Tal Arbel

cornelius.crijnen@mila.quebec

Cornelius Crijnen

Doctorat - McGill

Site web

oscar.cruzhernandez@mila.quebec

Oscar Cruzhernandez

Stagiaire de recherche - McGill

Charbel El Feghali

Stagiaire de recherche - McGill

charbel.elfeghali@mila.quebec

Carlotta Hoelzle

Stagiaire de recherche - McGill

carlotta.hoelzle@mila.quebec

elizabeth.janes@mila.quebec

Elizabeth Laura Janes

Maîtrise recherche - McGill

Emily Kaczmarek

Doctorat - McGill

emily.kaczmarek@mail.mcgill.ca

Google Scholar

Yusong Li

Collaborateur·rice de recherche - McGill University

yusong.li@mila.quebec

Toky Raharison Ralambomihanta

Google Scholar

Yik Yu Ng

Stagiaire de recherche - McGill

yik.ng@mila.quebec

Stagiaire de recherche - McGill

tokiniaina.raharisonralambomihan@mail.mcgill.ca

Ryan Rezai

Maîtrise recherche - McGill

ryan.rezai@mila.quebec

Rachel Ruddy

Stagiaire de recherche - McGill

rachel.ruddy@mila.quebec

PRISM : Un modèle d'IA générative explicable pour l'imagerie médicale

Minh To

Collaborateur·rice de recherche - UBC

Billets de blogue

Image of an Xray and the DDIM process to generate counterfactual version of Xrays

1 juillet 2025

par

Amar Kumar

Anita Kriz

Mohammed Havaei

Tal Arbel

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Publications

Identifying the Best Machine Learning Algorithms for Brain Tumor Segmentation, Progression Assessment, and Overall Survival Prediction in the BRATS Challenge

Spyridon Bakas

Mauricio Reyes

Andras Jakab

Stefan. Bauer

Markus Rempfler

Alessandro Crimi

Russell T. Shinohara

Christoph Berger

Sung-min Ha

Martin Rozycki

Marcel W. Prastawa

Esther Alberts

Jana Lipková

John Freymann

Justin Kirby

Michel Bilello

Hassan M. Fathallah-Shaykh

Roland Wiest

J. Kirschke

Benedikt Wiestler … (voir 31 de plus)

Rivka R. Colen

Aikaterini Kotrotsou

Pamela LaMontagne

D. Marcus

Mikhail Milchenko

Arash Nazeri

Marc-André Weber

Abhishek Mahajan

Ujjwal Baid

Dongjin Kwon

Manu Agarwal

Mahbubul Alam

Alberto Albiol

A. Albiol

Alex A. Varghese

T. Tuan

Aaron J. Avery

Bobade Pranjal

Subhashis Banerjee

Thomas H. Batchelder

Nematollah Batmanghelich

Enzo Battistella

Martin Bendszus

E. Benson

José Bernal

George Biros

Mariano Cabezas

Siddhartha Chandra

Yi-Ju Chang

et al.

Gliomas are the most common primary brain malignancies, with different degrees of aggressiveness, variable prognosis and various heterogeneo… (voir plus)us histologic sub-regions, i.e., peritumoral edematous/invaded tissue, necrotic core, active and non-enhancing core. This intrinsic heterogeneity is also portrayed in their radio-phenotype, as their sub-regions are depicted by varying intensity profiles disseminated across multi-parametric magnetic resonance imaging (mpMRI) scans, reflecting varying biological properties. Their heterogeneous shape, extent, and location are some of the factors that make these tumors difficult to resect, and in some cases inoperable. The amount of resected tumoris a factor also considered in longitudinal scans, when evaluating the apparent tumor for potential diagnosis of progression. Furthermore, there is mounting evidence that accurate segmentation of the various tumor sub-regions can offer the basis for quantitative image analysis towards prediction of patient overall survival. This study assesses thestate-of-the-art machine learning (ML) methods used for brain tumor image analysis in mpMRI scans, during the last seven instances of the International Brain Tumor Segmentation (BraTS) challenge, i.e., 2012-2018. Specifically, we focus on i) evaluating segmentations of the various glioma sub-regions in pre-operative mpMRI scans, ii) assessing potential tumor progression by virtue of longitudinal growth of tumor sub-regions, beyond use of the RECIST/RANO criteria, and iii) predicting the overall survival from pre-operative mpMRI scans of patients that underwent gross tota lresection. Finally, we investigate the challenge of identifying the best ML algorithms for each of these tasks, considering that apart from being diverse on each instance of the challenge, the multi-institutional mpMRI BraTS dataset has also been a continuously evolving/growing dataset.

2018-11-04

ArXiv (prépublication)

Exploring Uncertainty Measures in Deep Networks for Multiple Sclerosis Lesion Detection and Segmentation

Tanya Nair

Doina Precup

Douglas L. Arnold

Deep learning (DL) networks have recently been shown to outperform other segmentation methods on various public, medical-image challenge dat… (voir plus)asets [3,11,16], especially for large pathologies. However, in the context of diseases such as Multiple Sclerosis (MS), monitoring all the focal lesions visible on MRI sequences, even very small ones, is essential for disease staging, prognosis, and evaluating treatment efficacy. Moreover, producing deterministic outputs hinders DL adoption into clinical routines. Uncertainty estimates for the predictions would permit subsequent revision by clinicians. We present the first exploration of multiple uncertainty estimates based on Monte Carlo (MC) dropout [4] in the context of deep networks for lesion detection and segmentation in medical images. Specifically, we develop a 3D MS lesion segmentation CNN, augmented to provide four different voxel-based uncertainty measures based on MC dropout. We train the network on a proprietary, large-scale, multi-site, multi-scanner, clinical MS dataset, and compute lesion-wise uncertainties by accumulating evidence from voxel-wise uncertainties within detected lesions. We analyze the performance of voxel-based segmentation and lesion-level detection by choosing operating points based on the uncertainty. Empirical evidence suggests that uncertainty measures consistently allow us to choose superior operating points compared only using the network's sigmoid output as a probability.

2018-09-25

Medical Image Computing and Computer Assisted Intervention – MICCAI 2018 (publié)

Nazanin Mohammadi Sepahvand

CNN Prediction of Future Disease Activity for Multiple Sclerosis Patients from Baseline MRI and Lesion Labels

Tal Hassner

Douglas Arnold

2018-09-15

BrainLes@MICCAI (publié)

3D U-Net for Brain Tumour Segmentation

Raghav Mehta

2018-09-15

BrainLes@MICCAI (publié)

How to Exploit Weaknesses in Biomedical Challenge Design and Organization

Annika Reinke

Matthias Eisenmann

Sinan Onogur

Marko Stankovic

Patrick Scholz

Peter M. Full

Hrvoje Bogunovic

Bennett Landman

Oskar Maier

Bjoern Menze

Gregory C. Sharp

Korsuk Sirinukunwattana

Stefanie Speidel

F. V. D. Sommen

Guoyan Zheng

Henning Müller

Michal Kozubek

Andrew P. Bradley

Pierre Jannin … (voir 2 de plus)

Annette Kopp-Schneider

Lena Maier-Hein

2018-09-12

Medical Image Computing and Computer Assisted Intervention – MICCAI 2018 (publié)

RS-Net: Regression-Segmentation 3D CNN for Synthesis of Full Resolution Missing Brain MRI in the Presence of Tumours

Raghav Mehta

2018-09-11

Simulation and Synthesis in Medical Imaging (publié)

Structured deep Fisher pruning for efficient facial trait classification

Qing Tian

James J. Clark

2018-08-31

Image and Vision Computing (publié)

Fisher Pruning of Deep Nets for Facial Trait Classification

Qing Tian

James J. Clark

Although deep nets have resulted in high accuracies for various visual tasks, their computational and space requirements are prohibitively h… (voir plus)igh for inclusion on devices without high-end GPUs. In this paper, we introduce a neuron/filter level pruning framework based on Fisher's LDA which leads to high accuracies for a wide array of facial trait classification tasks, while significantly reducing space/computational complexities. The approach is general and can be applied to convolutional, fully-connected, and module-based deep structures, in all cases leveraging the high decorrelation of neuron activations found in the pre-decision layer and cross-layer deconv dependency. Experimental results on binary and multi-category facial traits from the LFWA and Adience datasets illustrate the framework's comparable/better performance to state-of-the-art pruning approaches and compact structures (e.g. SqueezeNet, MobileNet). Ours successfully maintains comparable accuracies even after discarding most parameters (98%-99% for VGG-16, 82% for GoogLeNet) and with significant FLOP reductions (83% for VGG-16, 64% for GoogLeNet).

2018-03-20

ArXiv (prépublication)

Task-specific Deep LDA pruning of neural networks

Qing Tian

James J. Clark

With deep learning's success, a limited number of popular deep nets have been widely adopted for various vision tasks. However, this usually… (voir plus) results in unnecessarily high complexities and possibly many features of low task utility. In this paper, we address this problem by introducing a task-dependent deep pruning framework based on Fisher's Linear Discriminant Analysis (LDA). The approach can be applied to convolutional, fully-connected, and module-based deep network structures, in all cases leveraging the high decorrelation of neuron motifs found in the pre-decision layer and cross-layer deconv dependency. Moreover, we examine our approach's potential in network architecture search for specific tasks and analyze the influence of our pruning on model robustness to noises and adversarial attacks. Experimental results on datasets of generic objects, as well as domain specific tasks (CIFAR100, Adience, and LFWA) illustrate our framework's superior performance over state-of-the-art pruning approaches and fixed compact nets (e.g. SqueezeNet, MobileNet). The proposed method successfully maintains comparable accuracies even after discarding most parameters (98%-99% for VGG16, up to 82% for the already compact InceptionNet) and with significant FLOP reductions (83% for VGG16, up to 64% for InceptionNet). Through pruning, we can also derive smaller, but more accurate and more robust models suitable for the task.

2018-03-20

(publié)

www.semanticscholar.org

Brain Tumor Segmentation Using a 3D FCN with Multi-scale Loss

Andrew Jesson

2018-02-16

Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries (publié)

Lesion Detection, Segmentation and Prediction in Multiple Sclerosis Clinical Trials

Andrew Doyle

Colm Elliott

Zahra Karimaghaloo

Nagesh K. Subbanna

Douglas Arnold

2018-02-16

Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries (publié)

Combining intraoperative ultrasound brain shift correction and augmented reality visualizations: a pilot study of eight cases

Ian J. Gerard

Marta Kersten-Oertel

Simon Drouin

Jeffery A. Hall

Kevin Petrecca

Dante De Nigris

Daniel A. Di Giovanni

D. Louis Collins

2018-01-25

Journal of Medical Imaging (publié)