arXiv subjects

Tal Arbel

Publications and source records attributed to Tal Arbel.

52 records · Page 3Linked to original sources

arXiv2022

Cohort Bias Adaptation in Aggregated Datasets for Lesion Segmentation

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 different cohorts. Surprisingly, training on this \it{big data} does not necessarily increase, and may even reduce, overall performance and model generalizability, due to the existence of cohort biases that affect label distributions. In this paper, we propose a generalized affine conditioning framework to learn and account for cohort biases across multi-source datasets, which we call Source-Conditioned Instance Normalization (SCIN). Through extensive experimentation on three different, large scale, multi-scanner, multi-centre Multiple Sclerosis (MS) clinical trial MRI datasets, we show that our cohort bias adaptation method (1) improves performance of the network on pooled datasets relative to naively pooling datasets and (2) can quickly adapt to a new cohort by fine-tuning the instance normalization parameters, thus learning the new cohort bias with only 10 labelled samples.

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arXiv2022

Segmentation-Consistent Probabilistic Lesion Counting

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 consistent manner. The proposed end-to-end approach--which consists of voxel clustering, lesion-level voxel probability aggregation, and Poisson-binomial counting--is non-parametric and thus offers a robust and consistent way to augment lesion segmentation models with post hoc counting capabilities. Experiments on Gadolinium-enhancing lesion counting demonstrate that our method outputs accurate and well-calibrated count distributions that capture meaningful uncertainty information. They also reveal that our model is suitable for multi-task learning of lesion segmentation, is efficient in low data regimes, and is robust to adversarial attacks.

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arXiv2021

Grow-Push-Prune: aligning deep discriminants for effective structural network compression

Most of today's popular deep architectures are hand-engineered to be generalists. However, this design procedure usually leads to massive redundant, useless, or even harmful features for specific tasks. Unnecessarily high complexities render deep nets impractical for many real-world applications, especially those without powerful GPU support. In this paper, we attempt to derive task-dependent compact models from a deep discriminant analysis perspective. We propose an iterative and proactive approach for classification tasks which alternates between (1) a pushing step, with an objective to simultaneously maximize class separation, penalize co-variances, and push deep discriminants into alignment with a compact set of neurons, and (2) a pruning step, which discards less useful or even interfering neurons. Deconvolution is adopted to reverse 'unimportant' filters' effects and recover useful contributing sources. A simple network growing strategy based on the basic Inception module is proposed for challenging tasks requiring larger capacity than what the base net can offer. Experiments on the MNIST, CIFAR10, and ImageNet datasets demonstrate our approach's efficacy. On ImageNet, by pushing and pruning our grown Inception-88 model, we achieve more accurate models than Inception nets generated during growing, residual nets, and popular compact nets at similar sizes. We also show that our grown Inception nets (without hard-coded dimension alignment) clearly outperform residual nets of similar complexities.

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arXiv2021

HAD-Net: A Hierarchical Adversarial Knowledge Distillation Network for Improved Enhanced Tumour Segmentation Without Post-Contrast Images

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. Although a number of modality-agnostic segmentation networks have been developed over the past few years, they have been met with limited success in the context of enhancing pathology segmentation. In this work, we present HAD-Net, a novel offline adversarial knowledge distillation (KD) technique, whereby a pre-trained teacher segmentation network, with access to all MRI sequences, teaches a student network, via hierarchical adversarial training, to better overcome the large domain shift presented when crucial images are absent during inference. In particular, we apply HAD-Net to the challenging task of enhancing tumour segmentation when access to post-contrast imaging is not available. The proposed network is trained and tested on the BraTS 2019 brain tumour segmentation challenge dataset, where it achieves performance improvements in the ranges of 16% - 26% over (a) recent modality-agnostic segmentation methods (U-HeMIS, U-HVED), (b) KD-Net adapted to this problem, (c) the pre-trained student network and (d) a non-hierarchical version of the network (AD-Net), in terms of Dice scores for enhancing tumour (ET). The network also shows improvements in tumour core (TC) Dice scores. Finally, the network outperforms both the baseline student network and AD-Net in terms of uncertainty quantification for enhancing tumour segmentation based on the BraTs 2019 uncertainty challenge metrics. Our code is publicly available at: https://github.com/SaverioVad/HAD_Net

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arXiv2021

Accounting for Variance in Machine Learning Benchmarks

Strong empirical evidence that one machine-learning algorithm A outperforms another one B ideally calls for multiple trials optimizing the learning pipeline over sources of variation such as data sampling, data augmentation, parameter initialization, and hyperparameters choices. This is prohibitively expensive, and corners are cut to reach conclusions. We model the whole benchmarking process, revealing that variance due to data sampling, parameter initialization and hyperparameter choice impact markedly the results. We analyze the predominant comparison methods used today in the light of this variance. We show a counter-intuitive result that adding more sources of variation to an imperfect estimator approaches better the ideal estimator at a 51 times reduction in compute cost. Building on these results, we study the error rate of detecting improvements, on five different deep-learning tasks/architectures. This study leads us to propose recommendations for performance comparisons.

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arXiv2020

Task dependent Deep LDA pruning of neural networks

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 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 space 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 (ImageNet, CIFAR100) as well as domain specific tasks (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.

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arXiv2020

Optimization over Random and Gradient Probabilistic Pixel Sampling for Fast, Robust Multi-Resolution Image Registration

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 schemes off-line during training, based on a small training dataset, using particle swarm optimization. We then test the proposed sampling approach on 3D rigid registration against two state-of-the-art approaches based on the popular, publicly available, Vanderbilt RIRE dataset. Our results indicate that the proposed sampling approach yields much faster, accurate and robust registration results when compared against the state-of-the-art.

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arXiv2020

Uncertainty driven probabilistic voxel selection for image registration

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 probability field (VSPF) is built based on the uncertainty on the transformation parameters. We then describe a practical, multi-scale registration algorithm, where, at each optimization iteration, different voxel subsets are sampled based on the VSPF. The approach maximizes accuracy without committing to a particular fixed subset of voxels. The probabilistic sampling scheme developed is shown to manage the tradeoff between the robustness of traditional random voxel selection (by permitting more exploration) and the accuracy of fixed voxel selection (by permitting a greater proportion of informative voxels).

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arXiv2020

BIAS: Transparent reporting of biomedical image analysis challenges

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 allow for adequate interpretation and reproducibility of results. To address the discrepancy between the impact of challenges and the quality (control), the Biomedical I mage Analysis ChallengeS (BIAS) initiative developed a set of recommendations for the reporting of challenges. The BIAS statement aims to improve the transparency of the reporting of a biomedical image analysis challenge regardless of field of application, image modality or task category assessed. This article describes how the BIAS statement was developed and presents a checklist which authors of biomedical image analysis challenges are encouraged to include in their submission when giving a paper on a challenge into review. The purpose of the checklist is to standardize and facilitate the review process and raise interpretability and reproducibility of challenge results by making relevant information explicit.

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arXiv2020

Medical Imaging with Deep Learning: MIDL 2020 -- Short Paper Track

This compendium gathers all the accepted extended abstracts from the Third International Conference on Medical Imaging with Deep Learning (MIDL 2020), held in Montreal, Canada, 6-9 July 2020. Note that only accepted extended abstracts are listed here, the Proceedings of the MIDL 2020 Full Paper Track are published in the Proceedings of Machine Learning Research (PMLR).

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arXiv2020

Uncertainty Evaluation Metric for Brain Tumour Segmentation

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 assigned low confidence and (2) penalize measures that have higher percentages of under-confident correct assertions. Here, the workings of the components of the metric are explored based on a number of popular uncertainty measures evaluated on the BraTS 2019 dataset.

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arXiv2019

Why rankings of biomedical image analysis competitions should be interpreted with care

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 challenges conducted up to now. We demonstrate the importance of challenges and show that the lack of quality control has critical consequences. First, reproducibility and interpretation of the results is often hampered as only a fraction of relevant information is typically provided. Second, the rank of an algorithm is generally not robust to a number of variables such as the test data used for validation, the ranking scheme applied and the observers that make the reference annotations. To overcome these problems, we recommend best practice guidelines and define open research questions to be addressed in the future.

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arXiv2019

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

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 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 tumor is 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 the state-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 total resection. 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.

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arXiv2018

Efficient Gender Classification Using a Deep LDA-Pruned Net

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 develop a 16-layer, yet lightweight, neural network which boosts efficiency while maintaining high accuracy. Our net is pruned from the VGG-16 model starting from the last convolutional (conv) layer where we find neuron activations are highly uncorrelated given the gender. Through Fisher's Linear Discriminant Analysis (LDA), we show that this high decorrelation makes it safe to discard directly last conv layer neurons with high within-class variance and low between-class variance. Combined with either Support Vector Machines (SVM) or Bayesian classification, the reduced CNNs are capable of achieving comparable (or even higher) accuracies on the LFW and CelebA datasets than the original net with fully connected layers. On LFW, only four Conv5_3 neurons are able to maintain a comparably high recognition accuracy, which results in a reduction of total network size by a factor of 70X with a 11 fold speedup. Comparisons with a state-of-the-art pruning method as well as two smaller nets in terms of accuracy loss and convolutional layers pruning rate are also provided.

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arXiv2018

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

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 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.

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arXiv2018

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

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 that takes a set of acquired MR image sequences (e.g. T1, T2, T1ce) as input and concurrently performs (1) regression of the missing full resolution 3D MRI (e.g. FLAIR) and (2) segmentation of the tumour into subtypes (e.g. enhancement, core). The hypothesis is that this would focus the network to perform accurate synthesis in the area of the tumour. Experiments on the BraTS 2015 and 2017 datasets [1] show that: (1) the proposed method gives better performance than state-of-the-art methods in terms of established global evaluation metrics (e.g. PSNR), (2) replacing real MR volumes with the synthesized MRI does not lead to significant degradation in tumour and sub-structure segmentation accuracy. The system further provides uncertainty estimates based on Monte Carlo (MC) dropout [11] for the synthesized volume at each voxel, permitting quantification of the system's confidence in the output at each location.

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