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

Speech data analysis for semantic indexing of video of simulated medical crises.

The Simulation for Pediatric Assessment, Resuscitation, and Communication (SPARC) group within the Department of Pediatrics at the University of Louisville, was established to enhance the care of children by using simulation based educational methodologies to improve patient safety and strengthen clinician-patient interactions. After each simulation session, the physician must manually review and annotate the recordings and then debrief the trainees. The physician responsible for the simulation has recorded 100s of videos, and is seeking solutions that can automate the process. This dissertation introduces our developed system for efficient segmentation and semantic indexing of videos of medical simulations using machine learning methods. It provides the physician with automated tools to review important sections of the simulation by identifying who spoke, when and what was his/her emotion. Only audio information is extracted and analyzed because the quality of the image recording is low and the visual environment is static for most parts. Our proposed system includes four main components: preprocessing, speaker segmentation, speaker identification, and emotion recognition. The preprocessing consists of first extracting the audio component from the video recording. Then, extracting various low-level audio features to detect and remove silence segments. We investigate and compare two different approaches for this task. The first one is threshold-based and the second one is classification-based. The second main component of the proposed system consists of detecting speaker changing points for the purpose of segmenting the audio stream. We propose two fusion methods for this task. The speaker identification and emotion recognition components of our system are designed to provide users the capability to browse the video and retrieve shots that identify ”who spoke, when, and the speaker’s emotion” for further analysis. For this component, we propose two feature representation methods that map audio segments of arbitary length to a feature vector with fixed dimensions. The first one is based on soft bag-of-word (BoW) feature representations. In particular, we define three types of BoW that are based on crisp, fuzzy, and possibilistic voting. The second feature representation is a generalization of the BoW and is based on Fisher Vector (FV). FV uses the Fisher Kernel principle and combines the benefits of generative and discriminative approaches. The proposed feature representations are used within two learning frameworks. The first one is supervised learning and assumes that a large collection of labeled training data is available. Within this framework, we use standard classifiers including K-nearest neighbor (K-NN), support vector machine (SVM), and Naive Bayes. The second framework is based on semi-supervised learning where only a limited amount of labeled training samples are available. We use an approach that is based on label propagation. Our proposed algorithms were evaluated using 15 medical simulation sessions. The results were analyzed and compared to those obtained using state-of-the-art algorithms. We show that our proposed speech segmentation fusion algorithms and feature mappings outperform existing methods. We also integrated all proposed algorithms and developed a GUI prototype system for subjective evaluation. This prototype processes medical simulation video and provides the user with a visual summary of the different speech segments. It also allows the user to browse videos and retrieve scenes that provide answers to semantic queries such as: who spoke and when; who interrupted who? and what was the emotion of the speaker? The GUI prototype can also provide summary statistics of each simulation video. Examples include: for how long did each person spoke? What is the longest uninterrupted speech segment? Is there an unusual large number of pauses within the speech segment of a given speaker

Weakly supervised deep learning method for vulnerable road user detection in FMCW radar

Millimeter-wave radar is currently the most effective automotive sensor capable of all-weather perception. In order to detect Vulnerable Road Users (VRUs) in cluttered radar data, it is necessary to model the time-frequency signal patterns of human motion, i.e. the micro-Doppler signature. In this paper we propose a spatio-temporal Convolutional Neural Network (CNN) capable of detecting VRUs in cluttered radar data. The main contribution is a weakly supervised training method which uses abundant, automatically generated labels from camera and lidar for training the model. The input to the network is a tensor of temporally concatenated range-azimuth-Doppler arrays, while the ground truth is an occupancy grid formed by objects detected jointly in-camera images and lidar. Lidar provides accurate ranging ground truth, while camera information helps distinguish between VRUs and background. Experimental evaluation shows that the CNN model has superior detection performance compared to classical techniques. Moreover, the model trained with imperfect, weak supervision labels outperforms the one trained with a limited number of perfect, hand-annotated labels. Finally, the proposed method has excellent scalability due to the low cost of automatic annotation

Webly Supervised Learning of Convolutional Networks

We present an approach to utilize large amounts of web data for learning CNNs. Specifically inspired by curriculum learning, we present a two-step approach for CNN training. First, we use easy images to train an initial visual representation. We then use this initial CNN and adapt it to harder, more realistic images by leveraging the structure of data and categories. We demonstrate that our two-stage CNN outperforms a fine-tuned CNN trained on ImageNet on Pascal VOC 2012. We also demonstrate the strength of webly supervised learning by localizing objects in web images and training a R-CNN style detector. It achieves the best performance on VOC 2007 where no VOC training data is used. Finally, we show our approach is quite robust to noise and performs comparably even when we use image search results from March 2013 (pre-CNN image search era)

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