Brennan Nichyporuk

SSL-AD: Spatiotemporal Self-Supervised Learning for Generalizability and Adaptability Across Alzheimer's Prediction Tasks and Datasets

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.

2025-09-12

ArXiv (preprint)

Imagining Alternatives: Towards High-Resolution 3D Counterfactual Medical Image Generation via Language Guidance

Mohamed Mohamed

Douglas Arnold

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.

2025-09-07

ArXiv (preprint)

Spatio-Temporal Conditional Diffusion Models for Forecasting Future Multiple Sclerosis Lesion Masks Conditioned on Treatments

Gian Mario Favero

Ge Ya Luo

Douglas Arnold

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)

Spatio-Temporal Conditional Diffusion Models for Forecasting Future Multiple Sclerosis Lesion Masks Conditioned on Treatments

Gian Mario Favero

Ge Ya Luo

Douglas Arnold

2025-08-09

ArXiv (preprint)

Conditional Diffusion Models are Medical Image Classifiers that Provide Explainability and Uncertainty for Free

Gian Mario Favero

2025-03-27

MIDL.io/2025/Conference (oral)

openreview.net

Conditional Diffusion Models are Medical Image Classifiers that Provide Explainability and Uncertainty for Free

Gian Mario Favero

Discriminative classifiers have become a foundational tool in deep learning for medical imaging, excelling at learning separable features of… (see more) complex data distributions. However, these models often need careful design, augmentation, and training techniques to ensure safe and reliable deployment. Recently, diffusion models have become synonymous with generative modeling in 2D. These models showcase robustness across a range of tasks including natural image classification, where classification is performed by comparing reconstruction errors across images generated for each possible conditioning input. This work presents the first exploration of the potential of class conditional diffusion models for 2D medical image classification. First, we develop a novel majority voting scheme shown to improve the performance of medical diffusion classifiers. Next, extensive experiments on the CheXpert and ISIC Melanoma skin cancer datasets demonstrate that foundation and trained-from-scratch diffusion models achieve competitive performance against SOTA discriminative classifiers without the need for explicit supervision. In addition, we show that diffusion classifiers are intrinsically explainable, and can be used to quantify the uncertainty of their predictions, increasing their trustworthiness and reliability in safety-critical, clinical contexts. Further information is available on our project page: https://faverogian.github.io/med-diffusion-classifier.github.io/

2025-02-06

ArXiv (preprint)

Improving Robustness and Reliability in Medical Image Classification with Latent-Guided Diffusion and Nested-Ensembles

Xing Shen

Hengguan Huang

2025-01-01

IEEE Transactions on Medical Imaging (published)

Exploring Compound Loss Functions for Brain Tumor Segmentation

Anita Kriz

Raghav Mehta

2024-12-28

Lecture Notes in Computer Science (published)

HyperFusion: A Hypernetwork Approach to Multimodal Integration of Tabular and Medical Imaging Data for Predictive Modeling

Daniel Duenias

Tammy Riklin-Raviv

The integration of diverse clinical modalities such as medical imaging and the tabular data obtained by the patients' Electronic Health Reco… (see more)rds (EHRs) is a crucial aspect of modern healthcare. The integrative analysis of multiple sources can provide a comprehensive understanding of a patient's condition and can enhance diagnoses and treatment decisions. Deep Neural Networks (DNNs) consistently showcase 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 the generality of our method on two different brain Magnetic Resonance Imaging (MRI) analysis tasks, namely, brain age prediction conditioned by subject's sex, and multiclass 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. The code, enclosed to this manuscript will be made publicly available.

2024-03-20

ArXiv (preprint)

DeCoDEx: Confounder Detector Guidance for Improved Diffusion-based Counterfactual Explanations

Mohammad Havaei

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.

2024-02-13

MIDL.io/2024/Conference/Submission (unknown)

openreview.net

Metrics reloaded: Pitfalls and 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

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

2024-02-12

Nature Methods (published)