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

Histopathological image analysis : a review

Over the past decade, dramatic increases in computational power and improvement in image analysis algorithms have allowed the development of powerful computer-assisted analytical approaches to radiological data. With the recent advent of whole slide digital scanners, tissue histopathology slides can now be digitized and stored in digital image form. Consequently, digitized tissue histopathology has now become amenable to the application of computerized image analysis and machine learning techniques. Analogous to the role of computer-assisted diagnosis (CAD) algorithms in medical imaging to complement the opinion of a radiologist, CAD algorithms have begun to be developed for disease detection, diagnosis, and prognosis prediction to complement the opinion of the pathologist. In this paper, we review the recent state of the art CAD technology for digitized histopathology. This paper also briefly describes the development and application of novel image analysis technology for a few specific histopathology related problems being pursued in the United States and Europe

Multi-Classifiers And Decision Fusion For Robust Statistical Pattern Recognition With Applications To Hyperspectral Classification

In this dissertation, a multi-classifier, decision fusion framework is proposed for robust classification of high dimensional data in small-sample-size conditions. Such datasets present two key challenges. (1) The high dimensional feature spaces compromise the classifiers’ generalization ability in that the classifier tends to overit decision boundaries to the training data. This phenomenon is commonly known as the Hughes phenomenon in the pattern classification community. (2) The small-sample-size of the training data results in ill-conditioned estimates of its statistics. Most classifiers rely on accurate estimation of these statistics for modeling training data and labeling test data, and hence ill-conditioned statistical estimates result in poorer classification performance. This dissertation tests the efficacy of the proposed algorithms to classify primarily remotely sensed hyperspectral data and secondarily diagnostic digital mammograms, since these applications naturally result in very high dimensional feature spaces and often do not have sufficiently large training datasets to support the dimensionality of the feature space. Conventional approaches, such as Stepwise LDA (S-LDA) are sub-optimal, in that they utilize a small subset of the rich spectral information provided by hyperspectral data for classification. In contrast, the approach proposed in this dissertation utilizes the entire high dimensional feature space for classification by identifying a suitable partition of this space, employing a bank-of-classifiers to perform “local” classification over this partition, and then merging these local decisions using an appropriate decision fusion mechanism. Adaptive classifier weight assignment and nonlinear pre-processing (in kernel induced spaces) are also proposed within this framework to improve its robustness over a wide range of fidelity conditions. Experimental results demonstrate that the proposed framework results in significant improvements in classification accuracies (as high as a 12% increase) over conventional approaches

Multi-Classifiers And Decision Fusion For Robust Statistical Pattern Recognition With Applications To Hyperspectral Classification

In this dissertation, a multi-classifier, decision fusion framework is proposed for robust classification of high dimensional data in small-sample-size conditions. Such datasets present two key challenges. (1) The high dimensional feature spaces compromise the classifiers’ generalization ability in that the classifier tends to overit decision boundaries to the training data. This phenomenon is commonly known as the Hughes phenomenon in the pattern classification community. (2) The small-sample-size of the training data results in ill-conditioned estimates of its statistics. Most classifiers rely on accurate estimation of these statistics for modeling training data and labeling test data, and hence ill-conditioned statistical estimates result in poorer classification performance. This dissertation tests the efficacy of the proposed algorithms to classify primarily remotely sensed hyperspectral data and secondarily diagnostic digital mammograms, since these applications naturally result in very high dimensional feature spaces and often do not have sufficiently large training datasets to support the dimensionality of the feature space. Conventional approaches, such as Stepwise LDA (S-LDA) are sub-optimal, in that they utilize a small subset of the rich spectral information provided by hyperspectral data for classification. In contrast, the approach proposed in this dissertation utilizes the entire high dimensional feature space for classification by identifying a suitable partition of this space, employing a bank-of-classifiers to perform “local” classification over this partition, and then merging these local decisions using an appropriate decision fusion mechanism. Adaptive classifier weight assignment and nonlinear pre-processing (in kernel induced spaces) are also proposed within this framework to improve its robustness over a wide range of fidelity conditions. Experimental results demonstrate that the proposed framework results in significant improvements in classification accuracies (as high as a 12% increase) over conventional approaches

Design of Machine Learning Algorithms with Applications to Breast Cancer Detection

Machine learning is concerned with the design and development of algorithms and techniques that allow computers to 'learn' from experience with respect to some class of tasks and performance measure. One application of machine learning is to improve the accuracy and efficiency of computer-aided diagnosis systems to assist physician, radiologists, cardiologists, neuroscientists, and health-care technologists. This thesis focuses on machine learning and the applications to breast cancer detection. Emphasis is laid on preprocessing of features, pattern classification, and model selection. Before the classification task, feature selection and feature transformation may be performed to reduce the dimensionality of the features and to improve the classification performance. Genetic algorithm (GA) can be employed for feature selection based on different measures of data separability or the estimated risk of a chosen classifier. A separate nonlinear transformation can be performed by applying kernel principal component analysis and kernel partial least squares. Different classifiers are proposed in this work: The SOM-RBF network combines self-organizing maps (SOMs) and radial basis function (RBF) networks, with the RBF centers set as the weight vectors of neurons from the competitive layer of a trained SaM. The pairwise Rayleigh quotient (PRQ) classifier seeks one discriminating boundary by maximizing an unconstrained optimization objective, named as the PRQ criterion, formed with a set of pairwise const~aints instead of individual training samples. The strict 2-surface proximal (S2SP) classifier seeks two proximal planes that are not necessary parallel to fit the distribution of the samples in the original feature space or a kernel-defined feature space, by ma-ximizing two strict optimization objectives with a 'square of sum' optimization factor. Two variations of the support vector data description (SVDD) with negative samples (NSVDD) are proposed by involving different forms of slack vectors, which learn a closed spherically shaped boundary, named as the supervised compact hypersphere (SCH), around a set of samples in the target class. \Ve extend the NSVDDs to solve the multi-class classification problems based on distances between the samples and the centers of the learned SCHs in a kernel-defined feature space, using a combination of linear discriminant analysis and the nearest-neighbor rule. The problem of model selection is studied to pick the best values of the hyperparameters for a parametric classifier. To choose the optimal kernel or regularization parameters of a classifier, we investigate different criteria, such as the validation error estimate and the leave-out-out bound, as well as different optimization methods, such as grid search, gradient descent, and GA. By viewing the tuning problem of the multiple parameters of an 2-norm support vector machine (SVM) as an identification problem of a nonlinear dynamic system, we design a tuning system by employing the extended Kalman filter based on cross validation. Independent kernel optimization based on different measures of data separability are a~so investigated for different kernel-based classifiers. Numerous computer experiments using the benchmark datasets verify the theoretical results, make comparisons among the techniques in measures of classification accuracy or area under the receiver operating characteristics curve. Computational requirements, such as the computing time and the number of hyper-parameters, are also discussed. All of the presented methods are applied to breast cancer detection from fine-needle aspiration and in mammograms, as well as screening of knee-joint vibroarthrographic signals and automatic monitoring of roller bearings with vibration signals. Experimental results demonstrate the excellence of these methods with improved classification performance. For breast cancer detection, instead of only providing a binary diagnostic decision of 'malignant' or 'benign', we propose methods to assign a measure of confidence of malignancy to an individual mass, by calculating probabilities of being benign and malignant with a single classifier or a set of classifiers

Medical imaging analysis with artificial neural networks

Given that neural networks have been widely reported in the research community of medical imaging, we provide a focused literature survey on recent neural network developments in computer-aided diagnosis, medical image segmentation and edge detection towards visual content analysis, and medical image registration for its pre-processing and post-processing, with the aims of increasing awareness of how neural networks can be applied to these areas and to provide a foundation for further research and practical development. Representative techniques and algorithms are explained in detail to provide inspiring examples illustrating: (i) how a known neural network with fixed structure and training procedure could be applied to resolve a medical imaging problem; (ii) how medical images could be analysed, processed, and characterised by neural networks; and (iii) how neural networks could be expanded further to resolve problems relevant to medical imaging. In the concluding section, a highlight of comparisons among many neural network applications is included to provide a global view on computational intelligence with neural networks in medical imaging

AI-enhanced diagnosis of challenging lesions in breast MRI: a methodology and application primer

Computer-aided diagnosis (CAD) systems have become an important tool in the assessment of breast tumors with magnetic resonance imaging (MRI). CAD systems can be used for the detection and diagnosis of breast tumors as a “second opinion” review complementing the radiologist’s review. CAD systems have many common parts such as image pre-processing, tumor feature extraction and data classification that are mostly based on machine learning (ML) techniques. In this review paper, we describe the application of ML-based CAD systems in MRI of the breast covering the detection of diagnostically challenging lesions such as non-mass enhancing (NME) lesions, multiparametric MRI, neo-adjuvant chemotherapy (NAC) and radiomics all applied to NME. Since ML has been widely used in the medical imaging community, we provide an overview about the state-ofthe-art and novel techniques applied as classifiers to CAD systems. The differences in the CAD systems in MRI of the breast for several standard and novel applications for NME are explained in detail to provide important examples illustrating: (i) CAD for the detection and diagnosis, (ii) CAD in multi-parametric imaging (iii) CAD in NAC and (iv) breast cancer radiomics. We aim to provide a comparison between these CAD applications and to illustrate a global view on intelligent CAD systems based on ANN in MRI of the breast

Ensemble Boosted Tree based Mammogram image classification using Texture features and extracted smart features of Deep Neural Network

/n This work proposes a technique of breast cancer detection from mammogram images. It is a multistage process which classifies the mammogram images into benign or malignant category. During preprocessing, images of Mammographic Image Analysis Society (MIAS) database are passed through a couple of filters for noise removal, thresholding and cropping techniques to extract the region of interest, followed by augmentation process on database to enhance its size. Features from Deep Convolution Neural Network (DCNN) are merged with texture features to form final feature vector. Using transfer learning, deep features are extracted from a modified DCNN, whose training is performed on 69% of randomly selected images of database from both categories. Features of Grey Level Co-Occurrence Matrix (GLCM) and Local Binary Pattern (LBP) are merged to form texture features. Mean and variance of four parameters (contrast, correlation, homogeneity and entropy) of GLCM are computed in four angular directions, at ten distances. Ensemble Boosted Tree classifier using five-fold cross-validation mode, achieved an accuracy, sensitivity, specificity of 98.8%, 100% and 92.55% respectively on this feature vector

Novel 3D Ultrasound Elastography Techniques for In Vivo Breast Tumor Imaging and Nonlinear Characterization

Breast cancer comprises about 29% of all types of cancer in women worldwide. This type of cancer caused what is equivalent to 14% of all female deaths due to cancer. Nowadays, tissue biopsy is routinely performed, although about 80% of the performed biopsies yield a benign result. Biopsy is considered the most costly part of breast cancer examination and invasive in nature. To reduce unnecessary biopsy procedures and achieve early diagnosis, ultrasound elastography was proposed.;In this research, tissue displacement fields were estimated using ultrasound waves, and used to infer the elastic properties of tissues. Ultrasound radiofrequency data acquired at consecutive increments of tissue compression were used to compute local tissue strains using a cross correlation method. In vitro and in vivo experiments were conducted on different tissue types to demonstrate the ability to construct 2D and 3D elastography that helps distinguish stiff from soft tissues. Based on the constructed strain volumes, a novel nonlinear classification method for human breast tumors is introduced. Multi-compression elastography imaging is elucidated in this study to differentiate malignant from benign tumors, based on their nonlinear mechanical behavior under compression. A pilot study on ten patients was performed in vivo, and classification results were compared with biopsy diagnosis - the gold standard. Various nonlinear parameters based on different models, were evaluated and compared with two commonly used parameters; relative stiffness and relative tumor size. Moreover, different types of strain components were constructed in 3D for strain imaging, including normal axial, first principal, maximum shear and Von Mises strains. Interactive segmentation algorithms were also evaluated and applied on the constructed volumes, to delineate the stiff tissue by showing its isolated 3D shape.;Elastography 3D imaging results were in good agreement with the biopsy outcomes, where the new classification method showed a degree of discrepancy between benign and malignant tumors better than the commonly used parameters. The results show that the nonlinear parameters were found to be statistically significant with p-value \u3c0.05. Moreover, one parameter; power-law exponent, was highly statistically significant having p-value \u3c 0.001. Additionally, volumetric strain images reconstructed using the maximum shear strains provided an enhanced tumor\u27s boundary from the surrounding soft tissues. This edge enhancement improved the overall segmentation performance, and diminished the boundary leakage effect. 3D segmentation provided an additional reliable means to determine the tumor\u27s size by estimating its volume.;In summary, the proposed elastographic techniques can help predetermine the tumor\u27s type, shape and size that are considered key features helping the physician to decide the sort and extent of the treatment. The methods can also be extended to diagnose other types of tumors, such as prostate and cervical tumors. This research is aimed toward the development of a novel \u27virtual biopsy\u27 method that may reduce the number of unnecessary painful biopsies, and diminish the increasingly risk of cancer