Active vision for deep visual learning: a unified pooling framework

Convolutional Neural Networks (CNNs) can be generally regarded as learning-based visual systems for computer vision tasks. By imitating the operating mechanism of the human visual system (HVS), CNNs can even achieve better results than human beings in some visual tasks. However, they are primary when compared to the HVS for the reason that the HVS has the ability of active vision to promptly analyze and adapt to specific tasks. In this study, a new unified pooling framework was proposed and a series of pooling methods were designed based on the framework to implement active vision to CNNs. In addition, an active selection pooling (ASP) was put forward to reorganize existing and newly proposed pooling methods. The CNN models with ASP tend to have a behavior of focus selection according to tasks during training process, which acts extrememly similar to the HVS

A dimension-reduction based multilayer perception method for supporting the medical decision making

Due to the rapid development of Medical IoT recently, how to effectively apply these huge amounts of IoT data to enhance the reliability of the clinical decision making has become an increasing issue in the medical field. These data usually comprise high-complicated features with tremendous volume, and it implies that the simple inference models may less powerful to be practiced. In deep learning, multilayer perceptron (MLP) is a kind of feed-forward artificial neural network, and it is one of the high-performance methods about stochastic scheme, fitness approximation, and regression analysis. To process these high uncertain data, the proposed work based on MLP structure in particular integrates the boosting scheme and dimension-reduction process. In this proposed work, the advanced ReLU-based activation function is used. Also, the weight initialization is applied to improve the stable prediction and convergence. After the improved dimension-reduction process is introduced, the proposed method can effectively learn the hidden information from the reformative data and the precise labels also can be recognized by stacking a small amount of neural network layers with paying few extra cost. The proposed work shows a possible path of embedding dimension reduction in deep learning structure with minor price. In addition to the prediction issue, the proposed method can also be applied to assess risk and forecast trend among different information systems

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

Nonparametric Bayesian Deep Learning for Scientific Data Analysis

Deep learning (DL) has emerged as the leading paradigm for predictive modeling in a variety of domains, especially those involving large volumes of high-dimensional spatio-temporal data such as images and text. With the rise of big data in scientific and engineering problems, there is now considerable interest in the research and development of DL for scientific applications. The scientific domain, however, poses unique challenges for DL, including special emphasis on interpretability and robustness. In particular, a priority of the Department of Energy (DOE) is the research and development of probabilistic ML methods that are robust to overfitting and offer reliable uncertainty quantification (UQ) on high-dimensional noisy data that is limited in size relative to its complexity. Gaussian processes (GPs) are nonparametric Bayesian models that are naturally robust to overfitting and offer UQ out-of-the-box. Unfortunately, traditional GP methods lack the balance of expressivity and domain-specific inductive bias that is key to the success of DL. Recently, however, a number of approaches have emerged to incorporate the DL paradigm into GP methods, including deep kernel learning (DKL), deep Gaussian processes (DGPs), and neural network Gaussian processes (NNGPs). In this work, we investigate DKL, DGPs, and NNGPs as paradigms for developing robust models for scientific applications. First, we develop DKL for text classification, and apply both DKL and Bayesian neural networks (BNNs) to the problem of classifying cancer pathology reports, with BNNs attaining new state-of-the-art results. Next, we introduce the deep ensemble kernel learning (DEKL) method, which is just as powerful as DKL while admitting easier model parallelism. Finally, we derive a new model called a ``bottleneck NNGP\u27\u27 by unifying the DGP and NNGP paradigms, thus laying the groundwork for a new class of methods for future applications

Design and Mining of Health Information Systems for Process and Patient Care Improvement

abstract: In healthcare facilities, health information systems (HISs) are used to serve different purposes. The radiology department adopts multiple HISs in managing their operations and patient care. In general, the HISs that touch radiology fall into two categories: tracking HISs and archive HISs. Electronic Health Records (EHR) is a typical tracking HIS, which tracks the care each patient receives at multiple encounters and facilities. Archive HISs are typically specialized databases to store large-size data collected as part of the patient care. A typical example of an archive HIS is the Picture Archive and Communication System (PACS), which provides economical storage and convenient access to diagnostic images from multiple modalities. How to integrate such HISs and best utilize their data remains a challenging problem due to the disparity of HISs as well as high-dimensionality and heterogeneity of the data. My PhD dissertation research includes three inter-connected and integrated topics and focuses on designing integrated HISs and further developing statistical models and machine learning algorithms for process and patient care improvement. Topic 1: Design of super-HIS and tracking of quality of care (QoC). My research developed an information technology that integrates multiple HISs in radiology, and proposed QoC metrics defined upon the data that measure various dimensions of care. The DDD assisted the clinical practices and enabled an effective intervention for reducing lengthy radiologist turnaround times for patients. Topic 2: Monitoring and change detection of QoC data streams for process improvement. With the super-HIS in place, high-dimensional data streams of QoC metrics are generated. I developed a statistical model for monitoring high- dimensional data streams that integrated Singular Vector Decomposition (SVD) and process control. The algorithm was applied to QoC metrics data, and additionally extended to another application of monitoring traffic data in communication networks. Topic 3: Deep transfer learning of archive HIS data for computer-aided diagnosis (CAD). The novelty of the CAD system is the development of a deep transfer learning algorithm that combines the ideas of transfer learning and multi- modality image integration under the deep learning framework. Our system achieved high accuracy in breast cancer diagnosis compared with conventional machine learning algorithms.Dissertation/ThesisDoctoral Dissertation Industrial Engineering 201

Spatio-temporal traffic anomaly detection for urban networks

Urban road networks are often affected by disruptions such as accidents and roadworks, giving rise to congestion and delays, which can, in turn, create a wide range of negative impacts to the economy, environment, safety and security. Accurate detection of the onset of traffic anomalies, specifically Recurrent Congestion (RC) and Nonrecurrent Congestion (NRC) in the traffic networks, is an important ITS function to facilitate proactive intervention measures to reduce the level of severity of congestion. A substantial body of literature is dedicated to models with varying levels of complexity that attempt to identify such anomalies. Given the complexity of the problem, however, very less effort is dedicated to the development of methods that attempt to detect traffic anomalies using spatio-temporal features. Driven both by the recent advances in deep learning techniques and the development of Traffic Incident Management Systems (TIMS), the aim of this research is to develop novel traffic anomaly detection models that can incorporate both spatial and temporal traffic information to detect traffic anomalies at a network level. This thesis first reviews the state of the art in traffic anomaly detection techniques, including the existing methods and emerging machine learning and deep learning methods, before identifying the gaps in the current understanding of traffic anomaly and its detection. One of the problems in terms of adapting the deep learning models to traffic anomaly detection is the translation of time series traffic data from multiple locations to the format necessary for the deep learning model to learn the spatial and temporal features effectively. To address this challenging problem and build a systematic traffic anomaly detection method at a network level, this thesis proposes a methodological framework consisting of (a) the translation layer (which is designed to translate the time series traffic data from multiple locations over the road network into a desired format with spatial and temporal features), (b) detection methods and (c) localisation. This methodological framework is subsequently tested for early RC detection and NRC detection. Three translation layers including connectivity matrix, geographical grid translation and spatial temporal translation are presented and evaluated for both RC and NRC detection. The early RC detection approach is a deep learning based method that combines Convolutional Neural Networks (CNN) and Long Short-Term Memory (LSTM). The NRC detection, on the other hand, involves only the application of the CNN. The performance of the proposed approach is compared against other conventional congestion detection methods, using a comprehensive evaluation framework that includes metrics such as detection rates and false positive rates, and the sensitivity analysis of time windows as well as prediction horizons. The conventional congestion detection methods used for the comparison include Multilayer Perceptron, Random Forest and Gradient Boost Classifier, all of which are commonly used in the literature. Real-world traffic data from the City of Bath are used for the comparative analysis of RC, while traffic data in conjunction with incident data extracted from Central London are used for NRC detection. The results show that while the connectivity matrix may be capable of extracting features of a small network, the increased sparsity in the matrix in a large network reduces its effectiveness in feature learning compared to geographical grid translation. The results also indicate that the proposed deep learning method demonstrates superior detection accuracy compared to alternative methods and that it can detect recurrent congestion as early as one hour ahead with acceptable accuracy. The proposed method is capable of being implemented within a real-world ITS system making use of traffic sensor data, thereby providing a practically useful tool for road network managers to manage traffic proactively. In addition, the results demonstrate that a deep learning-based approach may improve the accuracy of incident detection and locate traffic anomalies precisely, especially in a large urban network. Finally, the framework is further tested for robustness in terms of network topology, sensor faults and missing data. The robustness analysis demonstrates that the proposed traffic anomaly detection approaches are transferable to different sizes of road networks, and that they are robust in the presence of sensor faults and missing data.Open Acces

Advanced Computational Methods for Oncological Image Analysis

[Cancer is the second most common cause of death worldwide and encompasses highly variable clinical and biological scenarios. Some of the current clinical challenges are (i) early diagnosis of the disease and (ii) precision medicine, which allows for treatments targeted to specific clinical cases. The ultimate goal is to optimize the clinical workflow by combining accurate diagnosis with the most suitable therapies. Toward this, large-scale machine learning research can define associations among clinical, imaging, and multi-omics studies, making it possible to provide reliable diagnostic and prognostic biomarkers for precision oncology. Such reliable computer-assisted methods (i.e., artificial intelligence) together with clinicians’ unique knowledge can be used to properly handle typical issues in evaluation/quantification procedures (i.e., operator dependence and time-consuming tasks). These technical advances can significantly improve result repeatability in disease diagnosis and guide toward appropriate cancer care. Indeed, the need to apply machine learning and computational intelligence techniques has steadily increased to effectively perform image processing operations—such as segmentation, co-registration, classification, and dimensionality reduction—and multi-omics data integration.

Multimodal Biomedical Data Visualization: Enhancing Network, Clinical, and Image Data Depiction

In this dissertation, we present visual analytics tools for several biomedical applications. Our research spans three types of biomedical data: reaction networks, longitudinal multidimensional clinical data, and biomedical images. For each data type, we present intuitive visual representations and efficient data exploration methods to facilitate visual knowledge discovery. Rule-based simulation has been used for studying complex protein interactions. In a rule-based model, the relationships of interacting proteins can be represented as a network. Nevertheless, understanding and validating the intended behaviors in large network models are ineffective and error prone. We have developed a tool that first shows a network overview with concise visual representations and then shows relevant rule-specific details on demand. This strategy significantly improves visualization comprehensibility and disentangles the complex protein-protein relationships by showing them selectively alongside the global context of the network. Next, we present a tool for analyzing longitudinal multidimensional clinical datasets, that we developed for understanding Parkinson's disease progression. Detecting patterns involving multiple time-varying variables is especially challenging for clinical data. Conventional computational techniques, such as cluster analysis and dimension reduction, do not always generate interpretable, actionable results. Using our tool, users can select and compare patient subgroups by filtering patients with multiple symptoms simultaneously and interactively. Unlike conventional visualizations that use local features, many targets in biomedical images are characterized by high-level features. We present our research characterizing such high-level features through multiscale texture segmentation and deep-learning strategies. First, we present an efficient hierarchical texture segmentation approach that scales up well to gigapixel images to colorize electron microscopy (EM) images. This enhances visual comprehensibility of gigapixel EM images across a wide range of scales. Second, we use convolutional neural networks (CNNs) to automatically derive high-level features that distinguish cell states in live-cell imagery and voxel types in 3D EM volumes. In addition, we present a CNN-based 3D segmentation method for biomedical volume datasets with limited training samples. We use factorized convolutions and feature-level augmentations to improve model generalization and avoid overfitting

Deep Learning in Medical Image Analysis

The accelerating power of deep learning in diagnosing diseases will empower physicians and speed up decision making in clinical environments. Applications of modern medical instruments and digitalization of medical care have generated enormous amounts of medical images in recent years. In this big data arena, new deep learning methods and computational models for efficient data processing, analysis, and modeling of the generated data are crucially important for clinical applications and understanding the underlying biological process. This book presents and highlights novel algorithms, architectures, techniques, and applications of deep learning for medical image analysis