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

Towards generalizable machine learning models for computer-aided diagnosis in medicine

Hidden stratification represents a phenomenon in which a training dataset contains unlabeled (hidden) subsets of cases that may affect machine learning model performance. Machine learning models that ignore the hidden stratification phenomenon--despite promising overall performance measured as accuracy and sensitivity--often fail at predicting the low prevalence cases, but those cases remain important. In the medical domain, patients with diseases are often less common than healthy patients, and a misdiagnosis of a patient with a disease can have significant clinical impacts. Therefore, to build a robust and trustworthy CAD system and a reliable treatment effect prediction model, we cannot only pursue machine learning models with high overall accuracy, but we also need to discover any hidden stratification in the data and evaluate the proposing machine learning models with respect to both overall performance and the performance on certain subsets (groups) of the data, such as the ‘worst group’. In this study, I investigated three approaches for data stratification: a novel algorithmic deep learning (DL) approach that learns similarities among cases and two schema completion approaches that utilize domain expert knowledge. I further proposed an innovative way to integrate the discovered latent groups into the loss functions of DL models to allow for better model generalizability under the domain shift scenario caused by the data heterogeneity. My results on lung nodule Computed Tomography (CT) images and breast cancer histopathology images demonstrate that learning homogeneous groups within heterogeneous data significantly improves the performance of the computer-aided diagnosis (CAD) system, particularly for low-prevalence or worst-performing cases. This study emphasizes the importance of discovering and learning the latent stratification within the data, as it is a critical step towards building ML models that are generalizable and reliable. Ultimately, this discovery can have a profound impact on clinical decision-making, particularly for low-prevalence cases

Generalized Cross-domain Multi-label Few-shot Learning for Chest X-rays

Real-world application of chest X-ray abnormality classification requires dealing with several challenges: (i) limited training data; (ii) training and evaluation sets that are derived from different domains; and (iii) classes that appear during training may have partial overlap with classes of interest during evaluation. To address these challenges, we present an integrated framework called Generalized Cross-Domain Multi-Label Few-Shot Learning (GenCDML-FSL). The framework supports overlap in classes during training and evaluation, cross-domain transfer, adopts meta-learning to learn using few training samples, and assumes each chest X-ray image is either normal or associated with one or more abnormalities. Furthermore, we propose Generalized Episodic Training (GenET), a training strategy that equips models to operate with multiple challenges observed in the GenCDML-FSL scenario. Comparisons with well-established methods such as transfer learning, hybrid transfer learning, and multi-label meta-learning on multiple datasets show the superiority of our approach.Comment: 17 page

Improved Chest Anomaly Localization without Pixel-level Annotation via Image Translation Network Application in Pseudo-paired Registration Domain

Image translation based on a generative adversarial network (GAN-IT) is a promising method for the precise localization of abnormal regions in chest X-ray images (AL-CXR) even without pixel-level annotation. However, heterogeneous unpaired datasets undermine existing methods to extract key features and distinguish normal from abnormal cases, resulting in inaccurate and unstable AL-CXR. To address this problem, we propose an improved two-stage GAN-IT involving registration and data augmentation. For the first stage, we introduce an advanced deep-learning-based registration technique that virtually and reasonably converts unpaired data into paired data for learning registration maps, by sequentially utilizing linear-based global and uniform coordinate transformation and AI-based non-linear coordinate fine-tuning. This approach enables the independent and complex coordinate transformation of each detailed location of the lung while recognizing the entire lung structure, thereby achieving higher registration performance with resolving inherent artifacts caused by unpaired conditions. For the second stage, we apply data augmentation to diversify anomaly locations by swapping the left and right lung regions on the uniform registered frames, further improving the performance by alleviating imbalance in data distribution showing left and right lung lesions. The proposed method is model agnostic and shows consistent AL-CXR performance improvement in representative AI models. Therefore, we believe GAN-IT for AL-CXR can be clinically implemented by using our basis framework, even if learning data are scarce or difficult for the pixel-level disease annotation

A Modular Approach to Lung Nodule Detection from Computed Tomography Images Using Artificial Neural Networks and Content Based Image Representation

Lung cancer is one of the most lethal cancer types. Research in computer aided detection (CAD) and diagnosis for lung cancer aims at providing effective tools to assist physicians in cancer diagnosis and treatment to save lives. In this dissertation, we focus on developing a CAD framework for automated lung cancer nodule detection from 3D lung computed tomography (CT) images. Nodule detection is a challenging task that no machine intelligence can surpass human capability to date. In contrast, human recognition power is limited by vision capacity and may suffer from work overload and fatigue, whereas automated nodule detection systems can complement expert’s efforts to achieve better detection performance. The proposed CAD framework encompasses several desirable properties such as mimicking physicians by means of geometric multi-perspective analysis, computational efficiency, and the most importantly producing high performance in detection accuracy. As the central part of the framework, we develop a novel hierarchical modular decision engine implemented by Artificial Neural Networks. One advantage of this decision engine is that it supports the combination of spatial-level and feature-level information analysis in an efficient way. Our methodology overcomes some of the limitations of current lung nodule detection techniques by combining geometric multi-perspective analysis with global and local feature analysis. The proposed modular decision engine design is flexible to modifications in the decision modules; the engine structure can adopt the modifications without having to re-design the entire system. The engine can easily accommodate multi-learning scheme and parallel implementation so that each information type can be processed (in parallel) by the most adequate learning technique of its own. We have also developed a novel shape representation technique that is invariant under rigid-body transformation and we derived new features based on this shape representation for nodule detection. We implemented a prototype nodule detection system as a demonstration of the proposed framework. Experiments have been conducted to assess the performance of the proposed methodologies using real-world lung CT data. Several performance measures for detection accuracy are used in the assessment. The results show that the decision engine is able to classify patterns efficiently with very good classification performance