Publications

Galaxy cluster characterization with machine learning techniques
M. Sadikov
J. Hlavacek-Larrondo
Laurence Perreault-Levasseur
C. L. Rhea
M. McDonald
M. Ntampaka
J. ZuHone
We present an analysis of the X-ray properties of the galaxy cluster population in the z=0 snapshot of the IllustrisTNG simulations, utilizi… (see more)ng machine learning techniques to perform clustering and regression tasks. We examine five properties of the hot gas (the central cooling time, the central electron density, the central entropy excess, the concentration parameter, and the cuspiness) which are commonly used as classification metrics to identify cool core (CC), weak cool core (WCC) and non cool core (NCC) clusters of galaxies. Using mock Chandra X-ray images as inputs, we first explore an unsupervised clustering scheme to see how the resulting groups correlate with the CC/WCC/NCC classification based on the different criteria. We observe that the groups replicate almost exactly the separation of the galaxy cluster images when classifying them based on the concentration parameter. We then move on to a regression task, utilizing a ResNet model to predict the value of all five properties. The network is able to achieve a mean percentage error of 1.8% for the central cooling time, and a balanced accuracy of 0.83 on the concentration parameter, making them the best-performing metrics. Finally, we use simulation-based inference (SBI) to extract posterior distributions for the network predictions. Our neural network simultaneously predicts all five classification metrics using only mock Chandra X-ray images. This study demonstrates that machine learning is a viable approach for analyzing and classifying the large galaxy cluster datasets that will soon become available through current and upcoming X-ray surveys, such as eROSITA.
2025-06-03
The Astrophysical Journal (published)
doi.org
arxiv.org
It's the Thought that Counts: Evaluating the Attempts of Frontier LLMs to Persuade on Harmful Topics
Matthew Kowal
Jasper Timm
Jean-François Godbout
Thomas H Costello
Antonio A. Arechar
Gordon Pennycook
David Rand
Adam Gleave
Kellin Pelrine
Persuasion is a powerful capability of large language models (LLMs) that both enables beneficial applications (e.g. helping people quit smok… (see more)ing) and raises significant risks (e.g. large-scale, targeted political manipulation). Prior work has found models possess a significant and growing persuasive capability, measured by belief changes in simulated or real users. However, these benchmarks overlook a crucial risk factor: the propensity of a model to attempt to persuade in harmful contexts. Understanding whether a model will blindly ``follow orders'' to persuade on harmful topics (e.g. glorifying joining a terrorist group) is key to understanding the efficacy of safety guardrails. Moreover, understanding if and when a model will engage in persuasive behavior in pursuit of some goal is essential to understanding the risks from agentic AI systems. We propose the Attempt to Persuade Eval (APE) benchmark, that shifts the focus from persuasion success to persuasion attempts, operationalized as a model's willingness to generate content aimed at shaping beliefs or behavior. Our evaluation framework probes frontier LLMs using a multi-turn conversational setup between simulated persuader and persuadee agents. APE explores a diverse spectrum of topics including conspiracies, controversial issues, and non-controversially harmful content. We introduce an automated evaluator model to identify willingness to persuade and measure the frequency and context of persuasive attempts. We find that many open and closed-weight models are frequently willing to attempt persuasion on harmful topics and that jailbreaking can increase willingness to engage in such behavior. Our results highlight gaps in current safety guardrails and underscore the importance of evaluating willingness to persuade as a key dimension of LLM risk. APE is available at github.com/AlignmentResearch/AttemptPersuadeEval
2025-06-03
ArXiv (preprint)
arxiv.org
arxiv.org
Sociodemographic characteristics of SARS-CoV-2 serosurveillance studies with diverse recruitment strategies, Canada, 2020 to 2023
Matthew J Knight
Yuan Yu
Jiacheng Chen
Sheila F O’Brien
David Buckeridge
Carmen Charlton
W Alton Russell
2025-06-03
BMC Public Health (published)
doi.org
ToothForge: Automatic Dental Shape Generation using Synchronized Spectral Embeddings
Tibor Kubík
Franccois Guibault
Michal vSpanvel
Hervé Lombaert
We introduce ToothForge, a spectral approach for automatically generating novel 3D teeth, effectively addressing the sparsity of dental shap… (see more)e datasets. By operating in the spectral domain, our method enables compact machine learning modeling, allowing the generation of high-resolution tooth meshes in milliseconds. However, generating shape spectra comes with the instability of the decomposed harmonics. To address this, we propose modeling the latent manifold on synchronized frequential embeddings. Spectra of all data samples are aligned to a common basis prior to the training procedure, effectively eliminating biases introduced by the decomposition instability. Furthermore, synchronized modeling removes the limiting factor imposed by previous methods, which require all shapes to share a common fixed connectivity. Using a private dataset of real dental crowns, we observe a greater reconstruction quality of the synthetized shapes, exceeding those of models trained on unaligned embeddings. We also explore additional applications of spectral analysis in digital dentistry, such as shape compression and interpolation. ToothForge facilitates a range of approaches at the intersection of spectral analysis and machine learning, with fewer restrictions on mesh structure. This makes it applicable for shape analysis not only in dentistry, but also in broader medical applications, where guaranteeing consistent connectivity across shapes from various clinics is unrealistic. The code is available at https://github.com/tiborkubik/toothForge.
2025-06-03
ArXiv (preprint)
arxiv.org
arxiv.org
Self-Refining Training for Amortized Density Functional Theory
Majdi Hassan
Cristian Gabellini
Hatem Helal
Dominique Beaini
Kirill Neklyudov
Density Functional Theory (DFT) allows for predicting all the chemical and physical properties of molecular systems from first principles by… (see more) finding an approximate solution to the many-body Schr\"odinger equation. However, the cost of these predictions becomes infeasible when increasing the scale of the energy evaluations, e.g., when calculating the ground-state energy for simulating molecular dynamics. Recent works have demonstrated that, for substantially large datasets of molecular conformations, Deep Learning-based models can predict the outputs of the classical DFT solvers by amortizing the corresponding optimization problems. In this paper, we propose a novel method that reduces the dependency of amortized DFT solvers on large pre-collected datasets by introducing a self-refining training strategy. Namely, we propose an efficient method that simultaneously trains a deep-learning model to predict the DFT outputs and samples molecular conformations that are used as training data for the model. We derive our method as a minimization of the variational upper bound on the KL-divergence measuring the discrepancy between the generated samples and the target Boltzmann distribution defined by the ground state energy. To demonstrate the utility of the proposed scheme, we perform an extensive empirical study comparing it with the models trained on the pre-collected datasets. Finally, we open-source our implementation of the proposed algorithm, optimized with asynchronous training and sampling stages, which enables simultaneous sampling and training. Code is available at https://github.com/majhas/self-refining-dft.
2025-06-02
ArXiv (preprint)
arxiv.org
arxiv.org
Unpacking Softmax: How Temperature Drives Representation Collapse, Compression, and Generalization
Wojciech Masarczyk
Mateusz Ostaszewski
Tin Sum Cheng
Tomasz Trzci'nski
Aurélien Lucchi
Razvan Pascanu
The softmax function is a fundamental building block of deep neural networks, commonly used to define output distributions in classification… (see more) tasks or attention weights in transformer architectures. Despite its widespread use and proven effectiveness, its influence on learning dynamics and learned representations remains poorly understood, limiting our ability to optimize model behavior. In this paper, we study the pivotal role of the softmax function in shaping the model's representation. We introduce the concept of rank deficit bias - a phenomenon in which softmax-based deep networks find solutions of rank much lower than the number of classes. This bias depends on the softmax function's logits norm, which is implicitly influenced by hyperparameters or directly modified by softmax temperature. Furthermore, we demonstrate how to exploit the softmax dynamics to learn compressed representations or to enhance their performance on out-of-distribution data. We validate our findings across diverse architectures and real-world datasets, highlighting the broad applicability of temperature tuning in improving model performance. Our work provides new insights into the mechanisms of softmax, enabling better control over representation learning in deep neural networks.
2025-06-02
ArXiv (preprint)
arxiv.org
arxiv.org
Advancing global antifungal development to combat invasive fungal infection
Xiu-Li Wang
Jun Ding
Koon Ho Wong
Chen Ding
Chang-Bin Chen
Wen-Juan Wu
Ningning Liu
2025-06-01
hLife (published)
doi.org
Adversarial Attack Classification and Robustness Testing for Large Language Models for Code
Yang Liu
Armstrong Foundjem
Foutse Khomh
Heng Li
Large Language Models (LLMs) have become vital tools in software development tasks such as code generation, completion, and analysis. As the… (see more)ir integration into workflows deepens, ensuring robustness against vulnerabilities especially those triggered by diverse or adversarial inputs becomes increasingly important. Such vulnerabilities may lead to incorrect or insecure code generation when models encounter perturbed task descriptions, code, or comments. Prior research often overlooks the role of natural language in guiding code tasks. This study investigates how adversarial perturbations in natural language inputs including prompts, comments, and descriptions affect LLMs for Code (LLM4Code). It examines the effects of perturbations at the character, word, and sentence levels to identify the most impactful vulnerabilities. We analyzed multiple projects (e.g., ReCode, OpenAttack) and datasets (e.g., HumanEval, MBPP), establishing a taxonomy of adversarial attacks. The first dimension classifies the input type code, prompts, or comments while the second dimension focuses on granularity: character, word, or sentence-level changes. We adopted a mixed-methods approach, combining quantitative performance metrics with qualitative vulnerability analysis. LLM4Code models show varying robustness across perturbation types. Sentence-level attacks were least effective, suggesting models are resilient to broader contextual changes. In contrast, word-level perturbations posed serious challenges, exposing semantic vulnerabilities. Character-level effects varied, showing model sensitivity to subtle syntactic deviations.Our study offers a structured framework for testing LLM4Code robustness and emphasizes the critical role of natural language in adversarial evaluation. Improving model resilience to semantic-level disruptions is essential for secure and reliable code-generation systems.
2025-06-01
arXiv (published)
doi.org
arxiv.org
Are Large Language Models Good Temporal Graph Learners?
Shenyang Huang
Ali Parviz
Emma Kondrup
Zachary Yang
Zifeng Ding
Michael M. Bronstein
Reihaneh Rabbany
Guillaume Rabusseau
Large Language Models (LLMs) have recently driven significant advancements in Natural Language Processing and various other applications. Wh… (see more)ile a broad range of literature has explored the graph-reasoning capabilities of LLMs, including their use of predictors on graphs, the application of LLMs to dynamic graphs -- real world evolving networks -- remains relatively unexplored. Recent work studies synthetic temporal graphs generated by random graph models, but applying LLMs to real-world temporal graphs remains an open question. To address this gap, we introduce Temporal Graph Talker (TGTalker), a novel temporal graph learning framework designed for LLMs. TGTalker utilizes the recency bias in temporal graphs to extract relevant structural information, converted to natural language for LLMs, while leveraging temporal neighbors as additional information for prediction. TGTalker demonstrates competitive link prediction capabilities compared to existing Temporal Graph Neural Network (TGNN) models. Across five real-world networks, TGTalker performs competitively with state-of-the-art temporal graph methods while consistently outperforming popular models such as TGN and HTGN. Furthermore, TGTalker generates textual explanations for each prediction, thus opening up exciting new directions in explainability and interpretability for temporal link prediction. The code is publicly available at https://github.com/shenyangHuang/TGTalker.
2025-06-01
arXiv (published)
doi.org
arxiv.org
Bringing SAM to new heights: Leveraging elevation data for tree crown segmentation from drone imagery
Mélisande Teng
Arthur Ouaknine
Etienne Lalibert'e
Yoshua Bengio
David Rolnick
Hugo Larochelle
Information on trees at the individual level is crucial for monitoring forest ecosystems and planning forest management. Current monitoring … (see more)methods involve ground measurements, requiring extensive cost, time and labor. Advances in drone remote sensing and computer vision offer great potential for mapping individual trees from aerial imagery at broad-scale. Large pre-trained vision models, such as the Segment Anything Model (SAM), represent a particularly compelling choice given limited labeled data. In this work, we compare methods leveraging SAM for the task of automatic tree crown instance segmentation in high resolution drone imagery in three use cases: 1) boreal plantations, 2) temperate forests and 3) tropical forests. We also study the integration of elevation data into models, in the form of Digital Surface Model (DSM) information, which can readily be obtained at no additional cost from RGB drone imagery. We present BalSAM, a model leveraging SAM and DSM information, which shows potential over other methods, particularly in the context of plantations. We find that methods using SAM out-of-the-box do not outperform a custom Mask R-CNN, even with well-designed prompts. However, efficiently tuning SAM end-to-end and integrating DSM information are both promising avenues for tree crown instance segmentation models.
2025-06-01
arXiv (published)
doi.org
arxiv.org
Continual Learning in Vision-Language Models via Aligned Model Merging
Ghada Sokar
Gintare Karolina Dziugaite
Anurag Arnab
Ahmet Iscen
Pablo Samuel Castro
Cordelia Schmid
Continual learning is conventionally tackled through sequential fine-tuning, a process that, while enabling adaptation, inherently favors pl… (see more)asticity over the stability needed to retain prior knowledge. While existing approaches attempt to mitigate catastrophic forgetting, a bias towards recent tasks persists as they build upon this sequential nature. In this work we present a new perspective based on model merging to maintain stability while still retaining plasticity. Rather than just sequentially updating the model weights, we propose merging newly trained task parameters with previously learned ones, promoting a better balance. To maximize the effectiveness of the merging process, we propose a simple mechanism that promotes learning aligned weights with previous ones, thereby avoiding interference when merging. We evaluate this approach on large Vision-Language Models (VLMs), and demonstrate its effectiveness in reducing forgetting, increasing robustness to various task orders and similarities, and improving generalization.
2025-06-01
arXiv (published)
doi.org
arxiv.org
Ctrl-Crash: Controllable Diffusion for Realistic Car Crashes
Anthony Gosselin
Ge Ya Luo
Luis Lara
Florian Golemo
Derek Nowrouzezahrai
Liam Paull
Alexia Jolicoeur-Martineau
Chris Pal
Video diffusion techniques have advanced significantly in recent years; however, they struggle to generate realistic imagery of car crashes … (see more)due to the scarcity of accident events in most driving datasets. Improving traffic safety requires realistic and controllable accident simulations. To tackle the problem, we propose Ctrl-Crash, a controllable car crash video generation model that conditions on signals such as bounding boxes, crash types, and an initial image frame. Our approach enables counterfactual scenario generation where minor variations in input can lead to dramatically different crash outcomes. To support fine-grained control at inference time, we leverage classifier-free guidance with independently tunable scales for each conditioning signal. Ctrl-Crash achieves state-of-the-art performance across quantitative video quality metrics (e.g., FVD and JEDi) and qualitative measurements based on a human-evaluation of physical realism and video quality compared to prior diffusion-based methods.
2025-06-01
arXiv (published)
doi.org
arxiv.org