Deep Learning in Medical Image Analysis

The computer-assisted analysis for better interpreting images have been longstanding issues in the medical imaging field. On the image-understanding front, recent advances in machine learning, especially, in the way of deep learning, have made a big leap to help identify, classify, and quantify patterns in medical images. Specifically, exploiting hierarchical feature representations learned solely from data, instead of handcrafted features mostly designed based on domain-specific knowledge, lies at the core of the advances. In that way, deep learning is rapidly proving to be the state-of-the-art foundation, achieving enhanced performances in various medical applications. In this article, we introduce the fundamentals of deep learning methods; review their successes to image registration, anatomical/cell structures detection, tissue segmentation, computer-aided disease diagnosis or prognosis, and so on. We conclude by raising research issues and suggesting future directions for further improvements

Predicting radiologists' gaze with computational saliency models in mammogram reading

Previous studies have shown that there is a strong correlation between radiologists' diagnoses and their gaze when reading medical images. The extent to which gaze is attracted by content in a visual scene can be characterised as visual saliency. There is a potential for the use of visual saliency in computer-aided diagnosis in radiology. However, little is known about what methods are effective for diagnostic images, and how these methods could be adapted to address specific applications in diagnostic imaging. In this study, we investigate 20 state-of-the-art saliency models including 10 traditional models and 10 deep learning-based models in predicting radiologists' visual attention while reading 196 mammograms. We found that deep learning-based models represent the most effective type of methods for predicting radiologists' gaze in mammogram reading; and that the performance of these saliency models can be significantly improved by transfer learning. In particular, an enhanced model can be achieved by pre-training the model on a large-scale natural image saliency dataset and then fine-tuning it on the target medical image dataset. In addition, based on a systematic selection of backbone networks and network architectures, we proposed a parallel multi-stream encoded model which outperforms the state-of-the-art approaches for predicting saliency of mammograms

Physics-Informed Computer Vision: A Review and Perspectives

Incorporation of physical information in machine learning frameworks are opening and transforming many application domains. Here the learning process is augmented through the induction of fundamental knowledge and governing physical laws. In this work we explore their utility for computer vision tasks in interpreting and understanding visual data. We present a systematic literature review of formulation and approaches to computer vision tasks guided by physical laws. We begin by decomposing the popular computer vision pipeline into a taxonomy of stages and investigate approaches to incorporate governing physical equations in each stage. Existing approaches in each task are analyzed with regard to what governing physical processes are modeled, formulated and how they are incorporated, i.e. modify data (observation bias), modify networks (inductive bias), and modify losses (learning bias). The taxonomy offers a unified view of the application of the physics-informed capability, highlighting where physics-informed learning has been conducted and where the gaps and opportunities are. Finally, we highlight open problems and challenges to inform future research. While still in its early days, the study of physics-informed computer vision has the promise to develop better computer vision models that can improve physical plausibility, accuracy, data efficiency and generalization in increasingly realistic applications

Role of deep learning in infant brain MRI analysis

Deep learning algorithms and in particular convolutional networks have shown tremendous success in medical image analysis applications, though relatively few methods have been applied to infant MRI data due numerous inherent challenges such as inhomogenous tissue appearance across the image, considerable image intensity variability across the first year of life, and a low signal to noise setting. This paper presents methods addressing these challenges in two selected applications, specifically infant brain tissue segmentation at the isointense stage and presymptomatic disease prediction in neurodevelopmental disorders. Corresponding methods are reviewed and compared, and open issues are identified, namely low data size restrictions, class imbalance problems, and lack of interpretation of the resulting deep learning solutions. We discuss how existing solutions can be adapted to approach these issues as well as how generative models seem to be a particularly strong contender to address them

Deep Learning for Crowd Anomaly Detection

Today, public areas across the globe are monitored by an increasing amount of surveillance cameras. This widespread usage has presented an ever-growing volume of data that cannot realistically be examined in real-time. Therefore, efforts to understand crowd dynamics have brought light to automatic systems for the detection of anomalies in crowds. This thesis explores the methods used across literature for this purpose, with a focus on those fusing dense optical flow in a feature extraction stage to the crowd anomaly detection problem. To this extent, five different deep learning architectures are trained using optical flow maps estimated by three deep learning-based techniques. More specifically, a 2D convolutional network, a 3D convolutional network, and LSTM-based convolutional recurrent network, a pre-trained variant of the latter, and a ConvLSTM-based autoencoder is trained using both regular frames and optical flow maps estimated by LiteFlowNet3, RAFT, and GMA on the UCSD Pedestrian 1 dataset. The experimental results have shown that while prone to overfitting, the use of optical flow maps may improve the performance of supervised spatio-temporal architectures

Learnable latent embeddings for joint behavioral and neural analysis

Mapping behavioral actions to neural activity is a fundamental goal of neuroscience. As our ability to record large neural and behavioral data increases, there is growing interest in modeling neural dynamics during adaptive behaviors to probe neural representations. In particular, neural latent embeddings can reveal underlying correlates of behavior, yet, we lack non-linear techniques that can explicitly and flexibly leverage joint behavior and neural data. Here, we fill this gap with a novel method, CEBRA, that jointly uses behavioral and neural data in a hypothesis- or discovery-driven manner to produce consistent, high-performance latent spaces. We validate its accuracy and demonstrate our tool's utility for both calcium and electrophysiology datasets, across sensory and motor tasks, and in simple or complex behaviors across species. It allows for single and multi-session datasets to be leveraged for hypothesis testing or can be used label-free. Lastly, we show that CEBRA can be used for the mapping of space, uncovering complex kinematic features, and rapid, high-accuracy decoding of natural movies from visual cortex.Comment: Website: cebra.a

Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries

This two-volume set LNCS 12962 and 12963 constitutes the thoroughly refereed proceedings of the 7th International MICCAI Brainlesion Workshop, BrainLes 2021, as well as the RSNA-ASNR-MICCAI Brain Tumor Segmentation (BraTS) Challenge, the Federated Tumor Segmentation (FeTS) Challenge, the Cross-Modality Domain Adaptation (CrossMoDA) Challenge, and the challenge on Quantification of Uncertainties in Biomedical Image Quantification (QUBIQ). These were held jointly at the 23rd Medical Image Computing for Computer Assisted Intervention Conference, MICCAI 2020, in September 2021. The 91 revised papers presented in these volumes were selected form 151 submissions. Due to COVID-19 pandemic the conference was held virtually. This is an open access book

Combinatorial Generalisation in Machine Vision

The human capacity for generalisation, i.e. the fact that we are able to successfully perform a familiar task in novel contexts, is one of the hallmarks of our intelligent behaviour. But what mechanisms enable this capacity that is at the same time so impressive but comes so naturally to us? This is a question that has driven copious amounts of research in both Cognitive Science and Artificial Intelligence for almost a century, with some advocating the need for symbolic systems and others the benefits of distributed representations. In this thesis we will explore which principles help AI systems to generalise to novel combinations of previously observed elements (such as color and shape) in the context of machine vision. We will show that while approaches such as disentangled representation learning showed initial promise, they are fundamentally unable to solve this generalisation problem. In doing so we will illustrate the need to perform severe tests of models in order to properly assess their limitations. We will also see how such failures are robust across different datasets, training modalities and in the internal representations of the models. We then show that a different type of system that attempts to learn object-centric representations is capable of solving the generalisation challenges that previous models could not. We conclude by discussing the implications of these results for long-standing questions regarding the kinds of cognitive systems that are required to solve generalisation problems