robin Zbinden
Laura Pollock
Hugo Larochelle
Devis Tuia
David Rolnick
Species distribution models (SDMs) are widely used to predict species'geographic distributions, serving as critical tools for ecological res… (see more)earch and conservation planning. Typically, SDMs relate species occurrences to environmental variables representing abiotic factors, such as temperature, precipitation, and soil properties. However, species distributions are also strongly influenced by biotic interactions with other species, which are often overlooked. While some methods partially address this limitation by incorporating biotic interactions, they often assume symmetrical pairwise relationships between species and require consistent co-occurrence data. In practice, species observations are sparse, and the availability of information about the presence or absence of other species varies significantly across locations. To address these challenges, we propose CISO, a deep learning-based method for species distribution modeling Conditioned on Incomplete Species Observations. CISO enables predictions to be conditioned on a flexible number of species observations alongside environmental variables, accommodating the variability and incompleteness of available biotic data. We demonstrate our approach using three datasets representing different species groups: sPlotOpen for plants, SatBird for birds, and a new dataset, SatButterfly, for butterflies. Our results show that including partial biotic information improves predictive performance on spatially separate test sets. When conditioned on a subset of species within the same dataset, CISO outperforms alternative methods in predicting the distribution of the remaining species. Furthermore, we show that combining observations from multiple datasets can improve performance. CISO is a promising ecological tool, capable of incorporating incomplete biotic information and identifying potential interactions between species from disparate taxa.
2025-08-08
ArXiv (preprint)
arxiv.org
arxiv.org
Personalized Feature Translation for Expression Recognition: An Efficient Source-Free Domain Adaptation Method
Masoumeh Sharafi
Soufiane Belharbi
Houssem Ben Salem
Ali Etemad
Alessandro Lameiras Koerich
Marco Pedersoli
Simon Bacon
Eric Granger
Facial expression recognition (FER) models are employed in many video-based affective computing applications, such as human-computer interac… (see more)tion and healthcare monitoring. However, deep FER models often struggle with subtle expressions and high inter-subject variability, limiting their performance in real-world applications. To improve their performance, source-free domain adaptation (SFDA) methods have been proposed to personalize a pretrained source model using only unlabeled target domain data, thereby avoiding data privacy, storage, and transmission constraints. This paper addresses a challenging scenario where source data is unavailable for adaptation, and only unlabeled target data consisting solely of neutral expressions is available. SFDA methods are not typically designed to adapt using target data from only a single class. Further, using models to generate facial images with non-neutral expressions can be unstable and computationally intensive. In this paper, personalized feature translation (PFT) is proposed for SFDA. Unlike current image translation methods for SFDA, our lightweight method operates in the latent space. We first pre-train the translator on the source domain data to transform the subject-specific style features from one source subject into another. Expression information is preserved by optimizing a combination of expression consistency and style-aware objectives. Then, the translator is adapted on neutral target data, without using source data or image synthesis. By translating in the latent space, PFT avoids the complexity and noise of face expression generation, producing discriminative embeddings optimized for classification. Using PFT eliminates the need for image synthesis, reduces computational overhead (using a lightweight translator), and only adapts part of the model, making the method efficient compared to image-based translation.
2025-08-08
ArXiv (preprint)
arxiv.org
arxiv.org