Tal Arbel

Biographie

Tal Arbel est professeure titulaire au Département de génie électrique et informatique de l’Université McGill, où elle dirige le groupe de vision probabiliste et le laboratoire d'imagerie médicale du Centre sur les machines intelligentes.

Elle est titulaire d'une chaire en IA Canada-CIFAR et membre associée de Mila – Institut québécois d’intelligence artificielle ainsi que du Centre de recherche sur le cancer Goodman. Les recherches de la professeure Arbel portent sur le développement de méthodes probabilistes d'apprentissage profond dans les domaines de la vision par ordinateur et de l’analyse d'imagerie médicale pour un large éventail d'applications dans le monde réel, avec un accent particulier sur les maladies neurologiques.

Elle a remporté le prix de la recherche Christophe Pierre 2019 de McGill Engineering. Elle fait régulièrement partie de l'équipe organisatrice de grandes conférences internationales sur la vision par ordinateur et l'analyse d'imagerie médicale (par exemple celles de la Medical Image Computing and Computer-Assisted Intervention Society/MICCAI et de Medical Imaging with Deep Learning/MIDL, l’International Conference on Computer Vision/ICCV ou encore la Conference on Computer Vision and Pattern Recognition/CVPR). Elle est rédactrice en chef et cofondatrice de la revue Machine Learning for Biomedical Imaging (MELBA).

Étudiants actuels

Berardino Barile

Postdoctorat - McGill

Joshua Durso-finley

Doctorat - McGill

Nima Fathi

Maîtrise recherche - McGill

Gian Favero

Maîtrise recherche - McGill

elizabeth.janes@mila.quebec

Ethan Honey

Doctorat - McGill

ethan.honey@mila.quebec

Elizabeth Laura Janes

Maîtrise recherche - McGill

Emily Kaczmarek

Doctorat - McGill

emily.kaczmarek@mail.mcgill.ca

Anita Kriz

Maîtrise recherche - McGill

Amar Kumar

Doctorat - McGill

Mohamed Mohamed

Maîtrise recherche - McGill

Parham Saremi

Maîtrise recherche - McGill

Xing Shen

Maîtrise recherche - McGill

Maîtrise recherche - McGill

Mona Wang Wang

Baccalauréat - McGill

monaw7777@gmail.com

Ritchie Yu

Baccalauréat - McGill

Publications

Probabilistic Temporal Prediction of Continuous Disease Trajectories and Treatment Effects Using Neural SDEs

Joshua D. Durso-Finley

Berardino Barile

Jean-Pierre R. Falet

Douglas Arnold

Nick Pawlowski

Personalized medicine based on medical images, including predicting future individualized clinical disease progression and treatment respons… (voir plus)e, would have an enormous impact on healthcare and drug development, particularly for diseases (e.g. multiple sclerosis (MS)) with long term, complex, heterogeneous evolutions and no cure. In this work, we present the first stochastic causal temporal framework to model the continuous temporal evolution of disease progression via Neural Stochastic Differential Equations (NSDE). The proposed causal inference model takes as input the patient's high dimensional images (MRI) and tabular data, and predicts both factual and counterfactual progression trajectories on different treatments in latent space. The NSDE permits the estimation of high-confidence personalized trajectories and treatment effects. Extensive experiments were performed on a large, multi-centre, proprietary dataset of patient 3D MRI and clinical data acquired during several randomized clinical trials for MS treatments. Our results present the first successful uncertainty-based causal Deep Learning (DL) model to: (a) accurately predict future patient MS disability evolution (e.g. EDSS) and treatment effects leveraging baseline MRI, and (b) permit the discovery of subgroups of patients for which the model has high confidence in their response to treatment even in clinical trials which did not reach their clinical endpoints.

2024-10-03

Lecture Notes in Computer Science (publié)

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

Nima Fathi

Amar Kumar

Brennan Nichyporuk

Mohammad Havaei

Deep learning classifiers are prone to latching onto dominant confounders present in a dataset rather than on the causal markers associated … (voir plus)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.

2024-06-06

MIDL.io/2024/Conference (présentation orale)

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

Daniel Duenias

Brennan Nichyporuk

Tammy Riklin-Raviv

The integration of diverse clinical modalities such as medical imaging and the tabular data obtained by the patients' Electronic Health Reco… (voir plus)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 (prépublication)

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

Nima Fathi

Amar Kumar

Brennan Nichyporuk

Mohammad Havaei

2024-02-13

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

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 … (voir 47 de plus)

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

B. Calster

Gael Varoquaux

PAUL F. JÄGER

2024-02-12

Nature Methods (publié)

Understanding metric-related pitfalls in image analysis validation

Annika Reinke

Minu Dietlinde Tizabi

Michael Baumgartner

Matthias Eisenmann

DOREEN HECKMANN-NÖTZEL

A. EMRE KAVUR

TIM RÄDSCH

Carole H. Sudre

LAURA ACION

Michela Antonelli

Spyridon Bakas

Allison Benis

Arriel Benis

Matthew Blaschko

FLORIAN BUETTNER

Florian Buttner

M. Jorge Cardoso

Veronika Cheplygina

JIANXU CHEN … (voir 62 de plus)

Evangelia Christodoulou

BETH A. CIMINI

Gary S. Collins

Keyvan Farahani

LUCIANA FERRER

Adrian Galdran

Bram van Ginneken

Ben Glocker

PATRICK GODAU

Robert Cary Haase

Daniel A. Hashimoto

Michael M. Hoffman

Merel Huisman

Fabian Isensee

Pierre Jannin

CHARLES E. KAHN

DAGMAR KAINMUELLER

BERNHARD KAINZ

ALEXANDROS KARARGYRIS

Alan Karthikesalingam

H. Kenngott

Jens Kleesiek

Florian Kofler

THIJS KOOI

Annette Kopp-Schneider

Michal Kozubek

Anna Kreshuk

Tahsin Kurc

Bennett A. Landman

GEERT LITJENS

Amin Madani

Klaus Maier-Hein

Anne L. Martel

Peter Mattson

ERIK MEIJERING

Bjoern Menze

KAREL G.M. MOONS

Henning Müller

Brennan Nichyporuk

Felix Nickel

Jens Petersen

SUSANNE M. RAFELSKI

NASIR RAJPOOT

Mauricio Reyes

MICHAEL A. RIEGLER

Nicola Rieke

Julio Saez-Rodriguez

Ben Van Calster

Clara I. Sánchez

SHRAVYA SHETTY

ZIV R. YANIV

M. Smeden

Ronald M. Summers

Abdel Aziz Taha

ALEKSEI TIULPIN

Sotirios A. Tsaftaris

B. Calster

Gael Varoquaux

Manuel Wiesenfarth

Ziv Rafael Yaniv

PAUL F. JÄGER

Lena Maier-Hein

2024-02-12

Nature methods (publié)

Current AI applications in neurology: Brain imaging

Joshua D. Durso-Finley

Jean-Pierre R. Falet

Raghav Mehta

Douglas Arnold

Nick Pawlowski

2023-12-01

Journal of the Neurological Sciences (publié)

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

Xing Shen

Hengguan Huang

Brennan Nichyporuk

2023-10-24

ArXiv (prépublication)

Debiasing Counterfactuals in the Presence of Spurious Correlations

Amar Kumar

Nima Fathi

Raghav Mehta

Brennan Nichyporuk

Jean-Pierre R. Falet

Sotirios A. Tsaftaris

Deep learning models can perform well in complex medical imaging classification tasks, even when basing their conclusions on spurious correl… (voir plus)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.

2023-10-09

Clinical Image-Based Procedures, Fairness of AI in Medical Imaging, and Ethical and Philosophical Issues in Medical Imaging (publié)

Improving Image-Based Precision Medicine with Uncertainty-Aware Causal Models

Joshua D. Durso-Finley

Jean-Pierre R. Falet

Raghav Mehta

Douglas Arnold

Nick Pawlowski

Image-based precision medicine aims to personalize treatment decisions based on an individual's unique imaging features so as to improve the… (voir plus)ir clinical outcome. Machine learning frameworks that integrate uncertainty estimation as part of their treatment recommendations would be safer and more reliable. However, little work has been done in adapting uncertainty estimation techniques and validation metrics for precision medicine. In this paper, we use Bayesian deep learning for estimating the posterior distribution over factual and counterfactual outcomes on several treatments. This allows for estimating the uncertainty for each treatment option and for the individual treatment effects (ITE) between any two treatments. We train and evaluate this model to predict future new and enlarging T2 lesion counts on a large, multi-center dataset of MR brain images of patients with multiple sclerosis, exposed to several treatments during randomized controlled trials. We evaluate the correlation of the uncertainty estimate with the factual error, and, given the lack of ground truth counterfactual outcomes, demonstrate how uncertainty for the ITE prediction relates to bounds on the ITE error. Lastly, we demonstrate how knowledge of uncertainty could modify clinical decision-making to improve individual patient and clinical trial outcomes.

2023-10-08

OpenReview.net/Archive (publié)

Mitigating Calibration Bias Without Fixed Attribute Grouping for Improved Fairness in Medical Imaging Analysis

Changjian Shui

Justin Szeto

Raghav Mehta

Douglas Arnold