Learning For Medical Image Analysis Research Articles

Analysis of the ISIC image datasets: Usage, benchmarks and recommendations.

The International Skin Imaging Collaboration (ISIC) datasets have become a leading repository for researchers in machine learning for medical image analysis, especially in the field of skin cancer detection and malignancy assessment. They contain tens of thousands of dermoscopic photographs together with gold-standard lesion diagnosis metadata. The associated yearly challenges have resulted in major contributions to the field, with papers reporting measures well in excess of human experts. Skin cancers can be divided into two major groups - melanoma and non-melanoma. Although less prevalent, melanoma is considered to be more serious as it can quickly spread to other organs if not treated at an early stage. In this paper, we summarise the usage of the ISIC dataset images and present an analysis of yearly releases over a period of 2016 - 2020. Our analysis found a significant number of duplicate images, both within and between the datasets. Additionally, we also noted duplicates spread across testing and training sets. Due to these irregularities, we propose a duplicate removal strategy and recommend a curated dataset for researchers to use when working on ISIC datasets. Given that ISIC 2020 focused on melanoma classification, we conduct experiments to provide benchmark results on the ISIC 2020 test set, with additional analysis on the smaller ISIC 2017 test set. Testing was completed following the application of our duplicate removal strategy and an additional data balancing step. As a result of removing 14,310 duplicate images from the training set, our benchmark results show good levels of melanoma prediction with an AUC of 0.80 for the best performing model. As our aim was not to maximise network performance, we did not include additional steps in our experiments. Finally, we provide recommendations for future research by highlighting irregularities that may present research challenges. A list of image files with reference to the original ISIC dataset sources for the recommended curated training set will be shared on our GitHub repository (available at www.github.com/mmu-dermatology-research/isic_duplicate_removal_strategy).

Computer vision and machine learning for medical image analysis: recent advances, challenges, and way forward

The recent development in the areas of deep learning and deep convolutional neural networks has significantly progressed and advanced the field of computer vision (CV) and image analysis and understanding. Complex tasks such as classifying and segmenting medical images and localising and recognising objects of interest have become much less challenging. This progress has the potential of accelerating research and deployment of multitudes of medical applications that utilise CV. However, in reality, there are limited practical examples being physically deployed into front-line health facilities. In this paper, we examine the current state of the art in CV as applied to the medical domain. We discuss the main challenges in CV and intelligent data-driven medical applications and suggest future directions to accelerate research, development, and deployment of CV applications in health practices. First, we critically review existing literature in the CV domain that addresses complex vision tasks, including: medical image classification; shape and object recognition from images; and medical segmentation. Second, we present an in-depth discussion of the various challenges that are considered barriers to accelerating research, development, and deployment of intelligent CV methods in real-life medical applications and hospitals. Finally, we conclude by discussing future directions.

Comparison of the proposed DCNN model with standard CNN architectures for retinal diseases classification.

Deep learning in medical image analysis has indicated increasing interest in the classification of signs of abnormalities. In this study, a new convolutional neural network (CNN) architecture (MIDNet18) Medical Image Detection Network was proposed for the classification of retinal diseases using optical coherence tomography (OCT) images. The model consists of 14 convolutional layers, seven Max Pooling layers, four dense layers, and one classification layer. A multi-class classification layer in the MIDNet18 is used to classify the OCT images into either normal or any of the three abnormal types: Choroidal Neovascularization (CNV), Drusen, and Diabetic Macular Edema (DME). The dataset consists of 83,484 training images, 41,741 validation images, and 968 test images. According to the experimental results, MIDNet18 obtains an accuracy of 98.86%, and their performances are compared with other standard CNN models; ResNet-50 (83.26%), MobileNet (93.29%) and DenseNet (92.5%). Also, MIDNet18 with a p-value < 0.001 has been proved to be statistically significant than other standard CNN architectures in classifying retinal diseases using OCT images.

Deep Feature Learning for Medical Image Analysis with Convolutional Autoencoder Neural Network

At present, computed tomography (CT) is widely used to assist disease diagnosis. Especially, computer aided diagnosis (CAD) based on artificial intelligence (AI) recently exhibits its importance in intelligent healthcare. However, it is a great challenge to establish an adequate labeled dataset for CT analysis assistance, due to the privacy and security issues. Therefore, this paper proposes a convolutional autoencoder deep learning framework to support unsupervised image features learning for lung nodule through unlabeled data, which only needs a small amount of labeled data for efficient feature learning. Through comprehensive experiments, it shows that the proposed scheme is superior to other approaches, which effectively solves the intrinsic labor-intensive problem during artificial image labeling. Moreover, it verifies that the proposed convolutional autoencoder approach can be extended for similarity measurement of lung nodules images. Especially, the features extracted through unsupervised learning are also applicable in other related scenarios.

A review on deep learning in medical image analysis.

Ongoing improvements in AI, particularly concerning deep learning techniques, are assisting to identify, classify, and quantify patterns in clinical images. Deep learning is the quickest developing field in artificial intelligence and is effectively utilized lately in numerous areas, including medication. A brief outline is given on studies carried out on the region of application: neuro, brain, retinal, pneumonic, computerized pathology, bosom, heart, breast, bone, stomach, and musculoskeletal. For information exploration, knowledge deployment, and knowledge-based prediction, deep learning networks can be successfully applied to big data. In the field of medical image processing methods and analysis, fundamental information and state-of-the-art approaches with deep learning are presented in this paper. The primary goals of this paper are to present research on medical image processing as well as to define and implement the key guidelines that are identified and addressed.

A Tour of Unsupervised Deep Learning for Medical Image Analysis.

Interpretation of medical images for the diagnosis and treatment of complex diseases from high-dimensional and heterogeneous data remains a key challenge in transforming healthcare. In the last few years, both supervised and unsupervised deep learning achieved promising results in the area of medical image analysis. Several reviews on supervised deep learning are published, but hardly any rigorous review on unsupervised deep learning for medical image analysis is available. The objective of this review is to systematically present various unsupervised deep learning models, tools, and benchmark datasets applied to medical image analysis. Some of the discussed models are autoencoders and their variants, Restricted Boltzmann Machines (RBM), Deep Belief Networks (DBN), Deep Boltzmann Machine (DBM), and Generative Adversarial Network (GAN). Future research opportunities and challenges of unsupervised deep learning techniques for medical image analysis are also discussed. Currently, interpretation of medical images for diagnostic purposes is usually performed by human experts that may be replaced by computer-aided diagnosis due to advancement in machine learning techniques, including deep learning, and the availability of cheap computing infrastructure through cloud computing. Both supervised and unsupervised machine learning approaches are widely applied in medical image analysis, each of them having certain pros and cons. Since human supervisions are not always available or are inadequate or biased, therefore, unsupervised learning algorithms give a big hope with lots of advantages for biomedical image analysis.

A Tour of Unsupervised Deep Learning for Medical Image Analysis

A Tour of Unsupervised Deep Learning for Medical Image Analysis

The role of the quality control system for diagnostics of oncological diseases in radiomics: a review

Modern medical imaging methods allow for both qualitative and quantitative evaluations of tumors and issues surrounding them. Advances in computer science and big data processing are transforming any radiological study into analytic datasets, especially with the use of machine learning in medical image analysis. Among these datasets, statistically significant correlations with clinical events can then be searched for to subsequently assess their predictive value and ability to predict a particular clinical outcome. This concept, known as radiomics, was first described in 2012. It is particularly important in oncology because each type of tumor can be subdivided into many different molecular genetic subtypes, and simple visual characteristics are no longer sufficient. Moreover, as an absolutely noninvasive method, radiomics can provide a radiologist with additional information that would otherwise be unavailable without a histological examination of biopsy material. However, as with any methodology based on the use of big data, the question of the quality of the initial data becomes critical, because this can directly affect the outcome of the analysis and provide incorrect diagnostic information.&#x0D; In this literature review, we examine potential approaches to ensuring the quality of research at all stages, from technical control of the state of diagnostic equipment to the extraction of imaging markers in oncology and the calculation of their correlation with clinical data.

A survey on active learning and human-in-the-loop deep learning for medical image analysis.

Fully automatic deep learning has become the state-of-the-art technique for many tasks including image acquisition, analysis and interpretation, and for the extraction of clinically useful information for computer-aided detection, diagnosis, treatment planning, intervention and therapy. However, the unique challenges posed by medical image analysis suggest that retaining a human end-user in any deep learning enabled system will be beneficial. In this review we investigate the role that humans might play in the development and deployment of deep learning enabled diagnostic applications and focus on techniques that will retain a significant input from a human end user. Human-in-the-Loop computing is an area that we see as increasingly important in future research due to the safety-critical nature of working in the medical domain. We evaluate four key areas that we consider vital for deep learning in the clinical practice: (1) Active Learning to choose the best data to annotate for optimal model performance; (2) Interaction with model outputs - using iterative feedback to steer models to optima for a given prediction and offering meaningful ways to interpret and respond to predictions; (3) Practical considerations - developing full scale applications and the key considerations that need to be made before deployment; (4) Future Prospective and Unanswered Questions - knowledge gaps and related research fields that will benefit human-in-the-loop computing as they evolve. We offer our opinions on the most promising directions of research and how various aspects of each area might be unified towards common goals.

Deep learning classification of lung cancer histology using CT images

Tumor histology is an important predictor of therapeutic response and outcomes in lung cancer. Tissue sampling for pathologist review is the most reliable method for histology classification, however, recent advances in deep learning for medical image analysis allude to the utility of radiologic data in further describing disease characteristics and for risk stratification. In this study, we propose a radiomics approach to predicting non-small cell lung cancer (NSCLC) tumor histology from non-invasive standard-of-care computed tomography (CT) data. We trained and validated convolutional neural networks (CNNs) on a dataset comprising 311 early-stage NSCLC patients receiving surgical treatment at Massachusetts General Hospital (MGH), with a focus on the two most common histological types: adenocarcinoma (ADC) and Squamous Cell Carcinoma (SCC). The CNNs were able to predict tumor histology with an AUC of 0.71(p = 0.018). We also found that using machine learning classifiers such as k-nearest neighbors (kNN) and support vector machine (SVM) on CNN-derived quantitative radiomics features yielded comparable discriminative performance, with AUC of up to 0.71 (p = 0.017). Our best performing CNN functioned as a robust probabilistic classifier in heterogeneous test sets, with qualitatively interpretable visual explanations to its predictions. Deep learning based radiomics can identify histological phenotypes in lung cancer. It has the potential to augment existing approaches and serve as a corrective aid for diagnosticians.

Interpretability-Driven Sample Selection Using Self Supervised Learning for Disease Classification and Segmentation.

In supervised learning for medical image analysis, sample selection methodologies are fundamental to attain optimum system performance promptly and with minimal expert interactions (e.g. label querying in an active learning setup). In this article we propose a novel sample selection methodology based on deep features leveraging information contained in interpretability saliency maps. In the absence of ground truth labels for informative samples, we use a novel self supervised learning based approach for training a classifier that learns to identify the most informative sample in a given batch of images. We demonstrate the benefits of the proposed approach, termed Interpretability-Driven Sample Selection (IDEAL), in an active learning setup aimed at lung disease classification and histopathology image segmentation. We analyze three different approaches to determine sample informativeness from interpretability saliency maps: (i) an observational model stemming from findings on previous uncertainty-based sample selection approaches, (ii) a radiomics-based model, and (iii) a novel data-driven self-supervised approach. We compare IDEAL to other baselines using the publicly available NIH chest X-ray dataset for lung disease classification, and a public histopathology segmentation dataset (GLaS), demonstrating the potential of using interpretability information for sample selection in active learning systems. Results show our proposed self supervised approach outperforms other approaches in selecting informative samples leading to state of the art performance with fewer samples.

Transferable Visual Words: Exploiting the Semantics of Anatomical Patterns for Self-Supervised Learning.

This paper introduces a new concept called "transferable visual words" (TransVW), aiming to achieve annotation efficiency for deep learning in medical image analysis. Medical imaging-focusing on particular parts of the body for defined clinical purposes-generates images of great similarity in anatomy across patients and yields sophisticated anatomical patterns across images, which are associated with rich semantics about human anatomy and which are natural visual words. We show that these visual words can be automatically harvested according to anatomical consistency via self-discovery, and that the self-discovered visual words can serve as strong yet free supervision signals for deep models to learn semantics-enriched generic image representation via self-supervision (self-classification and self-restoration). Our extensive experiments demonstrate the annotation efficiency of TransVW by offering higher performance and faster convergence with reduced annotation cost in several applications. Our TransVW has several important advantages, including (1) TransVW is a fully autodidactic scheme, which exploits the semantics of visual words for self-supervised learning, requiring no expert annotation; (2) visual word learning is an add-on strategy, which complements existing self-supervised methods, boosting their performance; and (3) the learned image representation is semantics-enriched models, which have proven to be more robust and generalizable, saving annotation efforts for a variety of applications through transfer learning. Our code, pre-trained models, and curated visual words are available at https://github.com/JLiangLab/TransVW.

A survey on incorporating domain knowledge into deep learning for medical image analysis.

Although deep learning models like CNNs have achieved great success in medical image analysis, the small size of medical datasets remains a major bottleneck in this area. To address this problem, researchers have started looking for external information beyond current available medical datasets. Traditional approaches generally leverage the information from natural images via transfer learning. More recent works utilize the domain knowledge from medical doctors, to create networks that resemble how medical doctors are trained, mimic their diagnostic patterns, or focus on the features or areas they pay particular attention to. In this survey, we summarize the current progress on integrating medical domain knowledge into deep learning models for various tasks, such as disease diagnosis, lesion, organ and abnormality detection, lesion and organ segmentation. For each task, we systematically categorize different kinds of medical domain knowledge that have been utilized and their corresponding integrating methods. We also provide current challenges and directions for future research.

A Systematic Benchmarking Analysis of Transfer Learning for Medical Image Analysis.

Transfer learning from supervised ImageNet models has been frequently used in medical image analysis. Yet, no large-scale evaluation has been conducted to benchmark the efficacy of newly-developed pre-training techniques for medical image analysis, leaving several important questions unanswered. As the first step in this direction, we conduct a systematic study on the transferability of models pre-trained on iNat2021, the most recent large-scale fine-grained dataset, and 14 top self-supervised ImageNet models on 7 diverse medical tasks in comparison with the supervised ImageNet model. Furthermore, we present a practical approach to bridge the domain gap between natural and medical images by continually (pre-)training supervised ImageNet models on medical images. Our comprehensive evaluation yields new insights: (1) pre-trained models on fine-grained data yield distinctive local representations that are more suitable for medical segmentation tasks, (2) self-supervised ImageNet models learn holistic features more effectively than supervised ImageNet models, and (3) continual pre-training can bridge the domain gap between natural and medical images. We hope that this large-scale open evaluation of transfer learning can direct the future research of deep learning for medical imaging. As open science, all codes and pre-trained models are available on our GitHub page https://github.com/JLiangLab/BenchmarkTransferLearning.

A Tour of Unsupervised Deep Learning for Medical Image Analysis

A Tour of Unsupervised Deep Learning for Medical Image Analysis

A Tour of Unsupervised Deep Learning for Medical Image Analysis

Interpretation of medical images for diagnosis and treatment of complex disease from high-dimensional and heterogeneous data remains a key challenge in transforming healthcare. In the last few years, both supervised and unsupervised deep learning achieved promising results in the area of medical imaging and image analysis. Unlike supervised learning which is biased towards how it is being supervised and manual efforts to create class label for the algorithm, unsupervised learning derive insights directly from the data itself, group the data and help to make data driven decisions without any external bias. This review systematically presents various unsupervised models applied to medical image analysis, including autoencoders and its several variants, Restricted Boltzmann machines, Deep belief networks, Deep Boltzmann machine and Generative adversarial network. Future research opportunities and challenges of unsupervised techniques for medical image analysis have also been discussed.

Models Genesis.

Transfer learning from natural image to medical image has been established as one of the most practical paradigms in deep learning for medical image analysis. To fit this paradigm, however, 3D imaging tasks in the most prominent imaging modalities (e.g., CT and MRI) have to be reformulated and solved in 2D, losing rich 3D anatomical information, thereby inevitably compromising its performance. To overcome this limitation, we have built a set of models, called Generic Autodidactic Models, nicknamed Models Genesis, because they are created ex nihilo (with no manual labeling), self-taught (learnt by self-supervision), and generic (served as source models for generating application-specific target models). Our extensive experiments demonstrate that our Models Genesis significantly outperform learning from scratch and existing pre-trained 3D models in all five target 3D applications covering both segmentation and classification. More importantly, learning a model from scratch simply in 3D may not necessarily yield performance better than transfer learning from ImageNet in 2D, but our Models Genesis consistently top any 2D/2.5D approaches including fine-tuning the models pre-trained from ImageNet as well as fine-tuning the 2D versions of our Models Genesis, confirming the importance of 3D anatomical information and significance of Models Genesis for 3D medical imaging. This performance is attributed to our unified self-supervised learning framework, built on a simple yet powerful observation: the sophisticated and recurrent anatomy in medical images can serve as strong yet free supervision signals for deep models to learn common anatomical representation automatically via self-supervision. As open science, all codes and pre-trained Models Genesis are available at https://github.com/MrGiovanni/ModelsGenesis.

Application of deep learning in medical image analysis

Application of deep learning in medical image analysis

Deep learning for medical image analysis: a brief introduction.

Advances in deep learning have led to the development of neural network algorithms which today rival human performance in vision tasks, such as image classification or segmentation. Translation of these techniques into clinical science has also significantly advanced image analysis in neuro-oncology. This has created a need in the neuro-oncology community for understanding the mechanisms behind neural networks and deep learning, as close interaction of computer scientists and neuro-oncology researchers as well as realistic expectations about the possibilities (and limitations) of the current state-of-the-art is pivotal for successful translation of deep learning techniques into practice. In this review, we will briefly introduce the building blocks of neural networks with a particular focus on convolutional neural networks. We will explain why these networks excel at identifying relevant features and how they learn to associate these imaging features with (clinical) features of interest, such as genotype, or how they automatically segment structures of interest in the image volume. We will also discuss challenges for the more widespread use of these algorithms.

A descriptive framework for the field of deep learning applications in medical images

Deep learning in medical image analysis is a typical interdisciplinary application, which needs support and cooperation of computer techniques and medical experience, and has broad application prospects. Since 2017, the number of related published articles has increased exponentially, imposing a burden on the literature review in this field. In this survey, we clustered 2068 retrieved articles into 15 topics through Latent Dirichlet Allocation (LDA) and provided a rough overview on the application of deep learning in medical images. On this basis, we conducted a detailed review with 77 top representative articles. We built a descriptive review framework based on LDA and discussed classification, object detection, segmentation, and image generation applications in medical images for the field of deep learning from the perspective of image modalities. We ended with discussing current challenges and future research directions of deep learning in medical images analysis.