A Survey on Deep Learning in Medical Image Analysis

Deep learning algorithms, in particular convolutional networks, have rapidly become a methodology of choice for analyzing medical images. This paper reviews the major deep learning concepts pertinent to medical image analysis and summarizes over 300 contributions to the field, most of which appeared in the last year. We survey the use of deep learning for image classification, object detection, segmentation, registration, and other tasks and provide concise overviews of studies per application area. Open challenges and directions for future research are discussed.Comment: Revised survey includes expanded discussion section and reworked introductory section on common deep architectures. Added missed papers from before Feb 1st 201

Cancer diagnosis using deep learning: A bibliographic review

In this paper, we first describe the basics of the field of cancer diagnosis, which includes steps of cancer diagnosis followed by the typical classification methods used by doctors, providing a historical idea of cancer classification techniques to the readers. These methods include Asymmetry, Border, Color and Diameter (ABCD) method, seven-point detection method, Menzies method, and pattern analysis. They are used regularly by doctors for cancer diagnosis, although they are not considered very efficient for obtaining better performance. Moreover, considering all types of audience, the basic evaluation criteria are also discussed. The criteria include the receiver operating characteristic curve (ROC curve), Area under the ROC curve (AUC), F1 score, accuracy, specificity, sensitivity, precision, dice-coefficient, average accuracy, and Jaccard index. Previously used methods are considered inefficient, asking for better and smarter methods for cancer diagnosis. Artificial intelligence and cancer diagnosis are gaining attention as a way to define better diagnostic tools. In particular, deep neural networks can be successfully used for intelligent image analysis. The basic framework of how this machine learning works on medical imaging is provided in this study, i.e., pre-processing, image segmentation and post-processing. The second part of this manuscript describes the different deep learning techniques, such as convolutional neural networks (CNNs), generative adversarial models (GANs), deep autoencoders (DANs), restricted Boltzmann’s machine (RBM), stacked autoencoders (SAE), convolutional autoencoders (CAE), recurrent neural networks (RNNs), long short-term memory (LTSM), multi-scale convolutional neural network (M-CNN), multi-instance learning convolutional neural network (MIL-CNN). For each technique, we provide Python codes, to allow interested readers to experiment with the cited algorithms on their own diagnostic problems. The third part of this manuscript compiles the successfully applied deep learning models for different types of cancers. Considering the length of the manuscript, we restrict ourselves to the discussion of breast cancer, lung cancer, brain cancer, and skin cancer. The purpose of this bibliographic review is to provide researchers opting to work in implementing deep learning and artificial neural networks for cancer diagnosis a knowledge from scratch of the state-of-the-art achievements

Machine learning approaches for lung cancer diagnosis.

The enormity of changes and development in the field of medical imaging technology is hard to fathom, as it does not just represent the technique and process of constructing visual representations of the body from inside for medical analysis and to reveal the internal structure of different organs under the skin, but also it provides a noninvasive way for diagnosis of various disease and suggest an efficient ways to treat them. While data surrounding all of our lives are stored and collected to be ready for analysis by data scientists, medical images are considered a rich source that could provide us with a huge amount of data, that could not be read easily by physicians and radiologists, with valuable information that could be used in smart ways to discover new knowledge from these vast quantities of data. Therefore, the design of computer-aided diagnostic (CAD) system, that can be approved for use in clinical practice that aid radiologists in diagnosis and detecting potential abnormalities, is of a great importance. This dissertation deals with the development of a CAD system for lung cancer diagnosis, which is the second most common cancer in men after prostate cancer and in women after breast cancer. Moreover, lung cancer is considered the leading cause of cancer death among both genders in USA. Recently, the number of lung cancer patients has increased dramatically worldwide and its early detection doubles a patient’s chance of survival. Histological examination through biopsies is considered the gold standard for final diagnosis of pulmonary nodules. Even though resection of pulmonary nodules is the ideal and most reliable way for diagnosis, there is still a lot of different methods often used just to eliminate the risks associated with the surgical procedure. Lung nodules are approximately spherical regions of primarily high density tissue that are visible in computed tomography (CT) images of the lung. A pulmonary nodule is the first indication to start diagnosing lung cancer. Lung nodules can be benign (normal subjects) or malignant (cancerous subjects). Large (generally defined as greater than 2 cm in diameter) malignant nodules can be easily detected with traditional CT scanning techniques. However, the diagnostic options for small indeterminate nodules are limited due to problems associated with accessing small tumors. Therefore, additional diagnostic and imaging techniques which depends on the nodules’ shape and appearance are needed. The ultimate goal of this dissertation is to develop a fast noninvasive diagnostic system that can enhance the accuracy measures of early lung cancer diagnosis based on the well-known hypotheses that malignant nodules have different shape and appearance than benign nodules, because of the high growth rate of the malignant nodules. The proposed methodologies introduces new shape and appearance features which can distinguish between benign and malignant nodules. To achieve this goal a CAD system is implemented and validated using different datasets. This CAD system uses two different types of features integrated together to be able to give a full description to the pulmonary nodule. These two types are appearance features and shape features. For the appearance features different texture appearance descriptors are developed, namely the 3D histogram of oriented gradient, 3D spherical sector isosurface histogram of oriented gradient, 3D adjusted local binary pattern, 3D resolved ambiguity local binary pattern, multi-view analytical local binary pattern, and Markov Gibbs random field. Each one of these descriptors gives a good description for the nodule texture and the level of its signal homogeneity which is a distinguishable feature between benign and malignant nodules. For the shape features multi-view peripheral sum curvature scale space, spherical harmonics expansions, and different group of fundamental geometric features are utilized to describe the nodule shape complexity. Finally, the fusion of different combinations of these features, which is based on two stages is introduced. The first stage generates a primary estimation for every descriptor. Followed by the second stage that consists of an autoencoder with a single layer augmented with a softmax classifier to provide us with the ultimate classification of the nodule. These different combinations of descriptors are combined into different frameworks that are evaluated using different datasets. The first dataset is the Lung Image Database Consortium which is a benchmark publicly available dataset for lung nodule detection and diagnosis. The second dataset is our local acquired computed tomography imaging data that has been collected from the University of Louisville hospital and the research protocol was approved by the Institutional Review Board at the University of Louisville (IRB number 10.0642). These frameworks accuracy was about 94%, which make the proposed frameworks demonstrate promise to be valuable tool for the detection of lung cancer

Artificial Intelligence Techniques in Medical Imaging: A Systematic Review

This scientific review presents a comprehensive overview of medical imaging modalities and their diverse applications in artificial intelligence (AI)-based disease classification and segmentation. The paper begins by explaining the fundamental concepts of AI, machine learning (ML), and deep learning (DL). It provides a summary of their different types to establish a solid foundation for the subsequent analysis. The prmary focus of this study is to conduct a systematic review of research articles that examine disease classification and segmentation in different anatomical regions using AI methodologies. The analysis includes a thorough examination of the results reported in each article, extracting important insights and identifying emerging trends. Moreover, the paper critically discusses the challenges encountered during these studies, including issues related to data availability and quality, model generalization, and interpretability. The aim is to provide guidance for optimizing technique selection. The analysis highlights the prominence of hybrid approaches, which seamlessly integrate ML and DL techniques, in achieving effective and relevant results across various disease types. The promising potential of these hybrid models opens up new opportunities for future research in the field of medical diagnosis. Additionally, addressing the challenges posed by the limited availability of annotated medical images through the incorporation of medical image synthesis and transfer learning techniques is identified as a crucial focus for future research efforts

Segmentation of Pulmonary Nodules in Computed Tomography Using a Regression Neural Network Approach and Its Application to the Lung Image Database Consortium and Image Database Resource Initiative Dataset

We present new pulmonary nodule segmentation algorithms for computed tomography (CT). These include a fully-automated (FA) system, a semi-automated (SA) system, and a hybrid system. Like most traditional systems, the new FA system requires only a single user-supplied cue point. On the other hand, the SA system represents a new algorithm class requiring 8 user-supplied control points. This does increase the burden on the user, but we show that the resulting system is highly robust and can handle a variety of challenging cases. The proposed hybrid system starts with the FA system. If improved segmentation results are needed, the SA system is then deployed. The FA segmentation engine has 2 free parameters, and the SA system has 3. These parameters are adaptively determined for each nodule in a search process guided by a regression neural network (RNN). The RNN uses a number of features computed for each candidate segmentation. We train and test our systems using the new Lung Image Database Consortium and Image Database Resource Initiative (LIDC–IDRI) data. To the best of our knowledge, this is one of the first nodule-specific performance benchmarks using the new LIDC–IDRI dataset. We also compare the performance of the proposed methods with several previously reported results on the same data used by those other methods. Our results suggest that the proposed FA system improves upon the state-of-the-art, and the SA system offers a considerable boost over the FA system

Segmentation of Pulmonary Nodules in Computed Tomography using a Regression Neural Network Approach and its Application to the Lung Image Database Consortium and Image Database Resource Initiative Dataset

We present new pulmonary nodule segmentation algorithms for computed tomography (CT). These include a fully-automated (FA) system, a semi-automated (SA) system, and a hybrid system. Like most traditional systems, the new FA system requires only a single user-supplied cue point. On the other hand, the SA system represents a new algorithm class requiring 8 user-supplied control points. This does increase the burden on the user, but we show that the resulting system is highly robust and can handle a variety of challenging cases. The proposed hybrid system starts with the FA system. If improved segmentation results are needed, the SA system is then deployed. The FA segmentation engine has 2 free parameters, and the SA system has 3. These parameters are adaptively determined for each nodule in a search process guided by a regression neural network (RNN). The RNN uses a number of features computed for each candidate segmentation. We train and test our systems using the new Lung Image Database Consortium and Image Database Resource Initiative (LIDC–IDRI) data. To the best of our knowledge, this is one of the first nodule-specific performance benchmarks using the new LIDC–IDRI dataset. We also compare the performance of the proposed methods with several previously reported results on the same data used by those other methods. Our results suggest that the proposed FA system improves upon the state-of-the-art, and the SA system offers a considerable boost over the FA system

Segmentation of Pulmonary Nodules in Computed Tomography using a Regression Neural Network Approach and its Application to the Lung Image Database Consortium and Image Database Resource Initiative Dataset

We present new pulmonary nodule segmentation algorithms for computed tomography (CT). These include a fully-automated (FA) system, a semi-automated (SA) system, and a hybrid system. Like most traditional systems, the new FA system requires only a single user-supplied cue point. On the other hand, the SA system represents a new algorithm class requiring 8 user-supplied control points. This does increase the burden on the user, but we show that the resulting system is highly robust and can handle a variety of challenging cases. The proposed hybrid system starts with the FA system. If improved segmentation results are needed, the SA system is then deployed. The FA segmentation engine has 2 free parameters, and the SA system has 3. These parameters are adaptively determined for each nodule in a search process guided by a regression neural network (RNN). The RNN uses a number of features computed for each candidate segmentation. We train and test our systems using the new Lung Image Database Consortium and Image Database Resource Initiative (LIDC–IDRI) data. To the best of our knowledge, this is one of the first nodule-specific performance benchmarks using the new LIDC–IDRI dataset. We also compare the performance of the proposed methods with several previously reported results on the same data used by those other methods. Our results suggest that the proposed FA system improves upon the state-of-the-art, and the SA system offers a considerable boost over the FA system

Advanced machine learning methods for oncological image analysis

Cancer is a major public health problem, accounting for an estimated 10 million deaths worldwide in 2020 alone. Rapid advances in the field of image acquisition and hardware development over the past three decades have resulted in the development of modern medical imaging modalities that can capture high-resolution anatomical, physiological, functional, and metabolic quantitative information from cancerous organs. Therefore, the applications of medical imaging have become increasingly crucial in the clinical routines of oncology, providing screening, diagnosis, treatment monitoring, and non/minimally- invasive evaluation of disease prognosis. The essential need for medical images, however, has resulted in the acquisition of a tremendous number of imaging scans. Considering the growing role of medical imaging data on one side and the challenges of manually examining such an abundance of data on the other side, the development of computerized tools to automatically or semi-automatically examine the image data has attracted considerable interest. Hence, a variety of machine learning tools have been developed for oncological image analysis, aiming to assist clinicians with repetitive tasks in their workflow. This thesis aims to contribute to the field of oncological image analysis by proposing new ways of quantifying tumor characteristics from medical image data. Specifically, this thesis consists of six studies, the first two of which focus on introducing novel methods for tumor segmentation. The last four studies aim to develop quantitative imaging biomarkers for cancer diagnosis and prognosis. The main objective of Study I is to develop a deep learning pipeline capable of capturing the appearance of lung pathologies, including lung tumors, and integrating this pipeline into the segmentation networks to leverage the segmentation accuracy. The proposed pipeline was tested on several comprehensive datasets, and the numerical quantifications show the superiority of the proposed prior-aware DL framework compared to the state of the art. Study II aims to address a crucial challenge faced by supervised segmentation models: dependency on the large-scale labeled dataset. In this study, an unsupervised segmentation approach is proposed based on the concept of image inpainting to segment lung and head- neck tumors in images from single and multiple modalities. The proposed autoinpainting pipeline shows great potential in synthesizing high-quality tumor-free images and outperforms a family of well-established unsupervised models in terms of segmentation accuracy. Studies III and IV aim to automatically discriminate the benign from the malignant pulmonary nodules by analyzing the low-dose computed tomography (LDCT) scans. In Study III, a dual-pathway deep classification framework is proposed to simultaneously take into account the local intra-nodule heterogeneities and the global contextual information. Study IV seeks to compare the discriminative power of a series of carefully selected conventional radiomics methods, end-to-end Deep Learning (DL) models, and deep features-based radiomics analysis on the same dataset. The numerical analyses show the potential of fusing the learned deep features into radiomic features for boosting the classification power. Study V focuses on the early assessment of lung tumor response to the applied treatments by proposing a novel feature set that can be interpreted physiologically. This feature set was employed to quantify the changes in the tumor characteristics from longitudinal PET-CT scans in order to predict the overall survival status of the patients two years after the last session of treatments. The discriminative power of the introduced imaging biomarkers was compared against the conventional radiomics, and the quantitative evaluations verified the superiority of the proposed feature set. Whereas Study V focuses on a binary survival prediction task, Study VI addresses the prediction of survival rate in patients diagnosed with lung and head-neck cancer by investigating the potential of spherical convolutional neural networks and comparing their performance against other types of features, including radiomics. While comparable results were achieved in intra- dataset analyses, the proposed spherical-based features show more predictive power in inter-dataset analyses. In summary, the six studies incorporate different imaging modalities and a wide range of image processing and machine-learning techniques in the methods developed for the quantitative assessment of tumor characteristics and contribute to the essential procedures of cancer diagnosis and prognosis