Portrait of Brennan Nichyporuk is unavailable

Brennan Nichyporuk

nichypob@mila.quebec
Research Scientist, Innovation, Development and Technologies

Publications

Imagining Alternatives: Towards High-Resolution 3D Counterfactual Medical Image Generation via Language Guidance
Mohamed Mohamed
Brennan Nichyporuk
Douglas Arnold
Tal Arbel
Vision-language models have demonstrated impressive capabilities in generating 2D images under various conditions; however the impressive pe… (see more)rformance of these models in 2D is largely enabled by extensive, readily available pretrained foundation models. Critically, comparable pretrained foundation models do not exist for 3D, significantly limiting progress in this domain. As a result, the potential of vision-language models to produce high-resolution 3D counterfactual medical images conditioned solely on natural language descriptions remains completely unexplored. Addressing this gap would enable powerful clinical and research applications, such as personalized counterfactual explanations, simulation of disease progression scenarios, and enhanced medical training by visualizing hypothetical medical conditions in realistic detail. Our work takes a meaningful step toward addressing this challenge by introducing a framework capable of generating high-resolution 3D counterfactual medical images of synthesized patients guided by free-form language prompts. We adapt state-of-the-art 3D diffusion models with enhancements from Simple Diffusion and incorporate augmented conditioning to improve text alignment and image quality. To our knowledge, this represents the first demonstration of a language-guided native-3D diffusion model applied specifically to neurological imaging data, where faithful three-dimensional modeling is essential to represent the brain's three-dimensional structure. Through results on two distinct neurological MRI datasets, our framework successfully simulates varying counterfactual lesion loads in Multiple Sclerosis (MS), and cognitive states in Alzheimer's disease, generating high-quality images while preserving subject fidelity in synthetically generated medical images. Our results lay the groundwork for prompt-driven disease progression analysis within 3D medical imaging.
2025-10-11
Lecture Notes in Computer Science (published)
doi.org
arxiv.org
Building a General SimCLR Self-Supervised Foundation Model Across Neurological Diseases to Advance 3D Brain MRI Diagnoses
Emily Kaczmarek
Justin Szeto
Brennan Nichyporuk
Tal Arbel
3D structural Magnetic Resonance Imaging (MRI) brain scans are commonly acquired in clinical settings to monitor a wide range of neurologica… (see more)l conditions, including neurodegenerative disorders and stroke. While deep learning models have shown promising results analyzing 3D MRI across a number of brain imaging tasks, most are highly tailored for specific tasks with limited labeled data, and are not able to generalize across tasks and/or populations. The development of self-supervised learning (SSL) has enabled the creation of large medical foundation models that leverage diverse, unlabeled datasets ranging from healthy to diseased data, showing significant success in 2D medical imaging applications. However, even the very few foundation models for 3D brain MRI that have been developed remain limited in resolution, scope, or accessibility. In this work, we present a general, high-resolution SimCLR-based SSL foundation model for 3D brain structural MRI, pre-trained on 18,759 patients (44,958 scans) from 11 publicly available datasets spanning diverse neurological diseases. We compare our model to Masked Autoencoders (MAE), as well as two supervised baselines, on four diverse downstream prediction tasks in both in-distribution and out-of-distribution settings. Our fine-tuned SimCLR model outperforms all other models across all tasks. Notably, our model still achieves superior performance when fine-tuned using only 20% of labeled training samples for predicting Alzheimer's disease. We use publicly available code and data, and release our trained model at https://github.com/emilykaczmarek/3D-Neuro-SimCLR, contributing a broadly applicable and accessible foundation model for clinical brain MRI analysis.
2025-09-11
ArXiv (preprint)
doi.org
arxiv.org
SSL-AD: Spatiotemporal Self-Supervised Learning for Generalizability and Adaptability Across Alzheimer's Prediction Tasks and Datasets
Emily Kaczmarek
Justin Szeto
Brennan Nichyporuk
Tal Arbel
Alzheimer's disease is a progressive, neurodegenerative disorder that causes memory loss and cognitive decline. While there has been extensi… (see more)ve research in applying deep learning models to Alzheimer's prediction tasks, these models remain limited by lack of available labeled data, poor generalization across datasets, and inflexibility to varying numbers of input scans and time intervals between scans. In this study, we adapt three state-of-the-art temporal self-supervised learning (SSL) approaches for 3D brain MRI analysis, and add novel extensions designed to handle variable-length inputs and learn robust spatial features. We aggregate four publicly available datasets comprising 3,161 patients for pre-training, and show the performance of our model across multiple Alzheimer's prediction tasks including diagnosis classification, conversion detection, and future conversion prediction. Importantly, our SSL model implemented with temporal order prediction and contrastive learning outperforms supervised learning on six out of seven downstream tasks. It demonstrates adaptability and generalizability across tasks and number of input images with varying time intervals, highlighting its capacity for robust performance across clinical applications. We release our code and model publicly at https://github.com/emilykaczmarek/SSL-AD.
2025-09-11
ArXiv (preprint)
doi.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
Christopher Pal
Tal Arbel
2025-07-31
arXiv (published)
doi.org
arxiv.org
Conditional Diffusion Models are Medical Image Classifiers that Provide Explainability and Uncertainty for Free
Gian Mario Favero
Parham Saremi
Emily Kaczmarek
Brennan Nichyporuk
Tal Arbel
2025-03-26
MIDL.io/2025/Conference (oral)
doi.org
openreview.net
Improving Robustness and Reliability in Medical Image Classification with Latent-Guided Diffusion and Nested-Ensembles
Xing Shen
Hengguan Huang
Brennan Nichyporuk
Tal Arbel
Once deployed, medical image analysis methods are often faced with unexpected image corruptions and noise perturbations. These unknown covar… (see more)iate shifts present significant challenges to deep learning based methods trained on "clean" images. This often results in unreliable predictions and poorly calibrated confidence, hence hindering clinical applicability. While recent methods have been developed to address specific issues such as confidence calibration or adversarial robustness, no single framework effectively tackles all these challenges simultaneously. To bridge this gap, we propose LaDiNE, a novel ensemble learning method combining the robustness of Vision Transformers with diffusion-based generative models for improved reliability in medical image classification. Specifically, transformer encoder blocks are used as hierarchical feature extractors that learn invariant features from images for each ensemble member, resulting in features that are robust to input perturbations. In addition, diffusion models are used as flexible density estimators to estimate member densities conditioned on the invariant features, leading to improved modeling of complex data distributions while retaining properly calibrated confidence. Extensive experiments on tuberculosis chest X-rays and melanoma skin cancer datasets demonstrate that LaDiNE achieves superior performance compared to a wide range of state-of-the-art methods by simultaneously improving prediction accuracy and confidence calibration under unseen noise, adversarial perturbations, and resolution degradation.
2024-12-31
IEEE Transactions on Medical Imaging (unknown)
doi.org
arxiv.org
Exploring Compound Loss Functions for Brain Tumor Segmentation
Anita Kriz
Raghav Mehta
Brennan Nichyporuk
Tal Arbel
2024-12-27
Lecture Notes in Computer Science (published)
doi.org
Metrics reloaded: recommendations for image analysis validation.
Lena Maier-Hein
Annika Reinke
Evangelia Christodoulou
Ben Glocker
PATRICK GODAU
Fabian Isensee
Jens Kleesiek
Michal Kozubek
Mauricio Reyes
MICHAEL A. RIEGLER
Manuel Wiesenfarth
Michael Baumgartner
Matthias Eisenmann
DOREEN HECKMANN-NÖTZEL
A. EMRE KAVUR
TIM RÄDSCH
Minu Dietlinde Tizabi
Laura Acion
Michela Antonelli
Tal Arbel … (see 47 more)
Spyridon Bakas
Peter Bankhead
Allison Benis
M. Jorge Cardoso
Veronika Cheplygina
BETH A. CIMINI
Gary S. Collins
Keyvan Farahani
Bram van Ginneken
Daniel A. Hashimoto
Michael M. Hoffman
Merel Huisman
Pierre Jannin
CHARLES E. KAHN
Alexandros Karargyris
Alan Karthikesalingam
H. Kenngott
Annette Kopp-Schneider
Anna Kreshuk
Tahsin Kurc
Bennett Landman
GEERT LITJENS
Amin Madani
Klaus Maier-Hein
Anne L. Martel
Peter Mattson
Erik Meijering
Bjoern Menze
David Moher
Karel G.M. Moons
Henning Müller
Felix Nickel
Brennan Nichyporuk
Jens Petersen
Nasir Rajpoot
Nicola Rieke
Julio Saez-Rodriguez
Clarisa S'anchez Guti'errez
Shravya Shetty
M. Smeden
Carole H. Sudre
Ronald M. Summers
Abdel Aziz Taha
Sotirios A. Tsaftaris
Ben Van Calster
Gael Varoquaux
PAUL F. JÄGER
2024-02-11
Nature Methods (published)
doi.org
arxiv.org
Understanding metric-related pitfalls in image analysis validation
Annika Reinke
Minu D. Tizabi
Michael Baumgartner
Matthias Eisenmann
DOREEN HECKMANN-NÖTZEL
A. EMRE KAVUR
TIM RÄDSCH
Carole H. Sudre
Laura Acion
Michela Antonelli
Tal Arbel
Spyridon Bakas
Arriel Benis
Arriel Benis
Matthew B. Blaschko
Florian Buettner
M. Jorge Cardoso
Veronika Cheplygina
Jianxu Chen
Evangelia Christodoulou … (see 59 more)
BETH A. CIMINI
Keyvan Farahani
LUCIANA FERRER
Gary S. Collins
Adrian Galdran
Bram van Ginneken
Ben Glocker
PATRICK GODAU
Daniel A. Hashimoto
Michael M. Hoffman
Robert Haase
Merel Huisman
Fabian Isensee
Pierre Jannin
CHARLES E. KAHN
Dagmar Kainmueller
BERNHARD KAINZ
Alexandros Karargyris
Jens Kleesiek
Florian Kofler
Thijs Kooi
Annette Kopp-Schneider
Alan Karthikesalingam
Hannes Kenngott
Michal Kozubek
Anna Kreshuk
Tahsin Kurc
Bennett A. Landman
GEERT LITJENS
Amin Madani
Klaus Maier-Hein
Anne L. Martel
Erik Meijering
Bjoern Menze
Karel G.M. Moons
Henning Müller
Brennan Nichyporuk
Felix Nickel
Peter Mattson
Jens Petersen
Susanne M. Rafelski
Nasir Rajpoot
Mauricio Reyes
MICHAEL A. RIEGLER
Nicola Rieke
Julio Saez-Rodriguez
Clara I. Sánchez
Shravya Shetty
Ronald M. Summers
Abdel A. Taha
Aleksei Tiulpin
Sotirios A. Tsaftaris
Ben Van Calster
Gael Varoquaux
Amin Madani
Ziv R. Yaniv
PAUL F. JÄGER
Lena Maier-Hein
Anne L. Martel
Validation metrics are key for the reliable tracking of scientific progress and for bridging the current chasm between artificial intelligen… (see more)ce (AI) research and its translation into practice. However, increasing evidence shows that particularly in image analysis, metrics are often chosen inadequately in relation to the underlying research problem. This could be attributed to a lack of accessibility of metric-related knowledge: While taking into account the individual strengths, weaknesses, and limitations of validation metrics is a critical prerequisite to making educated choices, the relevant knowledge is currently scattered and poorly accessible to individual researchers. Based on a multi-stage Delphi process conducted by a multidisciplinary expert consortium as well as extensive community feedback, the present work provides the first reliable and comprehensive common point of access to information on pitfalls related to validation metrics in image analysis. Focusing on biomedical image analysis but with the potential of transfer to other fields, the addressed pitfalls generalize across application domains and are categorized according to a newly created, domain-agnostic taxonomy. To facilitate comprehension, illustrations and specific examples accompany each pitfall. As a structured body of information accessible to researchers of all levels of expertise, this work enhances global comprehension of a key topic in image analysis validation.
2024-01-31
Nature Methods (published)
doi.org
arxiv.org
DeCoDEx: Confounder Detector Guidance for Improved Diffusion-based Counterfactual Explanations
Nima Fathi
Amar Kumar
Brennan Nichyporuk
Mohammad Havaei
Tal Arbel
Deep learning classifiers are prone to latching onto dominant confounders present in a dataset rather than on the causal markers associated … (see more)with the target class, leading to poor generalization and biased predictions. Although explainability via counterfactual image generation has been successful at exposing the problem, bias mitigation strategies that permit accurate explainability in the presence of dominant and diverse artifacts remain unsolved. In this work, we propose the DeCoDEx framework and show how an external, pre-trained binary artifact detector can be leveraged during inference to guide a diffusion-based counterfactual image generator towards accurate explainability. Experiments on the CheXpert dataset, using both synthetic artifacts and real visual artifacts (support devices), show that the proposed method successfully synthesizes the counterfactual images that change the causal pathology markers associated with Pleural Effusion while preserving or ignoring the visual artifacts. Augmentation of ERM and Group-DRO classifiers with the DeCoDEx generated images substantially improves the results across underrepresented groups that are out of distribution for each class. The code is made publicly available at https://github.com/NimaFathi/DeCoDEx.
2023-12-31
MIDL (published)
doi.org
openreview.net
HyperFusion: A Hypernetwork Approach to Multimodal Integration of Tabular and Medical Imaging Data for Predictive Modeling
Daniel Duenias
Brennan Nichyporuk
Tal Arbel
Tammy Riklin Raviv
The integration of diverse clinical modalities such as medical imaging and the tabular data extracted from patients' Electronic Health Recor… (see more)ds (EHRs) is a crucial aspect of modern healthcare. Integrative analysis of multiple sources can provide a comprehensive understanding of the clinical condition of a patient, improving diagnosis and treatment decision. Deep Neural Networks (DNNs) consistently demonstrate outstanding performance in a wide range of multimodal tasks in the medical domain. However, the complex endeavor of effectively merging medical imaging with clinical, demographic and genetic information represented as numerical tabular data remains a highly active and ongoing research pursuit. We present a novel framework based on hypernetworks to fuse clinical imaging and tabular data by conditioning the image processing on the EHR's values and measurements. This approach aims to leverage the complementary information present in these modalities to enhance the accuracy of various medical applications. We demonstrate the strength and generality of our method on two different brain Magnetic Resonance Imaging (MRI) analysis tasks, namely, brain age prediction conditioned by subject's sex and multi-class Alzheimer's Disease (AD) classification conditioned by tabular data. We show that our framework outperforms both single-modality models and state-of-the-art MRI tabular data fusion methods. A link to our code can be found at https://github.com/daniel4725/HyperFusion
2023-12-31
arXiv (preprint)
doi.org
arxiv.org
Debiasing Counterfactuals in the Presence of Spurious Correlations
Amar Kumar
Nima Fathi
Raghav Mehta
Brennan Nichyporuk
Jean-Pierre R. Falet
Sotirios A. Tsaftaris
Tal Arbel
Deep learning models can perform well in complex medical imaging classification tasks, even when basing their conclusions on spurious correl… (see more)ations (i.e. confounders), should they be prevalent in the training dataset, rather than on the causal image markers of interest. This would thereby limit their ability to generalize across the population. Explainability based on counterfactual image generation can be used to expose the confounders but does not provide a strategy to mitigate the bias. In this work, we introduce the first end-to-end training framework that integrates both (i) popular debiasing classifiers (e.g. distributionally robust optimization (DRO)) to avoid latching onto the spurious correlations and (ii) counterfactual image generation to unveil generalizable imaging markers of relevance to the task. Additionally, we propose a novel metric, Spurious Correlation Latching Score (SCLS), to quantify the extent of the classifier reliance on the spurious correlation as exposed by the counterfactual images. Through comprehensive experiments on two public datasets (with the simulated and real visual artifacts), we demonstrate that the debiasing method: (i) learns generalizable markers across the population, and (ii) successfully ignores spurious correlations and focuses on the underlying disease pathology.
2023-10-08
Clinical Image-Based Procedures, Fairness of AI in Medical Imaging, and Ethical and Philosophical Issues in Medical Imaging (published)
doi.org
openreview.net