A survey on deep learning in medical image analysis

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.

Attention gated networks: Learning to leverage salient regions in medical images.

The health care sector is totally different from any other industry. It is a high priority sector and consumers expect the highest level of care and services regardless of cost. The health care sector has not achieved society’s expectations, even though the sector consumes a huge percentage of national budgets. Mostly, the interpretations of medical data are analyzed by medical experts. In terms of a medical expert interpreting images, this is quite limited due to its subjectivity and the complexity of the images; extensive variations exist between experts and fatigue sets in due to their heavy workload. Following the success of deep learning in other real-world applications, it is seen as also providing exciting and accurate solutions for medical imaging, and is seen as a key method for future applications in the health care sector. In this chapter, we discuss state-of-the-art deep learning architecture and its optimization when used for medical image segmentation and classification. The chapter closes with a discussion of the challenges of deep learning methods with regard to medical imaging and open research issue.

Deep Learning for Medical Image Processing: Overview, Challenges and the Future

Rapid advances in hardware-based technologies during the past decades have opened up new possibilities for life scientists to gather multimodal data in various application domains, such as omics , bioimaging , medical imaging , and (brain/body)–machine interfaces . These have generated novel opportunities for development of dedicated data-intensive machine learning techniques. In particular, recent research in deep learning (DL), reinforcement learning (RL), and their combination (deep RL) promise to revolutionize the future of artificial intelligence. The growth in computational power accompanied by faster and increased data storage, and declining computing costs have already allowed scientists in various fields to apply these techniques on data sets that were previously intractable owing to their size and complexity. This paper provides a comprehensive survey on the application of DL, RL, and deep RL techniques in mining biological data. In addition, we compare the performances of DL techniques when applied to different data sets across various application domains. Finally, we outline open issues in this challenging research area and discuss future development perspectives.

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Applications of Deep Learning and Reinforcement Learning to Biological Data

To extract patterns from neuroimaging data, various techniques, including statistical methods and machine learning algorithms, have been explored to ultimately aid in Alzheimer9s disease diagnosis of older adults in both clinical and research applications. However, identifying the distinctions between Alzheimer′s brain data and healthy brain data in older adults (age > 75) is challenging due to highly similar brain patterns and image intensities. Recently, cutting-edge deep learning technologies have been rapidly expanding into numerous fields, including medical image analysis. This work outlines state-of-the-art deep learning-based pipelines employed to distinguish Alzheimer′s magnetic resonance imaging (MRI) and functional MRI data from normal healthy control data for the same age group. Using these pipelines, which were executed on a GPU-based high performance computing platform, the data were strictly and carefully preprocessed. Next, scale and shift invariant low- to high-level features were obtained from a high volume of training images using convolutional neural network (CNN) architecture. In this study, functional MRI data were used for the first time in deep learning applications for the purposes of medical image analysis and Alzheimer′s disease prediction. These proposed and implemented pipelines, which demonstrate a significant improvement in classification output when compared to other studies, resulted in high and reproducible accuracy rates of 99.9% and 98.84% for the fMRI and MRI pipelines, respectively.

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DeepAD: Alzheimer′s Disease Classification via Deep Convolutional Neural Networks using MRI and fMRI

Over the past decade, machine learning techniques especially predictive modeling and pattern recognition in biomedical sciences from drug delivery system to medical imaging has become one of the important methods which are assisting researchers to have deeper understanding of entire issue and to solve complex medical problems. Deep learning is power learning machine learning algorithm in classification while extracting high-level features. In this paper, we used convolutional neural network to classify Alzheimer's brain from normal healthy brain. The importance of classifying this kind of medical data is to potentially develop a predict model or system in order to recognize the type disease from normal subjects or to estimate the stage of the disease. Classification of clinical data such as Alzheimer's disease has been always challenging and most problematic part has been always selecting the most discriminative features. Using Convolutional Neural Network (CNN) and the famous architecture LeNet-5, we successfully classified functional MRI data of Alzheimer's subjects from normal controls where the accuracy of test data on trained data reached 96.85%. This experiment suggests us the shift and scale invariant features extracted by CNN followed by deep learning classification is most powerful method to distinguish clinical data from healthy data in fMRI. This approach also enables us to expand our methodology to predict more complicated systems.

Classification of Alzheimer's Disease using fMRI Data and Deep Learning Convolutional Neural Networks

Over the past decade, machine learning techniques and in particular predictive modeling and pattern recognition in biomedical sciences, from drug delivery systems to medical imaging, have become one of the most important methods of assisting researchers in gaining a deeper understanding of issues in their entirety and solving complex medical problems. Deep learning is a powerful machine learning algorithm in classification that extracts low-to high-level features. In this paper, we employ a convolutional neural network to distinguish an Alzheimers brain from a normal, healthy brain. The importance of classifying this type of medical data lies in its potential to develop a predictive model or system in order to recognize the symptoms of Alzheimers disease when compared with normal subjects and to estimate the stages of the disease. Classification of clinical data for medical conditions such as Alzheimers disease has always been challenging, and the most problematic aspect has always been selecting the strongest discriminative features. Using the Convolutional Neural Network (CNN) and the famous architecture LeNet-5, we successfully classified functional MRI data of Alzheimers subjects from normal controls, where the accuracy of testing data reached 96.85%. This experiment suggests that the shift and scale invariant features extracted by CNN followed by deep learning classification represents the most powerful method of distinguishing clinical data from healthy data in fMRI. This approach also allows for expansion of the methodology to predict more complicated systems.

/pdf/deep-learning-based-pipeline-to-recognize-alzheimer-s-21b0be3tpt.pdf

Deep learning-based pipeline to recognize Alzheimer's disease using fMRI data

Recently, machine learning techniques especially predictive modeling and pattern recognition in biomedical sciences from drug delivery system to medical imaging has become one of the important methods which are assisting researchers to have deeper understanding of entire issue and to solve complex medical problems. Deep learning is a powerful machine learning algorithm in classification while extracting low to high-level features. In this paper, we used convolutional neural network to classify Alzheimer's brain from normal healthy brain. The importance of classifying this kind of medical data is to potentially develop a predict model or system in order to recognize the type disease from normal subjects or to estimate the stage of the disease. Classification of clinical data such as Alzheimer's disease has been always challenging and most problematic part has been always selecting the most discriminative features. Using Convolutional Neural Network (CNN) and the famous architecture LeNet-5, we successfully classified structural MRI data of Alzheimer's subjects from normal controls where the accuracy of test data on trained data reached 98.84%. This experiment suggests us the shift and scale invariant features extracted by CNN followed by deep learning classification is most powerful method to distinguish clinical data from healthy data in fMRI. This approach also enables us to expand our methodology to predict more complicated systems.

Classification of Alzheimer's Disease Structural MRI Data by Deep Learning Convolutional Neural Networks

In this paper, we propose a real-time vision-based hand posture recognition approach, based on appearance-based features of hand. Our approach has three main steps: hand segmentation, feature extraction and posture recognition. For the hand segmentation, we introduce “Adaptive Histogram Template of Skin” which tries to extract histogram of the subject hand by sampling its color and texture. With this template, we can use back projection method to find skin color areas in an image. In the feature extraction step, we extract global hand's features using hand's edge contour, and hand's edge convex hull. The hand can be classified into one of the ten posture classes in the recognition step. Each posture class has a representative template which is used as reference for comparing to subject hand features. This approach is simple and fast enough to provide real-time recognition.

Ghassem Tofighi

Papers

DeepAD: Alzheimer′s Disease Classification via Deep Convolutional Neural Networks using MRI and fMRI

Classification of Alzheimer's Disease using fMRI Data and Deep Learning Convolutional Neural Networks

Deep learning-based pipeline to recognize Alzheimer's disease using fMRI data

Classification of Alzheimer's Disease Structural MRI Data by Deep Learning Convolutional Neural Networks

Rapid hand posture recognition using Adaptive Histogram Template of Skin and hand edge contour