arXiv subjects

Ismail Ben Ayed

Publications and source records attributed to Ismail Ben Ayed.

At least 145 records · Page 8Linked to original sources

arXiv2020

Bounding boxes for weakly supervised segmentation: Global constraints get close to full supervision

We propose a novel weakly supervised learning segmentation based on several global constraints derived from box annotations. Particularly, we leverage a classical tightness prior to a deep learning setting via imposing a set of constraints on the network outputs. Such a powerful topological prior prevents solutions from excessive shrinking by enforcing any horizontal or vertical line within the bounding box to contain, at least, one pixel of the foreground region. Furthermore, we integrate our deep tightness prior with a global background emptiness constraint, guiding training with information outside the bounding box. We demonstrate experimentally that such a global constraint is much more powerful than standard cross-entropy for the background class. Our optimization problem is challenging as it takes the form of a large set of inequality constraints on the outputs of deep networks. We solve it with sequence of unconstrained losses based on a recent powerful extension of the log-barrier method, which is well-known in the context of interior-point methods. This accommodates standard stochastic gradient descent (SGD) for training deep networks, while avoiding computationally expensive and unstable Lagrangian dual steps and projections. Extensive experiments over two different public data sets and applications (prostate and brain lesions) demonstrate that the synergy between our global tightness and emptiness priors yield very competitive performances, approaching full supervision and outperforming significantly DeepCut. Furthermore, our approach removes the need for computationally expensive proposal generation. Our code is shared anonymously.

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arXiv2020

Semi-supervised few-shot learning for medical image segmentation

Recent years have witnessed the great progress of deep neural networks on semantic segmentation, particularly in medical imaging. Nevertheless, training high-performing models require large amounts of pixel-level ground truth masks, which can be prohibitive to obtain in the medical domain. Furthermore, training such models in a low-data regime highly increases the risk of overfitting. Recent attempts to alleviate the need for large annotated datasets have developed training strategies under the few-shot learning paradigm, which addresses this shortcoming by learning a novel class from only a few labeled examples. In this context, a segmentation model is trained on episodes, which represent different segmentation problems, each of them trained with a very small labeled dataset. In this work, we propose a novel few-shot learning framework for semantic segmentation, where unlabeled images are also made available at each episode. To handle this new learning paradigm, we propose to include surrogate tasks that can leverage very powerful supervisory signals --derived from the data itself-- for semantic feature learning. We show that including unlabeled surrogate tasks in the episodic training leads to more powerful feature representations, which ultimately results in better generability to unseen tasks. We demonstrate the efficiency of our method in the task of skin lesion segmentation in two publicly available datasets. Furthermore, our approach is general and model-agnostic, which can be combined with different deep architectures.

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arXiv2019

Deep clustering: On the link between discriminative models and K-means

In the context of recent deep clustering studies, discriminative models dominate the literature and report the most competitive performances. These models learn a deep discriminative neural network classifier in which the labels are latent. Typically, they use multinomial logistic regression posteriors and parameter regularization, as is very common in supervised learning. It is generally acknowledged that discriminative objective functions (e.g., those based on the mutual information or the KL divergence) are more flexible than generative approaches (e.g., K-means) in the sense that they make fewer assumptions about the data distributions and, typically, yield much better unsupervised deep learning results. On the surface, several recent discriminative models may seem unrelated to K-means. This study shows that these models are, in fact, equivalent to K-means under mild conditions and common posterior models and parameter regularization. We prove that, for the commonly used logistic regression posteriors, maximizing the $L_2$ regularized mutual information via an approximate alternating direction method (ADM) is equivalent to a soft and regularized K-means loss. Our theoretical analysis not only connects directly several recent state-of-the-art discriminative models to K-means, but also leads to a new soft and regularized deep K-means algorithm, which yields competitive performance on several image clustering benchmarks.

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arXiv2019

Adversarial Learning of General Transformations for Data Augmentation

Data augmentation (DA) is fundamental against overfitting in large convolutional neural networks, especially with a limited training dataset. In images, DA is usually based on heuristic transformations, like geometric or color transformations. Instead of using predefined transformations, our work learns data augmentation directly from the training data by learning to transform images with an encoder-decoder architecture combined with a spatial transformer network. The transformed images still belong to the same class but are new, more complex samples for the classifier. Our experiments show that our approach is better than previous generative data augmentation methods, and comparable to predefined transformation methods when training an image classifier.

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arXiv2019

Discretely-constrained deep network for weakly supervised segmentation

An efficient strategy for weakly-supervised segmentation is to impose constraints or regularization priors on target regions. Recent efforts have focused on incorporating such constraints in the training of convolutional neural networks (CNN), however this has so far been done within a continuous optimization framework. Yet, various segmentation constraints and regularization can be modeled and optimized more efficiently in a discrete formulation. This paper proposes a method, based on the alternating direction method of multipliers (ADMM) algorithm, to train a CNN with discrete constraints and regularization priors. This method is applied to the segmentation of medical images with weak annotations, where both size constraints and boundary length regularization are enforced. Experiments on a benchmark cardiac segmentation dataset show our method to yield a performance near to full supervision.

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arXiv2019

Curriculum semi-supervised segmentation

This study investigates a curriculum-style strategy for semi-supervised CNN segmentation, which devises a regression network to learn image-level information such as the size of a target region. These regressions are used to effectively regularize the segmentation network, constraining softmax predictions of the unlabeled images to match the inferred label distributions. Our framework is based on inequality constraints that tolerate uncertainties with inferred knowledge, e.g., regressed region size, and can be employed for a large variety of region attributes. We evaluated our proposed strategy for left ventricle segmentation in magnetic resonance images (MRI), and compared it to standard proposal-based semi-supervision strategies. Our strategy leverages unlabeled data in more efficiently, and achieves very competitive results, approaching the performance of full-supervision.

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arXiv2019

Beyond Gradient Descent for Regularized Segmentation Losses

The simplicity of gradient descent (GD) made it the default method for training ever-deeper and complex neural networks. Both loss functions and architectures are often explicitly tuned to be amenable to this basic local optimization. In the context of weakly-supervised CNN segmentation, we demonstrate a well-motivated loss function where an alternative optimizer (ADM) achieves the state-of-the-art while GD performs poorly. Interestingly, GD obtains its best result for a "smoother" tuning of the loss function. The results are consistent across different network architectures. Our loss is motivated by well-understood MRF/CRF regularization models in "shallow" segmentation and their known global solvers. Our work suggests that network design/training should pay more attention to optimization methods.

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arXiv2019

Decoupling Direction and Norm for Efficient Gradient-Based L2 Adversarial Attacks and Defenses

Research on adversarial examples in computer vision tasks has shown that small, often imperceptible changes to an image can induce misclassification, which has security implications for a wide range of image processing systems. Considering $L_2$ norm distortions, the Carlini and Wagner attack is presently the most effective white-box attack in the literature. However, this method is slow since it performs a line-search for one of the optimization terms, and often requires thousands of iterations. In this paper, an efficient approach is proposed to generate gradient-based attacks that induce misclassifications with low $L_2$ norm, by decoupling the direction and the norm of the adversarial perturbation that is added to the image. Experiments conducted on the MNIST, CIFAR-10 and ImageNet datasets indicate that our attack achieves comparable results to the state-of-the-art (in terms of $L_2$ norm) with considerably fewer iterations (as few as 100 iterations), which opens the possibility of using these attacks for adversarial training. Models trained with our attack achieve state-of-the-art robustness against white-box gradient-based $L_2$ attacks on the MNIST and CIFAR-10 datasets, outperforming the Madry defense when the attacks are limited to a maximum norm.

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arXiv2019

Isointense Infant Brain Segmentation with a Hyper-dense Connected Convolutional Neural Network

Neonatal brain segmentation in magnetic resonance (MR) is a challenging problem due to poor image quality and low contrast between white and gray matter regions. Most existing approaches for this problem are based on multi-atlas label fusion strategies, which are time-consuming and sensitive to registration errors. As alternative to these methods, we propose a hyper-densely connected 3D convolutional neural network that employs MR-T1 and T2 images as input, which are processed independently in two separated paths. An important difference with previous densely connected networks is the use of direct connections between layers from the same and different paths. Adopting such dense connectivity helps the learning process by including deep supervision and improving gradient flow. We evaluated our approach on data from the MICCAI Grand Challenge on 6-month infant Brain MRI Segmentation (iSEG), obtaining very competitive results. Among 21 teams, our approach ranked first or second in most metrics, translating into a state-of-the-art performance.

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arXiv2019

HyperDense-Net: A hyper-densely connected CNN for multi-modal image segmentation

Recently, dense connections have attracted substantial attention in computer vision because they facilitate gradient flow and implicit deep supervision during training. Particularly, DenseNet, which connects each layer to every other layer in a feed-forward fashion, has shown impressive performances in natural image classification tasks. We propose HyperDenseNet, a 3D fully convolutional neural network that extends the definition of dense connectivity to multi-modal segmentation problems. Each imaging modality has a path, and dense connections occur not only between the pairs of layers within the same path, but also between those across different paths. This contrasts with the existing multi-modal CNN approaches, in which modeling several modalities relies entirely on a single joint layer (or level of abstraction) for fusion, typically either at the input or at the output of the network. Therefore, the proposed network has total freedom to learn more complex combinations between the modalities, within and in-between all the levels of abstraction, which increases significantly the learning representation. We report extensive evaluations over two different and highly competitive multi-modal brain tissue segmentation challenges, iSEG 2017 and MRBrainS 2013, with the former focusing on 6-month infant data and the latter on adult images. HyperDenseNet yielded significant improvements over many state-of-the-art segmentation networks, ranking at the top on both benchmarks. We further provide a comprehensive experimental analysis of features re-use, which confirms the importance of hyper-dense connections in multi-modal representation learning. Our code is publicly available at https://www.github.com/josedolz/HyperDenseNet.

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arXiv2019

Constrained-CNN losses for weakly supervised segmentation

Weakly-supervised learning based on, e.g., partially labelled images or image-tags, is currently attracting significant attention in CNN segmentation as it can mitigate the need for full and laborious pixel/voxel annotations. Enforcing high-order (global) inequality constraints on the network output (for instance, to constrain the size of the target region) can leverage unlabeled data, guiding the training process with domain-specific knowledge. Inequality constraints are very flexible because they do not assume exact prior knowledge. However, constrained Lagrangian dual optimization has been largely avoided in deep networks, mainly for computational tractability reasons. To the best of our knowledge, the method of [Pathak et al., 2015] is the only prior work that addresses deep CNNs with linear constraints in weakly supervised segmentation. It uses the constraints to synthesize fully-labeled training masks (proposals) from weak labels, mimicking full supervision and facilitating dual optimization. We propose to introduce a differentiable penalty, which enforces inequality constraints directly in the loss function, avoiding expensive Lagrangian dual iterates and proposal generation. From constrained-optimization perspective, our simple penalty-based approach is not optimal as there is no guarantee that the constraints are satisfied. However, surprisingly, it yields substantially better results than the Lagrangian-based constrained CNNs in [Pathak et al., 2015], while reducing the computational demand for training. By annotating only a small fraction of the pixels, the proposed approach can reach a level of segmentation performance that is comparable to full supervision on three separate tasks. While our experiments focused on basic linear constraints such as the target-region size and image tags, our framework can be easily extended to other non-linear constraints.

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arXiv2018

Scalable Laplacian K-modes

We advocate Laplacian K-modes for joint clustering and density mode finding, and propose a concave-convex relaxation of the problem, which yields a parallel algorithm that scales up to large datasets and high dimensions. We optimize a tight bound (auxiliary function) of our relaxation, which, at each iteration, amounts to computing an independent update for each cluster-assignment variable, with guaranteed convergence. Therefore, our bound optimizer can be trivially distributed for large-scale data sets. Furthermore, we show that the density modes can be obtained as byproducts of the assignment variables via simple maximum-value operations whose additional computational cost is linear in the number of data points. Our formulation does not need storing a full affinity matrix and computing its eigenvalue decomposition, neither does it perform expensive projection steps and Lagrangian-dual inner iterates for the simplex constraints of each point. Furthermore, unlike mean-shift, our density-mode estimation does not require inner-loop gradient-ascent iterates. It has a complexity independent of feature-space dimension, yields modes that are valid data points in the input set and is applicable to discrete domains as well as arbitrary kernels. We report comprehensive experiments over various data sets, which show that our algorithm yields very competitive performances in term of optimization quality (i.e., the value of the discrete-variable objective at convergence) and clustering accuracy.

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arXiv2018

Multi-region segmentation of bladder cancer structures in MRI with progressive dilated convolutional networks

Precise segmentation of bladder walls and tumor regions is an essential step towards non-invasive identification of tumor stage and grade, which is critical for treatment decision and prognosis of patients with bladder cancer (BC). However, the automatic delineation of bladder walls and tumor in magnetic resonance images (MRI) is a challenging task, due to important bladder shape variations, strong intensity inhomogeneity in urine and very high variability across population, particularly on tumors appearance. To tackle these issues, we propose to use a deep fully convolutional neural network. The proposed network includes dilated convolutions to increase the receptive field without incurring extra cost nor degrading its performance. Furthermore, we introduce progressive dilations in each convolutional block, thereby enabling extensive receptive fields without the need for large dilation rates. The proposed network is evaluated on 3.0T T2-weighted MRI scans from 60 pathologically confirmed patients with BC. Experiments shows the proposed model to achieve high accuracy, with a mean Dice similarity coefficient of 0.98, 0.84 and 0.69 for inner wall, outer wall and tumor region, respectively. These results represent a very good agreement with reference contours and an increase in performance compared to existing methods. In addition, inference times are less than a second for a whole 3D volume, which is between 2-3 orders of magnitude faster than related state-of-the-art methods for this application. We showed that a CNN can yield precise segmentation of bladder walls and tumors in bladder cancer patients on MRI. The whole segmentation process is fully-automatic and yields results in very good agreement with the reference standard, demonstrating the viability of deep learning models for the automatic multi-region segmentation of bladder cancer MRI images.

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arXiv2018

IVD-Net: Intervertebral disc localization and segmentation in MRI with a multi-modal UNet

Accurate localization and segmentation of intervertebral disc (IVD) is crucial for the assessment of spine disease diagnosis. Despite the technological advances in medical imaging, IVD localization and segmentation are still manually performed, which is time-consuming and prone to errors. If, in addition, multi-modal imaging is considered, the burden imposed on disease assessments increases substantially. In this paper, we propose an architecture for IVD localization and segmentation in multi-modal MRI, which extends the well-known UNet. Compared to single images, multi-modal data brings complementary information, contributing to better data representation and discriminative power. Our contributions are three-fold. First, how to effectively integrate and fully leverage multi-modal data remains almost unexplored. In this work, each MRI modality is processed in a different path to better exploit their unique information. Second, inspired by HyperDenseNet, the network is densely-connected both within each path and across different paths, granting the model the freedom to learn where and how the different modalities should be processed and combined. Third, we improved standard U-Net modules by extending inception modules with two dilated convolutions blocks of different scale, which helps handling multi-scale context. We report experiments over the data set of the public MICCAI 2018 Challenge on Automatic Intervertebral Disc Localization and Segmentation, with 13 multi-modal MRI images used for training and 3 for validation. We trained IVD-Net on an NVidia TITAN XP GPU with 16 GBs RAM, using ADAM as optimizer and a learning rate of 10e-5 during 200 epochs. Training took about 5 hours, and segmentation of a whole volume about 2-3 seconds, on average. Several baselines, with different multi-modal fusion strategies, were used to demonstrate the effectiveness of the proposed architecture.

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arXiv2018

Dense Multi-path U-Net for Ischemic Stroke Lesion Segmentation in Multiple Image Modalities

Delineating infarcted tissue in ischemic stroke lesions is crucial to determine the extend of damage and optimal treatment for this life-threatening condition. However, this problem remains challenging due to high variability of ischemic strokes' location and shape. Recently, fully-convolutional neural networks (CNN), in particular those based on U-Net, have led to improved performances for this task. In this work, we propose a novel architecture that improves standard U-Net based methods in three important ways. First, instead of combining the available image modalities at the input, each of them is processed in a different path to better exploit their unique information. Moreover, the network is densely-connected (i.e., each layer is connected to all following layers), both within each path and across different paths, similar to HyperDenseNet. This gives our model the freedom to learn the scale at which modalities should be processed and combined. Finally, inspired by the Inception architecture, we improve standard U-Net modules by extending inception modules with two convolutional blocks with dilated convolutions of different scale. This helps handling the variability in lesion sizes. We split the 93 stroke datasets into training and validation sets containing 83 and 9 examples respectively. Our network was trained on a NVidia TITAN XP GPU with 16 GBs RAM, using ADAM as optimizer and a learning rate of 1$\times$10$^{-5}$ during 200 epochs. Training took around 5 hours and segmentation of a whole volume took between 0.2 and 2 seconds, as average. The performance on the test set obtained by our method is compared to several baselines, to demonstrate the effectiveness of our architecture, and to a state-of-art architecture that employs factorized dilated convolutions, i.e., ERFNet.

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arXiv2018

On Regularized Losses for Weakly-supervised CNN Segmentation

Minimization of regularized losses is a principled approach to weak supervision well-established in deep learning, in general. However, it is largely overlooked in semantic segmentation currently dominated by methods mimicking full supervision via "fake" fully-labeled training masks (proposals) generated from available partial input. To obtain such full masks the typical methods explicitly use standard regularization techniques for "shallow" segmentation, e.g. graph cuts or dense CRFs. In contrast, we integrate such standard regularizers directly into the loss functions over partial input. This approach simplifies weakly-supervised training by avoiding extra MRF/CRF inference steps or layers explicitly generating full masks, while improving both the quality and efficiency of training. This paper proposes and experimentally compares different losses integrating MRF/CRF regularization terms. We juxtapose our regularized losses with earlier proposal-generation methods using explicit regularization steps or layers. Our approach achieves state-of-the-art accuracy in semantic segmentation with near full-supervision quality.

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arXiv2018

An ILP Solver for Multi-label MRFs with Connectivity Constraints

Integer Linear Programming (ILP) formulations of Markov random fields (MRFs) models with global connectivity priors were investigated previously in computer vision, e.g., \cite{globalinter,globalconn}. In these works, only Linear Programing (LP) relaxations \cite{globalinter,globalconn} or simplified versions \cite{graphcutbase} of the problem were solved. This paper investigates the ILP of multi-label MRF with exact connectivity priors via a branch-and-cut method, which provably finds globally optimal solutions. The method enforces connectivity priors iteratively by a cutting plane method, and provides feasible solutions with a guarantee on sub-optimality even if we terminate it earlier. The proposed ILP can be applied as a post-processing method on top of any existing multi-label segmentation approach. As it provides globally optimal solution, it can be used off-line to generate ground-truth labeling, which serves as quality check for any fast on-line algorithm. Furthermore, it can be used to generate ground-truth proposals for weakly supervised segmentation. We demonstrate the power and usefulness of our model by several experiments on the BSDS500 and PASCAL image dataset, as well as on medical images with trained probability maps.

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arXiv2017

Deep CNN ensembles and suggestive annotations for infant brain MRI segmentation

Precise 3D segmentation of infant brain tissues is an essential step towards comprehensive volumetric studies and quantitative analysis of early brain developement. However, computing such segmentations is very challenging, especially for 6-month infant brain, due to the poor image quality, among other difficulties inherent to infant brain MRI, e.g., the isointense contrast between white and gray matter and the severe partial volume effect due to small brain sizes. This study investigates the problem with an ensemble of semi-dense fully convolutional neural networks (CNNs), which employs T1-weighted and T2-weighted MR images as input. We demonstrate that the ensemble agreement is highly correlated with the segmentation errors. Therefore, our method provides measures that can guide local user corrections. To the best of our knowledge, this work is the first ensemble of 3D CNNs for suggesting annotations within images. Furthermore, inspired by the very recent success of dense networks, we propose a novel architecture, SemiDenseNet, which connects all convolutional layers directly to the end of the network. Our architecture allows the efficient propagation of gradients during training, while limiting the number of parameters, requiring one order of magnitude less parameters than popular medical image segmentation networks such as 3D U-Net. Another contribution of our work is the study of the impact that early or late fusions of multiple image modalities might have on the performances of deep architectures. We report evaluations of our method on the public data of the MICCAI iSEG-2017 Challenge on 6-month infant brain MRI segmentation, and show very competitive results among 21 teams, ranking first or second in most metrics.

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