Publications

From Technical Excellence to Practical Adoption: Lessons Learned Building an ML-Enhanced Trace Analysis Tool
Kaveh Shahedi
Matthew Khouzam
Heng Li
Maxime Lamothe
Foutse Khomh
System tracing has become essential for understanding complex software behavior in modern systems, yet sophisticated trace analysis tools fa… (voir plus)ce significant adoption gaps in industrial settings. Through a year-long collaboration with Ericsson Montr\'eal, developing TMLL (Trace-Server Machine Learning Library, now in the Eclipse Foundation), we investigated barriers to trace analysis adoption. Contrary to assumptions about complexity or automation needs, practitioners struggled with translating expert knowledge into actionable insights, integrating analysis into their workflows, and trusting automated results they could not validate. We identified what we called the Excellence Paradox: technical excellence can actively impede adoption when conflicting with usability, transparency, and practitioner trust. TMLL addresses this through adoption-focused design that embeds expert knowledge in interfaces, provides transparent explanations, and enables incremental adoption. Validation through Ericsson's experts'feedback, Eclipse Foundation's integration, and a survey of 40 industry and academic professionals revealed consistent patterns: survey results showed that 77.5% prioritize quality and trust in results over technical sophistication, while 67.5% prefer semi-automated analysis with user control, findings supported by qualitative feedback from industrial collaboration and external peer review. Results validate three core principles: cognitive compatibility, embedded expertise, and transparency-based trust. This challenges conventional capability-focused tool development, demonstrating that sustainable adoption requires reorientation toward adoption-focused design with actionable implications for automated software engineering tools.
2025-08-02
ArXiv (prépublication)
arxiv.org
arxiv.org
Inhibition of epithelial cell YAP-TEAD/LOX signaling attenuates pulmonary fibrosis in preclinical models
Darcy Elizabeth Wagner
Hani N. Alsafadi
Nilay Mitash
Aurelien Justet
Qianjiang Hu
Ricardo Pineda
Claudia Staab-Weijnitz
Martina Korfei
Nika Gvazava
Kristin Wannemo
Ugochi Onwuka
Molly Mozurak
Adriana Estrada-Bernal
Juan Cala Garcia
Katrin Mutze
Rita Costa
Deniz Bölükbas
John Stegmayr
Wioletta Skronska-Wasek
Stephan Klee … (voir 14 de plus)
Chiharu Ota
Hoeke A. Baarsma
Jingtao Wang
John Sembrat
Anne Hilgendorff
Jun Ding
Andreas Günther
Rachel Chambers
Ivan O Rosas
Stijn de Langhe
Naftali Kaminski
Mareike Lehmann
Oliver Eickelberg
Melanie Königshoff
Idiopathic pulmonary fibrosis (IPF) is a progressive and lethal disease characterized by excessive extracellular matrix deposition. Current … (voir plus)IPF therapies slow disease progression but do not stop or reverse it. The (myo)fibroblasts are thought to be the main cellular contributors to excessive extracellular matrix production in IPF. Here we show that fibrotic alveolar type II cells regulate production and crosslinking of extracellular matrix via the co-transcriptional activator YAP. YAP leads to increased expression of Lysl oxidase (LOX) and subsequent LOX-mediated crosslinking by fibrotic alveolar type II cells. Pharmacological YAP inhibition via verteporfin reverses fibrotic alveolar type II cell reprogramming and LOX expression in experimental lung fibrosis in vivo and in human fibrotic tissue ex vivo. We thus identify YAP-TEAD/LOX inhibition in alveolar type II cells as a promising potential therapy for IPF patients.
2025-08-02
Nature Communications (publié)
doi.org
Inhibition of epithelial cell YAP-TEAD/LOX signaling attenuates pulmonary fibrosis in preclinical models
Darcy Elizabeth Wagner
Hani N. Alsafadi
Nilay Mitash
Aurelien Justet
Qianjiang Hu
Ricardo Pineda
Claudia Staab-Weijnitz
Martina Korfei
Nika Gvazava
Kristin Wannemo
Ugochi Onwuka
Molly Mozurak
Adriana Estrada-Bernal
Juan Cala Garcia
Katrin Mutze
Rita Costa
Deniz Bölükbas
John Stegmayr
Wioletta Skronska-Wasek
Stephan Klee … (voir 14 de plus)
Chiharu Ota
Hoeke A. Baarsma
Jingtao Wang
John Sembrat
Anne Hilgendorff
Jun Ding
Andreas Günther
Rachel Chambers
Ivan O Rosas
Stijn de Langhe
Naftali Kaminski
Mareike Lehmann
Oliver Eickelberg
Melanie Königshoff
Idiopathic pulmonary fibrosis (IPF) is a progressive and lethal disease characterized by excessive extracellular matrix deposition. Current … (voir plus)IPF therapies slow disease progression but do not stop or reverse it. The (myo)fibroblasts are thought to be the main cellular contributors to excessive extracellular matrix production in IPF. Here we show that fibrotic alveolar type II cells regulate production and crosslinking of extracellular matrix via the co-transcriptional activator YAP. YAP leads to increased expression of Lysl oxidase (LOX) and subsequent LOX-mediated crosslinking by fibrotic alveolar type II cells. Pharmacological YAP inhibition via verteporfin reverses fibrotic alveolar type II cell reprogramming and LOX expression in experimental lung fibrosis in vivo and in human fibrotic tissue ex vivo. We thus identify YAP-TEAD/LOX inhibition in alveolar type II cells as a promising potential therapy for IPF patients.
2025-08-02
Nature Communications (publié)
doi.org
Inhibition of epithelial cell YAP-TEAD/LOX signaling attenuates pulmonary fibrosis in preclinical models
Darcy Elizabeth Wagner
Hani N. Alsafadi
Nilay Mitash
Aurelien Justet
Qianjiang Hu
Ricardo Pineda
Claudia Staab-Weijnitz
Martina Korfei
Nika Gvazava
Kristin Wannemo
Ugochi Onwuka
Molly Mozurak
Adriana Estrada-Bernal
Juan Cala Garcia
Katrin Mutze
Rita Costa
Deniz Bölükbas
John Stegmayr
Wioletta Skronska-Wasek
Stephan Klee … (voir 14 de plus)
Chiharu Ota
Hoeke A. Baarsma
Jingtao Wang
John Sembrat
Anne Hilgendorff
Jun Ding
Andreas Günther
Rachel Chambers
Ivan O Rosas
Stijn de Langhe
Naftali Kaminski
Mareike Lehmann
Oliver Eickelberg
Melanie Königshoff
Idiopathic pulmonary fibrosis (IPF) is a progressive and lethal disease characterized by excessive extracellular matrix deposition. Current … (voir plus)IPF therapies slow disease progression but do not stop or reverse it. The (myo)fibroblasts are thought to be the main cellular contributors to excessive extracellular matrix production in IPF. Here we show that fibrotic alveolar type II cells regulate production and crosslinking of extracellular matrix via the co-transcriptional activator YAP. YAP leads to increased expression of Lysl oxidase (LOX) and subsequent LOX-mediated crosslinking by fibrotic alveolar type II cells. Pharmacological YAP inhibition via verteporfin reverses fibrotic alveolar type II cell reprogramming and LOX expression in experimental lung fibrosis in vivo and in human fibrotic tissue ex vivo. We thus identify YAP-TEAD/LOX inhibition in alveolar type II cells as a promising potential therapy for IPF patients.
2025-08-02
Nature Communications (publié)
doi.org
Adaptation, Comparison and Practical Implementation of Fairness Schemes in Kidney Exchange Programs
William St-Arnaud
Margarida Carvalho
Golnoosh Farnadi
In Kidney Exchange Programs (KEPs), each participating patient is registered together with an incompatible donor. Donors without an incompat… (voir plus)ible patient can also register. Then, KEPs typically maximize overall patient benefit through donor exchanges. This aggregation of benefits calls into question potential individual patient disparities in terms of access to transplantation in KEPs. Considering solely this utilitarian objective may become an issue in the case where multiple exchange plans are optimal or near-optimal. In fact, current KEP policies are all-or-nothing, meaning that only one exchange plan is determined. Each patient is either selected or not as part of that unique solution. In this work, we seek instead to find a policy that contemplates the probability of patients of being in a solution. To guide the determination of our policy, we adapt popular fairness schemes to KEPs to balance the usual approach of maximizing the utilitarian objective. Different combinations of fairness and utilitarian objectives are modelled as conic programs with an exponential number of variables. We propose a column generation approach to solve them effectively in practice. Finally, we make an extensive comparison of the different schemes in terms of the balance of utility and fairness score, and validate the scalability of our methodology for benchmark instances from the literature.
2025-08-01
European Journal of Operational Research (publié)
doi.org
arxiv.org
Amortized Sampling with Transferable Normalizing Flows
Charlie B. Tan
Majdi Hassan
Leon Klein
Saifuddin Syed
Dominique Beaini
Michael M. Bronstein
Alexander Tong
Kirill Neklyudov
Efficient equilibrium sampling of molecular conformations remains a core challenge in computational chemistry and statistical inference. Cla… (voir plus)ssical approaches such as molecular dynamics or Markov chain Monte Carlo inherently lack amortization; the computational cost of sampling must be paid in-full for each system of interest. The widespread success of generative models has inspired interest into overcoming this limitation through learning sampling algorithms. Despite performing on par with conventional methods when trained on a single system, learned samplers have so far demonstrated limited ability to transfer across systems. We prove that deep learning enables the design of scalable and transferable samplers by introducing Prose, a 280 million parameter all-atom transferable normalizing flow trained on a corpus of peptide molecular dynamics trajectories up to 8 residues in length. Prose draws zero-shot uncorrelated proposal samples for arbitrary peptide systems, achieving the previously intractable transferability across sequence length, whilst retaining the efficient likelihood evaluation of normalizing flows. Through extensive empirical evaluation we demonstrate the efficacy of Prose as a proposal for a variety of sampling algorithms, finding a simple importance sampling-based finetuning procedure to achieve superior performance to established methods such as sequential Monte Carlo on unseen tetrapeptides. We open-source the Prose codebase, model weights, and training dataset, to further stimulate research into amortized sampling methods and finetuning objectives.
2025-08-01
arXiv (publié)
doi.org
BiXSE: Improving Dense Retrieval via Probabilistic Graded Relevance Distillation
Christos Tsirigotis
Vaibhav Adlakha
Joao Monteiro
Aaron Courville
Perouz Taslakian
Neural sentence embedding models for dense retrieval typically rely on binary relevance labels, treating query-document pairs as either rele… (voir plus)vant or irrelevant. However, real-world relevance often exists on a continuum, and recent advances in large language models (LLMs) have made it feasible to scale the generation of fine-grained graded relevance labels. In this work, we propose BiXSE, a simple and effective pointwise training method that optimizes binary cross-entropy (BCE) over LLM-generated graded relevance scores. BiXSE interprets these scores as probabilistic targets, enabling granular supervision from a single labeled query-document pair per query. Unlike pairwise or listwise losses that require multiple annotated comparisons per query, BiXSE achieves strong performance with reduced annotation and compute costs by leveraging in-batch negatives. Extensive experiments across sentence embedding (MMTEB) and retrieval benchmarks (BEIR, TREC-DL) show that BiXSE consistently outperforms softmax-based contrastive learning (InfoNCE), and matches or exceeds strong pairwise ranking baselines when trained on LLM-supervised data. BiXSE offers a robust, scalable alternative for training dense retrieval models as graded relevance supervision becomes increasingly accessible.
2025-08-01
arXiv (publié)
doi.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… (voir plus)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.
2025-08-01
arXiv (publié)
doi.org
arxiv.org
Co-Producing AI: Toward an Augmented, Participatory Lifecycle
Rashid A. Mushkani
Hugo Berard
Toumadher Ammar
Cassandre Chatonnier
Shin (Alexandre) Koseki
Despite efforts to mitigate the inherent risks and biases of artificial intelligence (AI) algorithms, these algorithms can disproportionatel… (voir plus)y impact culturally marginalized groups. A range of approaches has been proposed to address or reduce these risks, including the development of ethical guidelines and principles for responsible AI, as well as technical solutions that promote algorithmic fairness. Drawing on design justice, expansive learning theory, and recent empirical work on participatory AI, we argue that mitigating these harms requires a fundamental re-architecture of the AI production pipeline. This re-design should center co-production, diversity, equity, inclusion (DEI), and multidisciplinary collaboration. We introduce an augmented AI lifecycle consisting of five interconnected phases: co-framing, co-design, co-implementation, co-deployment, and co-maintenance. The lifecycle is informed by four multidisciplinary workshops and grounded in themes of distributed authority and iterative knowledge exchange. Finally, we relate the proposed lifecycle to several leading ethical frameworks and outline key research questions that remain for scaling participatory governance.
2025-08-01
arXiv (publié)
doi.org
arxiv.org
Efficient Deep Reinforcement Learning-Based Supplementary Damping Control With a Coordinated RMS Training and EMT Testing Scheme
Tao Xue
Mingxuan Zhao
Ilhan Kocar
Mohsen Ghafouri
Antoine Lesage-Landry
Siqi Bu
Ziqing Zhu
Inverter-based resources (IBRs) can cause instability in weak AC grids. While supplementary damping controllers (SDCs) effectively mitigate … (voir plus)this instability, they are typically designed for specific resonance frequencies but struggle with large shifts caused by changing grid conditions. This paper proposes a deep reinforcement learning-based agent (DRL Agent) as an adaptive SDC to handle shifted resonance frequencies. To address the time-consuming nature of training DRL Agents in electromagnetic transient (EMT) simulations, we coordinate fast root mean square (RMS) and EMT simulations. Resonance frequencies of the weak grid instability are accurately reproduced by RMS simulations to support the training process. The DRL Agent’s efficacy is tested in unseen scenarios outside the training dataset. We then iteratively improve the DRL Agent’s performance by modifying the reward function and hyper-parameters.
2025-08-01
IEEE Transactions on Power Delivery (publié)
doi.org
Efficient Deep Reinforcement Learning-Based Supplementary Damping Control With a Coordinated RMS Training and EMT Testing Scheme
Tao Xue
Mingxuan Zhao
Ilhan Kocar
Mohsen Ghafouri
Antoine Lesage-Landry
Siqi Bu
Ziqing Zhu
Inverter-based resources (IBRs) can cause instability in weak AC grids. While supplementary damping controllers (SDCs) effectively mitigate … (voir plus)this instability, they are typically designed for specific resonance frequencies but struggle with large shifts caused by changing grid conditions. This paper proposes a deep reinforcement learning-based agent (DRL Agent) as an adaptive SDC to handle shifted resonance frequencies. To address the time-consuming nature of training DRL Agents in electromagnetic transient (EMT) simulations, we coordinate fast root mean square (RMS) and EMT simulations. Resonance frequencies of the weak grid instability are accurately reproduced by RMS simulations to support the training process. The DRL Agent’s efficacy is tested in unseen scenarios outside the training dataset. We then iteratively improve the DRL Agent’s performance by modifying the reward function and hyper-parameters.
2025-08-01
IEEE Transactions on Power Delivery (publié)
doi.org
Efficient Deep Reinforcement Learning-Based Supplementary Damping Control with a Coordinated RMS Training and EMT Testing Scheme
Tao Xue
Mingxuan Zhao
Ilhan Kocar
Mohsen Ghafouri
Antoine Lesage-Landry
Siqi Bu
Ziqing Zhu
2025-08-01
IEEE Transactions on Power Delivery (publié)
doi.org