arXiv subjects

Ghassan Hamarneh

Publications and source records attributed to Ghassan Hamarneh.

71 records · Page 4Linked to original sources

arXiv2019

Image Super Resolution via Bilinear Pooling: Application to Confocal Endomicroscopy

Recent developments in image acquisition literature have miniaturized the confocal laser endomicroscopes to improve usability and flexibility of the apparatus in actual clinical settings. However, miniaturized devices collect less light and have fewer optical components, resulting in pixelation artifacts and low resolution images. Owing to the strength of deep networks, many supervised methods known as super resolution have achieved considerable success in restoring low resolution images by generating the missing high frequency details. In this work, we propose a novel attention mechanism that, for the first time, combines 1st- and 2nd-order statistics for pooling operation, in the spatial and channel-wise dimensions. We compare the efficacy of our method to 11 other existing single image super resolution techniques that compensate for the reduction in image quality caused by the necessity of endomicroscope miniaturization. All evaluations are carried out on three publicly available datasets. Experimental results show that our method can produce competitive results against state-of-the-art in terms of PSNR, SSIM, and IFC metrics. Additionally, our proposed method contains small number of parameters, which makes it lightweight and fast for real-time applications.

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arXiv2019

Mask2Lesion: Mask-Constrained Adversarial Skin Lesion Image Synthesis

Skin lesion segmentation is a vital task in skin cancer diagnosis and further treatment. Although deep learning based approaches have significantly improved the segmentation accuracy, these algorithms are still reliant on having a large enough dataset in order to achieve adequate results. Inspired by the immense success of generative adversarial networks (GANs), we propose a GAN-based augmentation of the original dataset in order to improve the segmentation performance. In particular, we use the segmentation masks available in the training dataset to train the Mask2Lesion model, and use the model to generate new lesion images given any arbitrary mask, which are then used to augment the original training dataset. We test Mask2Lesion augmentation on the ISBI ISIC 2017 Skin Lesion Segmentation Challenge dataset and achieve an improvement of 5.17% in the mean Dice score as compared to a model trained with only classical data augmentation techniques.

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arXiv2019

Improved Inference via Deep Input Transfer

Although numerous improvements have been made in the field of image segmentation using convolutional neural networks, the majority of these improvements rely on training with larger datasets, model architecture modifications, novel loss functions, and better optimizers. In this paper, we propose a new segmentation performance boosting paradigm that relies on optimally modifying the network's input instead of the network itself. In particular, we leverage the gradients of a trained segmentation network with respect to the input to transfer it to a space where the segmentation accuracy improves. We test the proposed method on three publicly available medical image segmentation datasets: the ISIC 2017 Skin Lesion Segmentation dataset, the Shenzhen Chest X-Ray dataset, and the CVC-ColonDB dataset, for which our method achieves improvements of 5.8%, 0.5%, and 4.8% in the average Dice scores, respectively.

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arXiv2019

InfoMask: Masked Variational Latent Representation to Localize Chest Disease

The scarcity of richly annotated medical images is limiting supervised deep learning based solutions to medical image analysis tasks, such as localizing discriminatory radiomic disease signatures. Therefore, it is desirable to leverage unsupervised and weakly supervised models. Most recent weakly supervised localization methods apply attention maps or region proposals in a multiple instance learning formulation. While attention maps can be noisy, leading to erroneously highlighted regions, it is not simple to decide on an optimal window/bag size for multiple instance learning approaches. In this paper, we propose a learned spatial masking mechanism to filter out irrelevant background signals from attention maps. The proposed method minimizes mutual information between a masked variational representation and the input while maximizing the information between the masked representation and class labels. This results in more accurate localization of discriminatory regions. We tested the proposed model on the ChestX-ray8 dataset to localize pneumonia from chest X-ray images without using any pixel-level or bounding-box annotations.

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arXiv2019

Visual Diagnosis of Dermatological Disorders: Human and Machine Performance

Skin conditions are a global health concern, ranking the fourth highest cause of nonfatal disease burden when measured as years lost due to disability. As diagnosing, or classifying, skin diseases can help determine effective treatment, dermatologists have extensively researched how to diagnose conditions from a patient's history and the lesion's visual appearance. Computer vision researchers are attempting to encode this diagnostic ability into machines, and several recent studies report machine level performance comparable with dermatologists. This report reviews machine approaches to classify skin images and consider their performance when compared to human dermatologists. Following an overview of common image modalities, dermatologists' diagnostic approaches and common tasks, and publicly available datasets, we discuss approaches to machine skin lesion classification. We then review works that directly compare human and machine performance. Finally, this report addresses the limitations and sources of errors in image-based skin disease diagnosis, applicable to both machines and dermatologists in a teledermatology setting.

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arXiv2019

A Kernelized Manifold Mapping to Diminish the Effect of Adversarial Perturbations

The linear and non-flexible nature of deep convolutional models makes them vulnerable to carefully crafted adversarial perturbations. To tackle this problem, we propose a non-linear radial basis convolutional feature mapping by learning a Mahalanobis-like distance function. Our method then maps the convolutional features onto a linearly well-separated manifold, which prevents small adversarial perturbations from forcing a sample to cross the decision boundary. We test the proposed method on three publicly available image classification and segmentation datasets namely, MNIST, ISBI ISIC 2017 skin lesion segmentation, and NIH Chest X-Ray-14. We evaluate the robustness of our method to different gradient (targeted and untargeted) and non-gradient based attacks and compare it to several non-gradient masking defense strategies. Our results demonstrate that the proposed method can increase the resilience of deep convolutional neural networks to adversarial perturbations without accuracy drop on clean data.

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arXiv2019

Fully Convolutional Neural Networks to Detect Clinical Dermoscopic Features

The presence of certain clinical dermoscopic features within a skin lesion may indicate melanoma, and automatically detecting these features may lead to more quantitative and reproducible diagnoses. We reformulate the task of classifying clinical dermoscopic features within superpixels as a segmentation problem, and propose a fully convolutional neural network to detect clinical dermoscopic features from dermoscopy skin lesion images. Our neural network architecture uses interpolated feature maps from several intermediate network layers, and addresses imbalanced labels by minimizing a negative multi-label Dice-F$_1$ score, where the score is computed across the mini-batch for each label. Our approach ranked first place in the 2017 ISIC-ISBI Part 2: Dermoscopic Feature Classification Task challenge over both the provided validation and test datasets, achieving a 0.895% area under the receiver operator characteristic curve score. We show how simple baseline models can outrank state-of-the-art approaches when using the official metrics of the challenge, and propose to use a fuzzy Jaccard Index that ignores the empty set (i.e., masks devoid of positive pixels) when ranking models. Our results suggest that (i) the classification of clinical dermoscopic features can be effectively approached as a segmentation problem, and (ii) the current metrics used to rank models may not well capture the efficacy of the model. We plan to make our trained model and code publicly available.

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arXiv2018

Vulnerability Analysis of Chest X-Ray Image Classification Against Adversarial Attacks

Recently, there have been several successful deep learning approaches for automatically classifying chest X-ray images into different disease categories. However, there is not yet a comprehensive vulnerability analysis of these models against the so-called adversarial perturbations/attacks, which makes deep models more trustful in clinical practices. In this paper, we extensively analyzed the performance of two state-of-the-art classification deep networks on chest X-ray images. These two networks were attacked by three different categories (ten methods in total) of adversarial methods (both white- and black-box), namely gradient-based, score-based, and decision-based attacks. Furthermore, we modified the pooling operations in the two classification networks to measure their sensitivities against different attacks, on the specific task of chest X-ray classification.

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arXiv2018

Can Deep Learning Relax Endomicroscopy Hardware Miniaturization Requirements?

Confocal laser endomicroscopy (CLE) is a novel imaging modality that provides in vivo histological cross-sections of examined tissue. Recently, attempts have been made to develop miniaturized in vivo imaging devices, specifically confocal laser microscopes, for both clinical and research applications. However, current implementations of miniature CLE components, such as confocal lenses, compromise image resolution, signal-to-noise ratio, or both, which negatively impacts the utility of in vivo imaging. In this work, we demonstrate that software-based techniques can be used to recover lost information due to endomicroscopy hardware miniaturization and reconstruct images of higher resolution. Particularly, a densely connected convolutional neural network is used to reconstruct a high-resolution CLE image from a low-resolution input. In the proposed network, each layer is directly connected to all subsequent layers, which results in an effective combination of low-level and high-level features and efficient information flow throughout the network. To train and evaluate our network, we use a dataset of 181 high-resolution CLE images. Both quantitative and qualitative results indicate superiority of the proposed network compared to traditional interpolation techniques and competing learning-based methods. This work demonstrates that software-based super-resolution is a viable approach to compensate for loss of resolution due to endoscopic hardware miniaturization.

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arXiv2018

Star Shape Prior in Fully Convolutional Networks for Skin Lesion Segmentation

Semantic segmentation is an important preliminary step towards automatic medical image interpretation. Recently deep convolutional neural networks have become the first choice for the task of pixel-wise class prediction. While incorporating prior knowledge about the structure of target objects has proven effective in traditional energy-based segmentation approaches, there has not been a clear way for encoding prior knowledge into deep learning frameworks. In this work, we propose a new loss term that encodes the star shape prior into the loss function of an end-to-end trainable fully convolutional network (FCN) framework. We penalize non-star shape segments in FCN prediction maps to guarantee a global structure in segmentation results. Our experiments demonstrate the advantage of regularizing FCN parameters by the star shape prior and our results on the ISBI 2017 skin segmentation challenge data set achieve the first rank in the segmentation task among $21$ participating teams.

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arXiv2018

Select, Attend, and Transfer: Light, Learnable Skip Connections

Skip connections in deep networks have improved both segmentation and classification performance by facilitating the training of deeper network architectures, and reducing the risks for vanishing gradients. They equip encoder-decoder-like networks with richer feature representations, but at the cost of higher memory usage, computation, and possibly resulting in transferring non-discriminative feature maps. In this paper, we focus on improving skip connections used in segmentation networks (e.g., U-Net, V-Net, and The One Hundred Layers Tiramisu (DensNet) architectures). We propose light, learnable skip connections which learn to first select the most discriminative channels and then attend to the most discriminative regions of the selected feature maps. The output of the proposed skip connections is a unique feature map which not only reduces the memory usage and network parameters to a high extent, but also improves segmentation accuracy. We evaluate the proposed method on three different 2D and volumetric datasets and demonstrate that the proposed light, learnable skip connections can outperform the traditional heavy skip connections in terms of segmentation accuracy, memory usage, and number of network parameters.

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arXiv2016

Machine Learning on Human Connectome Data from MRI

Functional MRI (fMRI) and diffusion MRI (dMRI) are non-invasive imaging modalities that allow in-vivo analysis of a patient's brain network (known as a connectome). Use of these technologies has enabled faster and better diagnoses and treatments of neurological disorders and a deeper understanding of the human brain. Recently, researchers have been exploring the application of machine learning models to connectome data in order to predict clinical outcomes and analyze the importance of subnetworks in the brain. Connectome data has unique properties, which present both special challenges and opportunities when used for machine learning. The purpose of this work is to review the literature on the topic of applying machine learning models to MRI-based connectome data. This field is growing rapidly and now encompasses a large body of research. To summarize the research done to date, we provide a comparative, structured summary of 77 relevant works, tabulated according to different criteria, that represent the majority of the literature on this topic. (We also published a living version of this table online at http://connectomelearning.cs.sfu.ca that the community can continue to contribute to.) After giving an overview of how connectomes are constructed from dMRI and fMRI data, we discuss the variety of machine learning tasks that have been explored with connectome data. We then compare the advantages and drawbacks of different machine learning approaches that have been employed, discussing different feature selection and feature extraction schemes, as well as the learning models and regularization penalties themselves. Throughout this discussion, we focus particularly on how the methods are adapted to the unique nature of graphical connectome data. Finally, we conclude by summarizing the current state of the art and by outlining what we believe are strategic directions for future research.

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arXiv2016

Adaptable Precomputation for Random Walker Image Segmentation and Registration

The random walker (RW) algorithm is used for both image segmentation and registration, and possesses several useful properties that make it popular in medical imaging, such as being globally optimizable, allowing user interaction, and providing uncertainty information. The RW algorithm defines a weighted graph over an image and uses the graph's Laplacian matrix to regularize its solutions. This regularization reduces to solving a large system of equations, which may be excessively time consuming in some applications, such as when interacting with a human user. Techniques have been developed that precompute eigenvectors of a Laplacian offline, after image acquisition but before any analysis, in order speed up the RW algorithm online, when segmentation or registration is being performed. However, precomputation requires certain algorithm parameters be fixed offline, limiting their flexibility. In this paper, we develop techniques to update the precomputed data online when RW parameters are altered. Specifically, we dynamically determine the number of eigenvectors needed for a desired accuracy based on user input, and derive update equations for the eigenvectors when the edge weights or topology of the image graph are changed. We present results demonstrating that our techniques make RW with precomputation much more robust to offline settings while only sacrificing minimal accuracy.

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arXiv2016

Incorporating prior knowledge in medical image segmentation: a survey

Medical image segmentation, the task of partitioning an image into meaningful parts, is an important step toward automating medical image analysis and is at the crux of a variety of medical imaging applications, such as computer aided diagnosis, therapy planning and delivery, and computer aided interventions. However, the existence of noise, low contrast and objects' complexity in medical images are critical obstacles that stand in the way of achieving an ideal segmentation system. Incorporating prior knowledge into image segmentation algorithms has proven useful for obtaining more accurate and plausible results. This paper surveys the different types of prior knowledge that have been utilized in different segmentation frameworks. We focus our survey on optimization-based methods that incorporate prior information into their frameworks. We review and compare these methods in terms of the types of prior employed, the domain of formulation (continuous vs. discrete), and the optimization techniques (global vs. local). We also created an interactive online database of existing works and categorized them based on the type of prior knowledge they use. Our website is interactive so that researchers can contribute to keep the database up to date. We conclude the survey by discussing different aspects of designing an energy functional for image segmentation, open problems, and future perspectives.

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arXiv2015

Multi-Region Probabilistic Dice Similarity Coefficient using the Aitchison Distance and Bipartite Graph Matching

Validation of image segmentation methods is of critical importance. Probabilistic image segmentation is increasingly popular as it captures uncertainty in the results. Image segmentation methods that support multi-region (as opposed to binary) delineation are more favourable as they capture interactions between the different objects in the image. The Dice similarity coefficient (DSC) has been a popular metric for evaluating the accuracy of automated or semi-automated segmentation methods by comparing their results to the ground truth. In this work, we develop an extension of the DSC to multi-region probabilistic segmentations (with unordered labels). We use bipartite graph matching to establish label correspondences and propose two functions that extend the DSC, one based on absolute probability differences and one based on the Aitchison distance. These provide a robust and accurate measure of multi-region probabilistic segmentation accuracy.

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arXiv2009

Multi-Label MRF Optimization via Least Squares s-t Cuts

There are many applications of graph cuts in computer vision, e.g. segmentation. We present a novel method to reformulate the NP-hard, k-way graph partitioning problem as an approximate minimal s-t graph cut problem, for which a globally optimal solution is found in polynomial time. Each non-terminal vertex in the original graph is replaced by a set of ceil(log_2(k)) new vertices. The original graph edges are replaced by new edges connecting the new vertices to each other and to only two, source s and sink t, terminal nodes. The weights of the new edges are obtained using a novel least squares solution approximating the constraints of the initial k-way setup. The minimal s-t cut labels each new vertex with a binary (s vs t) "Gray" encoding, which is then decoded into a decimal label number that assigns each of the original vertices to one of k classes. We analyze the properties of the approximation and present quantitative as well as qualitative segmentation results.

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arXiv2009

Automatic Spatially-Adaptive Balancing of Energy Terms for Image Segmentation

Image segmentation techniques are predominately based on parameter-laden optimization. The objective function typically involves weights for balancing competing image fidelity and segmentation regularization cost terms. Setting these weights suitably has been a painstaking, empirical process. Even if such ideal weights are found for a novel image, most current approaches fix the weight across the whole image domain, ignoring the spatially-varying properties of object shape and image appearance. We propose a novel technique that autonomously balances these terms in a spatially-adaptive manner through the incorporation of image reliability in a graph-based segmentation framework. We validate on synthetic data achieving a reduction in mean error of 47% (p-value << 0.05) when compared to the best fixed parameter segmentation. We also present results on medical images (including segmentations of the corpus callosum and brain tissue in MRI data) and on natural images.

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