Tal Arbel

Tal Arbel
McGill University | McGill · Department of Electrical & Computer Engineering

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164
Publications
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Publications

Publications (164)
Article
Full-text available
Disability progression in multiple sclerosis remains resistant to treatment. The absence of a suitable biomarker to allow for phase 2 clinical trials presents a high barrier for drug development. We propose to enable short proof-of-concept trials by increasing statistical power using a deep-learning predictive enrichment strategy. Specifically, a m...
Chapter
In many clinical contexts, detecting all lesions is imperative for evaluating disease activity. Standard approaches pose lesion detection as a segmentation problem despite the time-consuming nature of acquiring segmentation labels. In this paper, we present a lesion detection method which relies only on point labels. Our model, which is trained via...
Chapter
Large, annotated datasets are not widely available in medical image analysis due to the prohibitive time, costs, and challenges associated with labelling large datasets. Unlabelled datasets are easier to obtain, and in many contexts, it would be feasible for an expert to provide labels for a small subset of images. This work presents an information...
Preprint
In many clinical contexts, detecting all lesions is imperative for evaluating disease activity. Standard approaches pose lesion detection as a segmentation problem despite the time-consuming nature of acquiring segmentation labels. In this paper, we present a lesion detection method which relies only on point labels. Our model, which is trained via...
Preprint
The discovery of patient-specific imaging markers that are predictive of future disease outcomes can help us better understand individual-level heterogeneity of disease evolution. In fact, deep learning models that can provide data-driven personalized markers are much more likely to be adopted in medical practice. In this work, we demonstrate that...
Preprint
Full-text available
Large, annotated datasets are not widely available in medical image analysis due to the prohibitive time, costs, and challenges associated with labelling large datasets. Unlabelled datasets are easier to obtain, and in many contexts, it would be feasible for an expert to provide labels for a small subset of images. This work presents an information...
Preprint
Full-text available
The field of automatic biomedical image analysis crucially depends on robust and meaningful performance metrics for algorithm validation. Current metric usage, however, is often ill-informed and does not reflect the underlying domain interest. Here, we present a comprehensive framework that guides researchers towards choosing performance metrics in...
Preprint
Lesion counts are important indicators of disease severity, patient prognosis, and treatment efficacy, yet counting as a task in medical imaging is often overlooked in favor of segmentation. This work introduces a novel continuously differentiable function that maps lesion segmentation predictions to lesion count probability distributions in a cons...
Preprint
Full-text available
Precision medicine for chronic diseases such as multiple sclerosis (MS) involves choosing a treatment which best balances efficacy and side effects/preferences for individual patients. Making this choice as early as possible is important, as delays in finding an effective therapy can lead to irreversible disability accrual. To this end, we present...
Preprint
Full-text available
Deep learning (DL) models have provided the state-of-the-art performance in a wide variety of medical imaging benchmarking challenges, including the Brain Tumor Segmentation (BraTS) challenges. However, the task of focal pathology multi-compartment segmentation (e.g., tumor and lesion sub-regions) is particularly challenging, and potential errors h...
Preprint
Full-text available
Progressive forms of multiple sclerosis (MS) remain resistant to treatment. Since there are currently no suitable biomarkers to allow for phase 2 trials, pharmaceutical companies must proceed directly to financially risky phase 3 trials, presenting a high barrier to drug development. We address this problem through predictive enrichment, which rand...
Article
Although deep networks have been shown to perform very well on a variety of medical imaging tasks, inference in the presence of pathology presents several challenges to common models. These challenges impede the integration of deep learning models into real clinical workflows, where the customary process of cascading deterministic outputs from a se...
Chapter
Many automatic machine learning models developed for focal pathology (e.g. lesions, tumours) detection and segmentation perform well, but do not generalize as well to new patient cohorts, impeding their widespread adoption into real clinical contexts. One strategy to create a more diverse, generalizable training set is to naively pool datasets from...
Preprint
Many automatic machine learning models developed for focal pathology (e.g. lesions, tumours) detection and segmentation perform well, but do not generalize as well to new patient cohorts, impeding their widespread adoption into real clinical contexts. One strategy to create a more diverse, generalizable training set is to naively pool datasets from...
Preprint
There are many clinical contexts which require accurate detection and segmentation of all focal pathologies (e.g. lesions, tumours) in patient images. In cases where there are a mix of small and large lesions, standard binary cross entropy loss will result in better segmentation of large lesions at the expense of missing small ones. Adjusting the o...
Preprint
Full-text available
While the importance of automatic image analysis is increasing at an enormous pace, recent meta-research revealed major flaws with respect to algorithm validation. Specifically, performance metrics are key for objective, transparent and comparative performance assessment, but relatively little attention has been given to the practical pitfalls when...
Preprint
Full-text available
Segmentation of enhancing tumours or lesions from MRI is important for detecting new disease activity in many clinical contexts. However, accurate segmentation requires the inclusion of medical images (e.g., T1 post contrast MRI) acquired after injecting patients with a contrast agent (e.g., Gadolinium), a process no longer thought to be safe. Alth...
Article
With deep learning’s success, a limited number of popular deep nets have been widely adopted for various vision tasks. However, this usually 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...
Preprint
With deep learning's success, a limited number of popular deep nets have been widely adopted for various vision tasks. However, this usually 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...
Preprint
Full-text available
This paper presents a novel probabilistic voxel selection strategy for medical image registration in time-sensitive contexts, where the goal is aggressive voxel sampling (e.g. using less than 1% of the total number) while maintaining registration accuracy and low failure rate. We develop a Bayesian framework whereby, first, a voxel sampling probabi...
Preprint
This paper presents an approach to fast image registration through probabilistic pixel sampling. We propose a practical scheme to leverage the benefits of two state-of-the-art pixel sampling approaches: gradient magnitude based pixel sampling and uniformly random sampling. Our framework involves learning the optimal balance between the two sampling...
Preprint
Most of today's popular deep architectures are hand-engineered for general purpose applications. However, this design procedure usually leads to massive redundant, useless, or even harmful features for specific tasks. Such unnecessarily high complexities render deep nets impractical for many real-world applications, especially those without powerfu...
Article
Full-text available
The number of biomedical image analysis challenges organized per year is steadily increasing. These international competitions have the purpose of benchmarking algorithms on common data sets, typically to identify the best method for a given problem. Recent research, however, revealed that common practice related to challenge reporting does not all...
Preprint
In this paper, we develop a metric designed to assess and rank uncertainty measures for the task of brain tumour sub-tissue segmentation in the BraTS 2019 sub-challenge on uncertainty quantification. The metric is designed to: (1) reward uncertainty measures where high confidence is assigned to correct assertions, and where incorrect assertions are...
Article
Full-text available
The Sørensen-Dice index (SDI) is a widely used measure for evaluating medical image segmentation algorithms. It offers a standardized measure of segmentation accuracy which has proven useful. However, it offers diminishing insight when the number of objects is unknown, such as in white matter lesion segmentation of multiple sclerosis (MS) patients....
Chapter
The appearance of contrast-enhanced pathologies (e.g. lesion, cancer) is an important marker of disease activity, stage and treatment efficacy in clinical trials. The automatic detection and segmentation of these enhanced pathologies remains a difficult challenge, as they can be very small and visibly similar to other non-pathological enhancements...
Book
This book constitutes the refereed proceedings of the Second International Workshop on Uncertainty for Safe Utilization of Machine Learning in Medical Imaging, UNSURE 2020, and the Third International Workshop on Graphs in Biomedical Image Analysis, GRAIL 2020, held in conjunction with MICCAI 2020, in Lima, Peru, in October 2020. The workshops were...
Preprint
Full-text available
The number of biomedical image analysis challenges organized per year is steadily increasing. These international competitions have the purpose of benchmarking algorithms on common data sets, typically to identify the best method for a given problem. Recent research, however, revealed that common practice related to challenge reporting does not all...
Chapter
Although deep networks have been shown to perform very well on a variety of tasks, inference in the presence of pathology in medical images presents challenges to traditional networks. Given that medical image analysis typically requires a sequence of inference tasks to be performed (e.g. registration, segmentation), this results in an accumulation...
Chapter
One of the biggest challenges in developing robust machine learning techniques for medical image analysis is the lack of access to large-scale annotated image datasets needed for supervised learning. When the task is to segment pathological structures (e.g. lesions, tumors) from patient images, training on a dataset with few samples is very challen...
Article
Deep learning networks have recently been shown to outperform other segmentation methods on various public, medical-image challenge datasets, particularly on metrics focused on large pathologies. For diseases such as Multiple Sclerosis (MS), however, monitoring all the focal lesions visible on MRI sequences, even very small ones, is essential for d...
Article
Full-text available
Robust and reliable stroke lesion segmentation is a crucial step toward employing lesion volume as an independent endpoint for randomized trials. The aim of this work was to develop and evaluate a novel method to segment sub-acute ischemic stroke lesions from fluid-attenuated inversion recovery (FLAIR) magnetic resonance imaging (MRI) datasets. Aft...
Preprint
Full-text available
Gliomas are the most common primary brain malignancies, with different degrees of aggressiveness, variable prognosis and various heterogeneous 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...
Article
Full-text available
Our research [Team Name: URAN] of 'Neuromorphic Neural Network for Multimodal Brain Tumor Segmentation and Survival analysis' demonstrates its performance on 'Overall Survival Prediction', without any prior training using multi-modal MRI Image segmentation by medical doctors (though provided by BraTS 2018 challenge data). Two segmentation categorie...
Article
Full-text available
In the original version of this Article the values in the rightmost column of Table 1 were inadvertently shifted relative to the other columns. This has now been corrected in the PDF and HTML versions of the Article.
Book
This book constitutes the refereed proceedings of the First International Workshop on Uncertainty for Safe Utilization of Machine Learning in Medical Imaging, UNSURE 2019, and the 8th International Workshop on Clinical Image-Based Procedures, CLIP 2019, held in conjunction with MICCAI 2019, in Shenzhen, China, in October 2019. For UNSURE 2019, 8 pa...
Article
Full-text available
International challenges have become the standard for validation of biomedical image analysis methods. Given their scientific impact, it is surprising that a critical analysis of common practices related to the organization of challenges has not yet been performed. In this paper, we present a comprehensive analysis of biomedical image analysis chal...
Preprint
Full-text available
Gliomas are the most common primary brain malignancies, with different degrees of aggressiveness, variable prognosis and various heterogeneous 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...
Article
Full-text available
Since the first MICCAI grand challenge was organized in 2007 [1], the impact of biomedical image analysis challenges on both the research field as well as on individual careers has been steadily growing. For example, the acceptance of a journal article today often depends on the performance of a new algorithm being assessed against the state-of-the...
Conference Paper
Full-text available
Since the first MICCAI grand challenge organized in 2007 in Brisbane, challenges have become an integral part of MICCAI conferences. In the meantime, challenge datasets have become widely recognized as international benchmarking datasets and thus have a great influence on the research community and individual careers. In this paper, we show several...
Chapter
Accurate synthesis of a full 3D MR image containing tumours from available MRI (e.g. to replace an image that is currently unavailable or corrupted) would provide a clinician as well as downstream inference methods with important complementary information for disease analysis. In this paper, we present an end-to-end 3D convolution neural network th...
Article
High efficiency is desirable for many interactive biometrics tasks, including facial trait recognition. Although deep convolutional nets are effective for a multitude of classification tasks, their high space and time demands make them impractical for PCs and mobile devices without a powerful GPU. In this paper, we propose a structured filter-level...
Chapter
In this work, we use a 3D Fully Connected Network (FCN) architecture for brain tumor segmentation. Our method includes a multi-scale loss function on predictions given at each resolution of the FCN. Using this approach, the higher resolution features can be combined with the initial segmentation at a lower resolution so that the FCN models context...
Chapter
A variety of automatic segmentation techniques have been successfully applied to the delineation of larger T2 lesions in patient MRI in the context of Multiple Sclerosis (MS), assisting in the estimation of lesion volume, a common clinical measure of disease activity and stage. In the context of clinical trials, however, a wider number of metrics a...
Chapter
Deep learning (DL) networks have recently been shown to outperform other segmentation methods on various public, medical-image challenge datasets [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 esse...
Preprint
Deep learning (DL) networks have recently been shown to outperform other segmentation methods on various public, medical-image challenge datasets [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 essent...
Preprint
Full-text available
Accurate synthesis of a full 3D MR image containing tumours from available MRI (e.g. to replace an image that is currently unavailable or corrupted) would provide a clinician as well as downstream inference methods with important complementary information for disease analysis. In this paper, we present an end-to-end 3D convolution neural network th...
Preprint
Full-text available
International challenges have become the standard for validation of biomedical image analysis methods. Given their scientific impact, it is surprising that a critical analysis of common practices related to the organization of challenges has not yet been performed. In this paper, we present a comprehensive analysis of biomedical image analysis chal...
Article
Full-text available
We present our work investigating the feasibility of combining intraoperative ultrasound for brain shift correction and augmented reality (AR) visualization for intraoperative interpretation of patient-specific models in image-guided neurosurgery (IGNS) of brain tumors. We combine two imaging technologies for image-guided brain tumor neurosurgery....
Conference Paper
The growth of lesions and the development of new lesions in MRI are markers of new disease activity in Multiple Sclerosis (MS) patients. Successfully predicting future lesion activity could lead to a better understanding of disease worsening, as well as prediction of treatment efficacy. We introduce the first, fully automatic, probabilistic framewo...
Conference Paper
Many real-time tasks, such as human-computer interaction, require fast and efficient facial gender classification. Although deep CNN nets have been very effective for a multitude of classification tasks, their high space and time demands make them impractical for personal computers and mobile devices without a powerful GPU. In this paper, we develo...
Preprint
Published conference paper: https://openaccess.thecvf.com/content_cvpr_2017_workshops/w6/html/Tian_Deep_LDA-Pruned_Nets_CVPR_2017_paper.html
Article
In conjunction with the ISBI 2015 conference, we organized a longitudinal lesion segmentation challenge providing training and test data to registered participants. The training data consisted of five subjects with a mean of 4.4 time-points, and test data of fourteen subjects with a mean of 4.4 time-points. All 82 data sets had the white matter les...
Book
This book constitutes the refereed joint proceedings of the 6th Joint International Workshop on Computing and Visualization for Intravascular Imaging and Computer Assisted Stenting, CVII-STENT 2017, and the Second International Workshop on Large-Scale Annotation of Biomedical Data and Expert Label Synthesis, LABELS 2017, held in conjunction with th...
Book
This book constitutes the refereed joint proceedings of the International Workshop on Bio-Imaging and Visualization for Patient-Customized Simulations, BIVPCS 2017, and the International Workshop on Point-of-Care Ultrasound, POCUS 2017, held in conjunction with the 20th International Conference on Medical Imaging and Computer-Assisted Intervention,...
Book
This book constitutes the refereed joint proceedings of the International Workshop on Fetal and Infant Image Analysis, FIFI 2017, and the 6th International Workshop on Ophthalmic Medical Image Analysis, OMIA 2017, held in conjunction with the 20th International Conference on Medical Imaging and Computer-Assisted Intervention, MICCAI 2017, in Québec...
Book
This book constitutes the refereed joint proceedings of the Third International Workshop on Deep Learning in Medical Image Analysis, DLMIA 2017, and the 6th International Workshop on Multimodal Learning for Clinical Decision Support, ML-CDS 2017, held in conjunction with the 20th International Conference on Medical Imaging and Computer-Assisted Int...
Book
This book constitutes the refereed joint proceedings of the International Workshop on Computational Methods for Molecular Imaging, CMMI 2017, the International Workshop on Reconstruction and Analysis of Moving Body Organs, RAMBO 2017, and the International Stroke Workshop: Imaging and Treatment Challenges, SWITCH 2017, held in conjunction with the...
Book
This book constitutes the refereed joint proceedings of the 4th International Workshop on Computer Assisted and Robotic Endoscopy, CARE 2017, and the 6th International Workshop on Clinical Image-Based Procedures: Translational Research in Medical Imaging, CLIP 2017, held in conjunction with the 20th International Conference on Medical Imaging and C...
Book
This book constitutes the thoroughly refereed post-workshop proceedings of the International Workshop on Medical Computer Vision, MCV 2016, and of the International Workshop on Bayesian and grAphical Models for Biomedical Imaging, BAMBI 2016, held in Athens, Greece, in October 2016, held in conjunction with the 19th International Conference on Medi...