Deep Learning in Cardiology

The medical field is creating large amount of data that physicians are unable to decipher and use efficiently. Moreover, rule-based expert systems are inefficient in solving complicated medical tasks or for creating insights using big data. Deep learning has emerged as a more accurate and effective technology in a wide range of medical problems such as diagnosis, prediction and intervention. Deep learning is a representation learning method that consists of layers that transform the data non-linearly, thus, revealing hierarchical relationships and structures. In this review we survey deep learning application papers that use structured data, signal and imaging modalities from cardiology. We discuss the advantages and limitations of applying deep learning in cardiology that also apply in medicine in general, while proposing certain directions as the most viable for clinical use.Comment: 27 pages, 2 figures, 10 table

CNN-SLAM: Real-time dense monocular SLAM with learned depth prediction

Given the recent advances in depth prediction from Convolutional Neural Networks (CNNs), this paper investigates how predicted depth maps from a deep neural network can be deployed for accurate and dense monocular reconstruction. We propose a method where CNN-predicted dense depth maps are naturally fused together with depth measurements obtained from direct monocular SLAM. Our fusion scheme privileges depth prediction in image locations where monocular SLAM approaches tend to fail, e.g. along low-textured regions, and vice-versa. We demonstrate the use of depth prediction for estimating the absolute scale of the reconstruction, hence overcoming one of the major limitations of monocular SLAM. Finally, we propose a framework to efficiently fuse semantic labels, obtained from a single frame, with dense SLAM, yielding semantically coherent scene reconstruction from a single view. Evaluation results on two benchmark datasets show the robustness and accuracy of our approach.Comment: 10 pages, 6 figures, IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR), Hawaii, USA, June, 2017. The first two authors contribute equally to this pape

A Reminiscence of ”Mastermind”: Iris/Periocular Biometrics by ”In-Set” CNN Iterative Analysis

Convolutional neural networks (CNNs) have emerged as the most popular classification models in biometrics research. Under the discriminative paradigm of pattern recognition, CNNs are used typically in one of two ways: 1) verification mode (”are samples from the same person?”), where pairs of images are provided to the network to distinguish between genuine and impostor instances; and 2) identification mode (”whom is this sample from?”), where appropriate feature representations that map images to identities are found. This paper postulates a novel mode for using CNNs in biometric identification, by learning models that answer to the question ”is the query’s identity among this set?”. The insight is a reminiscence of the classical Mastermind game: by iteratively analysing the network responses when multiple random samples of k gallery elements are compared to the query, we obtain weakly correlated matching scores that - altogether - provide solid cues to infer the most likely identity. In this setting, identification is regarded as a variable selection and regularization problem, with sparse linear regression techniques being used to infer the matching probability with respect to each gallery identity. As main strength, this strategy is highly robust to outlier matching scores, which are known to be a primary error source in biometric recognition. Our experiments were carried out in full versions of two well known irises near-infrared (CASIA-IrisV4-Thousand) and periocular visible wavelength (UBIRIS.v2) datasets, and confirm that recognition performance can be solidly boosted-up by the proposed algorithm, when compared to the traditional working modes of CNNs in biometrics.info:eu-repo/semantics/publishedVersio

Reasoning with Uncertainty in Deep Learning for Safer Medical Image Computing

Deep learning is now ubiquitous in the research field of medical image computing. As such technologies progress towards clinical translation, the question of safety becomes critical. Once deployed, machine learning systems unavoidably face situations where the correct decision or prediction is ambiguous. However, the current methods disproportionately rely on deterministic algorithms, lacking a mechanism to represent and manipulate uncertainty. In safety-critical applications such as medical imaging, reasoning under uncertainty is crucial for developing a reliable decision making system. Probabilistic machine learning provides a natural framework to quantify the degree of uncertainty over different variables of interest, be it the prediction, the model parameters and structures, or the underlying data (images and labels). Probability distributions are used to represent all the uncertain unobserved quantities in a model and how they relate to the data, and probability theory is used as a language to compute and manipulate these distributions. In this thesis, we explore probabilistic modelling as a framework to integrate uncertainty information into deep learning models, and demonstrate its utility in various high-dimensional medical imaging applications. In the process, we make several fundamental enhancements to current methods. We categorise our contributions into three groups according to the types of uncertainties being modelled: (i) predictive; (ii) structural and (iii) human uncertainty. Firstly, we discuss the importance of quantifying predictive uncertainty and understanding its sources for developing a risk-averse and transparent medical image enhancement application. We demonstrate how a measure of predictive uncertainty can be used as a proxy for the predictive accuracy in the absence of ground-truths. Furthermore, assuming the structure of the model is flexible enough for the task, we introduce a way to decompose the predictive uncertainty into its orthogonal sources i.e. aleatoric and parameter uncertainty. We show the potential utility of such decoupling in providing a quantitative “explanations” into the model performance. Secondly, we introduce our recent attempts at learning model structures directly from data. One work proposes a method based on variational inference to learn a posterior distribution over connectivity structures within a neural network architecture for multi-task learning, and share some preliminary results in the MR-only radiotherapy planning application. Another work explores how the training algorithm of decision trees could be extended to grow the architecture of a neural network to adapt to the given availability of data and the complexity of the task. Lastly, we develop methods to model the “measurement noise” (e.g., biases and skill levels) of human annotators, and integrate this information into the learning process of the neural network classifier. In particular, we show that explicitly modelling the uncertainty involved in the annotation process not only leads to an improvement in robustness to label noise, but also yields useful insights into the patterns of errors that characterise individual experts

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