Deep learning describes a class of machine learning algorithms that are capable of combining raw inputs into layers of intermediate features. These algorithms have recently shown impressive results across a variety of domains. Biology and medicine are data-rich disciplines, but the data are complex and often ill-understood. Hence, deep learning techniques may be particularly well suited to solve problems of these fields. We examine applications of deep learning to a variety of biomedical problems-patient classification, fundamental biological processes and treatment of patients-and discuss whether deep learning will be able to transform these tasks or if the biomedical sphere poses unique challenges. Following from an extensive literature review, we find that deep learning has yet to revolutionize biomedicine or definitively resolve any of the most pressing challenges in the field, but promising advances have been made on the prior state of the art. Even though improvements over previous baselines have been modest in general, the recent progress indicates that deep learning methods will provide valuable means for speeding up or aiding human investigation. Though progress has been made linking a specific neural network's prediction to input features, understanding how users should interpret these models to make testable hypotheses about the system under study remains an open challenge. Furthermore, the limited amount of labelled data for training presents problems in some domains, as do legal and privacy constraints on work with sensitive health records. Nonetheless, we foresee deep learning enabling changes at both bench and bedside with the potential to transform several areas of biology and medicine.

https://royalsocietypublishing.org/doi/pdf/10.1098/rsif.2017.0387

Opportunities and obstacles for deep learning in biology and medicine.

The goals of this review paper on deep learning (DL) in medical imaging and radiation therapy are to (a) summarize what has been achieved to date; (b) identify common and unique challenges, and strategies that researchers have taken to address these challenges; and (c) identify some of the promising avenues for the future both in terms of applications as well as technical innovations. We introduce the general principles of DL and convolutional neural networks, survey five major areas of application of DL in medical imaging and radiation therapy, identify common themes, discuss methods for dataset expansion, and conclude by summarizing lessons learned, remaining challenges, and future directions.

https://aapm.onlinelibrary.wiley.com/doi/epdf/10.1002/mp.13264

Deep learning in medical imaging and radiation therapy.

Automatic skin lesion segmentation in dermoscopic images is a challenging task due to the low contrast between lesion and the surrounding skin, the irregular and fuzzy lesion borders, the existence of various artifacts, and various imaging acquisition conditions. In this paper, we present a fully automatic method for skin lesion segmentation by leveraging 19-layer deep convolutional neural networks that is trained end-to-end and does not rely on prior knowledge of the data. We propose a set of strategies to ensure effective and efficient learning with limited training data. Furthermore, we design a novel loss function based on Jaccard distance to eliminate the need of sample re-weighting, a typical procedure when using cross entropy as the loss function for image segmentation due to the strong imbalance between the number of foreground and background pixels. We evaluated the effectiveness, efficiency, as well as the generalization capability of the proposed framework on two publicly available databases. One is from ISBI 2016 skin lesion analysis towards melanoma detection challenge, and the other is the PH2 database. Experimental results showed that the proposed method outperformed other state-of-the-art algorithms on these two databases. Our method is general enough and only needs minimum pre- and post-processing, which allows its adoption in a variety of medical image segmentation tasks.

Automatic Skin Lesion Segmentation Using Deep Fully Convolutional Networks With Jaccard Distance

Deep learning for image-based cancer detection and diagnosis − A survey

Colonoscopy is an effective technique for detecting colorectal polyps, which are highly related to colorectal cancer. In clinical practice, segmenting polyps from colonoscopy images is of great importance since it provides valuable information for diagnosis and surgery. However, accurate polyp segmentation is a challenging task, for two major reasons: (i) the same type of polyps has a diversity of size, color and texture; and (ii) the boundary between a polyp and its surrounding mucosa is not sharp. To address these challenges, we propose a parallel reverse attention network (PraNet) for accurate polyp segmentation in colonoscopy images. Specifically, we first aggregate the features in high-level layers using a parallel partial decoder (PPD). Based on the combined feature, we then generate a global map as the initial guidance area for the following components. In addition, we mine the boundary cues using a reverse attention (RA) module, which is able to establish the relationship between areas and boundary cues. Thanks to the recurrent cooperation mechanism between areas and boundaries, our PraNet is capable of calibrating any misaligned predictions, improving the segmentation accuracy. Quantitative and qualitative evaluations on five challenging datasets across six metrics show that our PraNet improves the segmentation accuracy significantly, and presents a number of advantages in terms of generalizability, and real-time segmentation efficiency.

PraNet: Parallel Reverse Attention Network for Polyp Segmentation

Melanoma, most threatening type of skin cancer, is on the rise. In this paper an implementation of a deep-learning system on a computer server, equipped with graphic processing unit (GPU), is proposed for detection of melanoma lesions. Clinical (non-dermoscopic) images are used in the proposed system, which could assist a dermatologist in early diagnosis of this type of skin cancer. In the proposed system, input clinical images, which could contain illumination and noise effects, are preprocessed in order to reduce such artifacts. Afterward, the enhanced images are fed to a pre-trained convolutional neural network (CNN) which is a member of deep learning models. The CNN classifier, which is trained by large number of training samples, distinguishes between melanoma and benign cases. Experimental results show that the proposed method is superior in terms of diagnostic accuracy in comparison with the state-of-the-art methods.

Melanoma detection by analysis of clinical images using convolutional neural network

Colorectal cancer is one of the highest causes of cancer-related death, especially in men. Polyps are one of the main causes of colorectal cancer, and early diagnosis of polyps by colonoscopy could result in successful treatment. Diagnosis of polyps in colonoscopy videos is a challenging task due to variations in the size and shape of polyps. In this paper, we proposed a polyp segmentation method based on the convolutional neural network. Two strategies enhance the performance of the method. First, we perform a novel image patch selection method in the training phase of the network. Second, in the test phase, we perform effective post-processing on the probability map that is produced by the network. Evaluation of the proposed method using the CVC-ColonDB database shows that our proposed method achieves more accurate results in comparison with previous colonoscopy video-segmentation methods.

Polyp Segmentation in Colonoscopy Images Using Fully Convolutional Network

Melanoma is the most aggressive form of skin cancer and is on rise. There exists a research trend for computerized analysis of suspicious skin lesions for malignancy using images captured by digital cameras. Analysis of these images is usually challenging due to existence of disturbing factors such as illumination variations and light reflections from skin surface. One important stage in diagnosis of melanoma is segmentation of lesion region from normal skin. In this paper, a method for accurate extraction of lesion region is proposed that is based on deep learning approaches. The input image, after being preprocessed to reduce noisy artifacts, is applied to a deep convolutional neural network (CNN). The CNN combines local and global contextual information and outputs a label for each pixel, producing a segmentation mask that shows the lesion region. This mask will be further refined by some post processing operations. The experimental results show that our proposed method can outperform the existing state-of-the-art algorithms in terms of segmentation accuracy.

Skin lesion segmentation in clinical images using deep learning

Computerized prescreening of suspicious moles and lesions for malignancy is of great importance for assessing the need and the priority of the removal surgery. Detection can be done by images captured by standard cameras, which are more preferable due to low cost and availability. One important step in computerized evaluation is accurate detection of lesion’s region, i.e., segmentation of an image into two regions as lesion and normal skin. In this paper, a new method based on deep neural networks is proposed for accurate extraction of a lesion region. The input image is preprocessed, and then, its patches are fed to a convolutional neural network. Local texture and global structure of the patches are processed in order to assign pixels to lesion or normal classes. A method for effective selection of training patches is proposed for more accurate detection of a lesion’s border. Our results indicate that the proposed method could reach the accuracy of 98.7% and the sensitivity of 95.2% in segmentation of lesion regions over the dataset of clinical images. The experimental results of qualitative and quantitative evaluations demonstrate that our method can outperform other state-of-the-art algorithms exist in the literature.

Extraction of skin lesions from non-dermoscopic images for surgical excision of melanoma.

Coronary artery disease (CAD) is the most common type of heart disease which is the leading cause of death all over the world. X-ray angiography is currently the gold standard imaging technique for CAD diagnosis. These images usually suffer from low quality and presence of noise. Therefore, vessel enhancement and vessel segmentation play important roles in CAD diagnosis. In this paper a deep learning approach using convolutional neural networks (CNN) is proposed for detecting vessel regions in angiography images. Initially, an input angiogram is preprocessed to enhance its contrast. Afterward, the image is evaluated using patches of pixels and the network determines the vessel and background regions. A set of 1,040,000 patches is used in order to train the deep CNN. Experimental results on angiography images of a dataset show that our proposed method has a superior performance in extraction of vessel regions.

Ebrahim Nasr-Esfahani

Papers

Melanoma detection by analysis of clinical images using convolutional neural network

Polyp Segmentation in Colonoscopy Images Using Fully Convolutional Network

Skin lesion segmentation in clinical images using deep learning

Extraction of skin lesions from non-dermoscopic images for surgical excision of melanoma.

Vessel extraction in X-ray angiograms using deep learning