A Survey of the Impact of Self-Supervised Pretraining for Diagnostic Tasks with Radiological Images

Self-supervised pretraining has been observed to be effective at improving feature representations for transfer learning, leveraging large amounts of unlabelled data. This review summarizes recent research into its usage in X-ray, computed tomography, magnetic resonance, and ultrasound imaging, concentrating on studies that compare self-supervised pretraining to fully supervised learning for diagnostic tasks such as classification and segmentation. The most pertinent finding is that self-supervised pretraining generally improves downstream task performance compared to full supervision, most prominently when unlabelled examples greatly outnumber labelled examples. Based on the aggregate evidence, recommendations are provided for practitioners considering using self-supervised learning. Motivated by limitations identified in current research, directions and practices for future study are suggested, such as integrating clinical knowledge with theoretically justified self-supervised learning methods, evaluating on public datasets, growing the modest body of evidence for ultrasound, and characterizing the impact of self-supervised pretraining on generalization.Comment: 32 pages, 6 figures, a literature survey submitted to BMC Medical Imagin

Generating semantically enriched diagnostics for radiological images using machine learning

Development of Computer Aided Diagnostic (CAD) tools to aid radiologists in pathology detection and decision making relies considerably on manually annotated images. With the advancement of deep learning techniques for CAD development, these expert annotations no longer need to be hand-crafted, however, deep learning algorithms require large amounts of data in order to generalise well. One way in which to access large volumes of expert-annotated data is through radiological exams consisting of images and reports. Using past radiological exams obtained from hospital archiving systems has many advantages: they are expert annotations available in large quantities, covering a population-representative variety of pathologies, and they provide additional context to pathology diagnoses, such as anatomical location and severity. Learning to auto-generate such reports from images presents many challenges such as the difficulty in representing and generating long, unstructured textual information, accounting for spelling errors and repetition or redundancy, and the inconsistency across different annotators. In this thesis, the problem of learning to automate disease detection from radiological exams is approached from three directions. Firstly, a report generation model is developed such that it is conditioned on radiological image features. Secondly, a number of approaches are explored aimed at extracting diagnostic information from free-text reports. Finally, an alternative approach to image latent space learning from current state-of-the-art is developed that can be applied to accelerated image acquisition.Open Acces

Generative Adversarial Network (GAN) for Medical Image Synthesis and Augmentation

Medical image processing aided by artificial intelligence (AI) and machine learning (ML) significantly improves medical diagnosis and decision making. However, the difficulty to access well-annotated medical images becomes one of the main constraints on further improving this technology. Generative adversarial network (GAN) is a DNN framework for data synthetization, which provides a practical solution for medical image augmentation and translation. In this study, we first perform a quantitative survey on the published studies on GAN for medical image processing since 2017. Then a novel adaptive cycle-consistent adversarial network (Ad CycleGAN) is proposed. We respectively use a malaria blood cell dataset (19,578 images) and a COVID-19 chest X-ray dataset (2,347 images) to test the new Ad CycleGAN. The quantitative metrics include mean squared error (MSE), root mean squared error (RMSE), peak signal-to-noise ratio (PSNR), universal image quality index (UIQI), spatial correlation coefficient (SCC), spectral angle mapper (SAM), visual information fidelity (VIF), Frechet inception distance (FID), and the classification accuracy of the synthetic images. The CycleGAN and variant autoencoder (VAE) are also implemented and evaluated as comparison. The experiment results on malaria blood cell images indicate that the Ad CycleGAN generates more valid images compared to CycleGAN or VAE. The synthetic images by Ad CycleGAN or CycleGAN have better quality than those by VAE. The synthetic images by Ad CycleGAN have the highest accuracy of 99.61%. In the experiment on COVID-19 chest X-ray, the synthetic images by Ad CycleGAN or CycleGAN have higher quality than those generated by variant autoencoder (VAE). However, the synthetic images generated through the homogenous image augmentation process have better quality than those synthesized through the image translation process. The synthetic images by Ad CycleGAN have higher accuracy of 95.31% compared to the accuracy of the images by CycleGAN of 93.75%. In conclusion, the proposed Ad CycleGAN provides a new path to synthesize medical images with desired diagnostic or pathological patterns. It is considered a new approach of conditional GAN with effective control power upon the synthetic image domain. The findings offer a new path to improve the deep neural network performance in medical image processing

Uncertainty Quantification, Image Synthesis and Deformation Prediction for Image Registration

Image registration is essential for medical image analysis to provide spatial correspondences. It is a difficult problem due to the modeling complexity of image appearance and the computational complexity of the deformable registration models. Thus, several techniques are needed: Uncertainty measurements of the high-dimensional parameter space of the registration methods for the evaluation of the registration result; Registration methods for registering healthy medical images to pathological images with large appearance changes; Fast registration prediction techniques for uni-modal and multi-modal images. This dissertation addresses these problems and makes the following contributions: 1) A frame- work for uncertainty quantification of image registration results is proposed. The proposed method for uncertainty quantification utilizes a low-rank Hessian approximation to evaluate the variance/co- variance of the variational Gaussian distribution of the registration parameters. The method requires significantly less storage and computation time than computing the Hessian via finite difference while achieving excellent approximation accuracy, facilitating the computation of the variational approximation; 2) An image synthesis deep network for pathological image registration is developed. The network transforms a pathological image into a ‘quasi-normal’ image, making registrations more accurate; 3) A patch-based deep learning framework for registration parameter prediction using image appearances only is created. The network is capable of accurately predicting the initial momentum for the Large Deformation Diffeomorphic Metric Mapping (LDDMM) model for both uni-modal and multi-modal registration problems, while increasing the registration speed by at least an order of magnitude compared with optimization-based approaches and maintaining the theoretical properties of LDDMM. Applications of the methods include 1) Uncertainty quantification of LDDMM for 2D and 3D medical image registrations, which could be used for uncertainty-based image smoothing and subsequent analysis; 2) Quasi-normal image synthesis for the registration of brain images with tumors with potential extensions to other image registration problems with pathologies and 3) deformation prediction for various brain datasets and T1w/T2w magnetic resonance images (MRI), which could be incorporated into other medical image analysis tasks such as fast multi-atlas image segmentation, fast geodesic image regression, fast atlas construction and fast user-interactive registration refinement.Doctor of Philosoph

Data efficient deep learning for medical image analysis: A survey

The rapid evolution of deep learning has significantly advanced the field of medical image analysis. However, despite these achievements, the further enhancement of deep learning models for medical image analysis faces a significant challenge due to the scarcity of large, well-annotated datasets. To address this issue, recent years have witnessed a growing emphasis on the development of data-efficient deep learning methods. This paper conducts a thorough review of data-efficient deep learning methods for medical image analysis. To this end, we categorize these methods based on the level of supervision they rely on, encompassing categories such as no supervision, inexact supervision, incomplete supervision, inaccurate supervision, and only limited supervision. We further divide these categories into finer subcategories. For example, we categorize inexact supervision into multiple instance learning and learning with weak annotations. Similarly, we categorize incomplete supervision into semi-supervised learning, active learning, and domain-adaptive learning and so on. Furthermore, we systematically summarize commonly used datasets for data efficient deep learning in medical image analysis and investigate future research directions to conclude this survey.Comment: Under Revie

Semantics-driven Abstractive Document Summarization

The evolution of the Web over the last three decades has led to a deluge of scientific and news articles on the Internet. Harnessing these publications in different fields of study is critical to effective end user information consumption. Similarly, in the domain of healthcare, one of the key challenges with the adoption of Electronic Health Records (EHRs) for clinical practice has been the tremendous amount of clinical notes generated that can be summarized without which clinical decision making and communication will be inefficient and costly. In spite of the rapid advances in information retrieval and deep learning techniques towards abstractive document summarization, the results of these efforts continue to resemble extractive summaries, achieving promising results predominantly on lexical metrics but performing poorly on semantic metrics. Thus, abstractive summarization that is driven by intrinsic and extrinsic semantics of documents is not adequately explored. Resources that can be used for generating semantics-driven abstractive summaries include: • Abstracts of multiple scientific articles published in a given technical field of study to generate an abstractive summary for topically-related abstracts within the field, thus reducing the load of having to read semantically duplicate abstracts on a given topic. • Citation contexts from different authoritative papers citing a reference paper can be used to generate utility-oriented abstractive summary for a scientific article. • Biomedical articles and the named entities characterizing the biomedical articles along with background knowledge bases to generate entity and fact-aware abstractive summaries. • Clinical notes of patients and clinical knowledge bases for abstractive clinical text summarization using knowledge-driven multi-objective optimization. In this dissertation, we develop semantics-driven abstractive models based on intra- document and inter-document semantic analyses along with facts of named entities retrieved from domain-specific knowledge bases to produce summaries. Concretely, we propose a sequence of frameworks leveraging semantics at various granularity (e.g., word, sentence, document, topic, citations, and named entities) levels, by utilizing external resources. The proposed frameworks have been applied to a range of tasks including 1. Abstractive summarization of topic-centric multi-document scientific articles and news articles. 2. Abstractive summarization of scientific articles using crowd-sourced citation contexts. 3. Abstractive summarization of biomedical articles clustered based on entity-relatedness. 4. Abstractive summarization of clinical notes of patients with heart failure and Chest X-Rays recordings. The proposed approaches achieve impressive performance in terms of preserving semantics in abstractive summarization while paraphrasing. For summarization of topic-centric multiple scientific/news articles, we propose a three-stage approach where abstracts of scientific articles or news articles are clustered based on their topical similarity determined from topics generated using Latent Dirichlet Allocation (LDA), followed by extractive phase and abstractive phase. Then, in the next stage, we focus on abstractive summarization of biomedical literature where we leverage named entities in biomedical articles to 1) cluster related articles; and 2) leverage the named entities towards guiding abstractive summarization. Finally, in the last stage, we turn to external resources such as citation contexts pointing to a scientific article to generate a comprehensive and utility-centric abstractive summary of a scientific article, domain-specific knowledge bases to fill gaps in information about entities in a biomedical article to summarize and clinical notes to guide abstractive summarization of clinical text. Thus, the bottom-up progression of exploring semantics towards abstractive summarization in this dissertation starts with (i) Semantic Analysis of Latent Topics; builds on (ii) Internal and External Knowledge-I (gleaned from abstracts and Citation Contexts); and extends it to make it comprehensive using (iii) Internal and External Knowledge-II (Named Entities and Knowledge Bases)