Publications

The impact of statistical adjustment for assay performance on inferences from SARS-CoV-2 serological surveillance studies
Jiacheng Chen
Yuan Yu
Sheila F O’Brien
Carmen Charlton
Steven J. Drews
Jane M Heffernan
Amber M Smith
Yu Nakagama
Yasutoshi Kido
David Buckeridge
W Alton Russell
2025-07-22
American Journal of Epidemiology (published)
doi.org
The impact of statistical adjustment for assay performance on inferences from SARS-CoV-2 serological surveillance studies
Jiacheng Chen
Yuan Yu
Sheila F O’Brien
Carmen Charlton
Steven J. Drews
Jane M Heffernan
Amber M Smith
Y. Nakagama
Yasutoshi Kido
David Buckeridge
W Alton Russell
Choice of immunoassay influences population seroprevalence estimates. Post-hoc adjustments for assay performance could improve comparability… (see more) of estimates across studies and enable pooled analyses. We assessed post-hoc adjustment methods using data from 2021–2023 SARS-CoV-2 serosurveillance studies in Alberta, Canada: one that tested 124,008 blood donations using Roche immunoassays (SARS-CoV-2 nucleocapsid total antibody and anti-SARS-CoV-2 S) and another that tested 214,780 patient samples using Abbott immunoassays (SARS-CoV-2 IgG and anti-SARS-CoV-2 S). Comparing datasets, seropositivity for antibodies against nucleocapsid (anti-N) diverged after May 2022 due to differential loss of sensitivity as a function of time since infection. The commonly used Rogen-Gladen adjustment did not reduce this divergence. Regression-based adjustments using the assays’ semi-quantitative results produced more similar estimates of anti-N seroprevalence and rolling incidence proportion (proportion of individuals infected in recent months). Seropositivity for antibodies targeting SARS-CoV-2 spike protein was similar without adjustment, and concordance was not improved when applying an alternative, functional threshold. These findings suggest that assay performance substantially impacted population inferences from SARS-CoV-2 serosurveillance studies in the Omicron period. Unlike methods that ignore time-varying assay sensitivity, regression-based methods using the semi-quantitative assay resulted in increased concordance in estimated anti-N seropositivity and rolling incidence between cohorts using different assays.
2025-07-22
American Journal of Epidemiology (published)
doi.org
Corrigendum to "Child- and Proxy-reported Differences in Patient-reported Outcome and Experience Measures in Pediatric Surgery: Systematic Review and Meta-analysis" [Journal of Pediatric Surgery 60 (2025) 162172].
Zanib Nafees
Siena O'Neill
Alexandra Dimmer
Elena Guadagno
Julia Ferreira
Nancy Mayo
Dan Poenaru
2025-07-21
Journal of Pediatric Surgery (published)
doi.org
Corrigendum to "Child- and Proxy-reported Differences in Patient-reported Outcome and Experience Measures in Pediatric Surgery: Systematic Review and Meta-analysis" [Journal of Pediatric Surgery 60 (2025) 162172].
Zanib Nafees
Siena O'Neill
Alexandra Dimmer
Elena Guadagno
Julia Ferreira
Nancy Mayo
Dan Poenaru
2025-07-21
Journal of Pediatric Surgery (published)
doi.org
Corrigendum to "Virtual Reality for Pediatric Trauma Education - A Preliminary Face and Content Validation Study" [Journal of Pediatric Surgery 60 (2025) 161951].
F. Botelho
Said Ashkar
Shreenik Kundu
Tj Matthews
Elena Guadagno
Dan Poenaru
2025-07-21
Journal of Pediatric Surgery (published)
doi.org
Corrigendum to "Virtual Reality for Pediatric Trauma Education - A Preliminary Face and Content Validation Study" [Journal of Pediatric Surgery 60 (2025) 161951].
F. Botelho
Said Ashkar
Shreenik Kundu
Tj Matthews
Elena Guadagno
Dan Poenaru
2025-07-21
Journal of Pediatric Surgery (published)
doi.org
Employing Machine Learning to Predict Medical Trainees’ Psychophysiological Responses and Self- and Socially- Shared Regulated Learning Strategies While Completing Medical Simulations
Matthew Moreno
Keerat Grewal
Maria Cutumisu
Jason M. Harley
2025-07-18
Educational Psychology Review (published)
doi.org
Quantification of head and neck cancer patients'anatomical changes during radiotherapy: prediction of replanning need
Odette Rios-Ibacache
James Manalad
Kayla O'Sullivan‐Steben
Emily Poon
Luc Galarneau
Julia Khriguian
Georges Shenouda
John Kildea
2025-07-18
ArXiv (preprint)
arxiv.org
arxiv.org
Adaptive Resolution Residual Networks — Generalizing Across Resolutions Easily and Efficiently
Léa Demeule
Mahtab Sandhu
Glen Berseth
The majority of signal data captured in the real world uses numerous sensors with different resolutions. In practice, most deep learning arc… (see more)hitectures are fixed-resolution; they consider a single resolution at training and inference time. This is convenient to implement but fails to fully take advantage of the diverse signal data that exists. In contrast, other deep learning architectures are adaptive-resolution; they directly allow various resolutions to be processed at training and inference time. This provides computational adaptivity but either sacrifices robustness or compatibility with mainstream layers, which hinders their use. In this work, we introduce Adaptive Resolution Residual Networks (ARRNs) to surpass this tradeoff. We construct ARRNs from Laplacian residuals, which serve as generic adaptive-resolution adapters for fixed-resolution layers. We use smoothing filters within Laplacian residuals to linearly separate input signals over a series of resolution steps. We can thereby skip Laplacian residuals to cast high-resolution ARRNs into low-resolution ARRNs that are computationally cheaper yet numerically identical over low-resolution signals. We guarantee this result when Laplacian residuals are implemented with perfect smoothing kernels. We complement this novel component with Laplacian dropout, which randomly omits Laplacian residuals during training. This regularizes for robustness to a distribution of lower resolutions. This also regularizes for numerical errors that may occur when Laplacian residuals are implemented with approximate smoothing kernels. We provide a solid grounding for the advantageous properties of ARRNs through a theoretical analysis based on neural operators, and empirically show that ARRNs embrace the challenge posed by diverse resolutions with computational adaptivity, robustness, and compatibility with mainstream layers.
2025-07-17
TMLR (accepted)
openreview.net
openreview.net
Pixel Perfect MegaMed: A Megapixel-Scale Vision-Language Foundation Model for Generating High Resolution Medical Images
Zahra TehraniNasab
Amar Kumar
Tal Arbel
Medical image synthesis presents unique challenges due to the inherent complexity and high-resolution details required in clinical contexts.… (see more) Traditional generative architectures such as Generative Adversarial Networks (GANs) or Variational Auto Encoder (VAEs) have shown great promise for high-resolution image generation but struggle with preserving fine-grained details that are key for accurate diagnosis. To address this issue, we introduce Pixel Perfect MegaMed, the first vision-language foundation model to synthesize images at resolutions of 1024x1024. Our method deploys a multi-scale transformer architecture designed specifically for ultra-high resolution medical image generation, enabling the preservation of both global anatomical context and local image-level details. By leveraging vision-language alignment techniques tailored to medical terminology and imaging modalities, Pixel Perfect MegaMed bridges the gap between textual descriptions and visual representations at unprecedented resolution levels. We apply our model to the CheXpert dataset and demonstrate its ability to generate clinically faithful chest X-rays from text prompts. Beyond visual quality, these high-resolution synthetic images prove valuable for downstream tasks such as classification, showing measurable performance gains when used for data augmentation, particularly in low-data regimes. Our code is accessible through the project website - https://tehraninasab.github.io/pixelperfect-megamed.
2025-07-17
ArXiv (preprint)
arxiv.org
arxiv.org
Sample, Predict, then Proceed: Self-Verification Sampling for Tool Use of LLMs
Shangmin Guo
Omar Darwiche Domingues
Raphaël Avalos
Aaron Courville
Florian Strub
Tool use in stateful environments presents unique challenges for large language models (LLMs), where existing test-time compute strategies r… (see more)elying on repeated trials in the environment are impractical. We propose dynamics modelling (DyMo), a method that augments LLMs with a state prediction capability alongside function calling during post-training. This enables LLMs to predict the future states of their actions through an internal environment model. On the Berkeley Function Calling Leaderboard V2, DyMo improves success rates and significantly reduces hallucinations. We further integrate the internal environment model into self-verification sampling (SVS), and show that this substantially improves pass^k over number of trials k, and allows the model to refuse unreliable outputs. Together, DyMo and SVS greatly enhance the effectiveness and reliability of LLMs for tool use. We believe this work charts a path towards scalable planning RL methods for LLM inference without repeatedly querying the oracle environment.
2025-07-17
EWRL/2025/Workshop (poster)
openreview.net
openreview.net
Compositional Discrete Latent Code for High Fidelity, Productive Diffusion Models
Samuel Lavoie
Michael Noukhovitch
Aaron Courville
We argue that diffusion models'success in modeling complex distributions is, for the most part, coming from their input conditioning. This p… (see more)aper investigates the representation used to condition diffusion models from the perspective that ideal representations should improve sample fidelity, be easy to generate, and be compositional to allow out-of-training samples generation. We introduce Discrete Latent Code (DLC), an image representation derived from Simplicial Embeddings trained with a self-supervised learning objective. DLCs are sequences of discrete tokens, as opposed to the standard continuous image embeddings. They are easy to generate and their compositionality enables sampling of novel images beyond the training distribution. Diffusion models trained with DLCs have improved generation fidelity, establishing a new state-of-the-art for unconditional image generation on ImageNet. Additionally, we show that composing DLCs allows the image generator to produce out-of-distribution samples that coherently combine the semantics of images in diverse ways. Finally, we showcase how DLCs can enable text-to-image generation by leveraging large-scale pretrained language models. We efficiently finetune a text diffusion language model to generate DLCs that produce novel samples outside of the image generator training distribution.
2025-07-16
ArXiv (preprint)
arxiv.org
arxiv.org