Exploiting the potential of large databases of electronic health records for research using rapid search algorithms and an intuitive query interface.

Objective: UK primary care databases, which contain diagnostic, demographic and prescribing information for millions of patients geographically representative of the UK, represent a significant resource for health services and clinical research. They can be used to identify patients with a specified disease or condition (phenotyping) and to investigate patterns of diagnosis and symptoms. Currently, extracting such information manually is time-consuming and requires considerable expertise. In order to exploit more fully the potential of these large and complex databases, our interdisciplinary team developed generic methods allowing access to different types of user. Materials and methods: Using the Clinical Practice Research Datalink database, we have developed an online user-focused system (TrialViz), which enables users interactively to select suitable medical general practices based on two criteria: suitability of the patient base for the intended study (phenotyping) and measures of data quality. Results: An end-to-end system, underpinned by an innovative search algorithm, allows the user to extract information in near real-time via an intuitive query interface and to explore this information using interactive visualization tools. A usability evaluation of this system produced positive results. Discussion: We present the challenges and results in the development of TrialViz and our plans for its extension for wider applications of clinical research. Conclusions: Our fast search algorithms and simple query algorithms represent a significant advance for users of clinical research databases

The Signal Data Explorer: A high performance Grid based signal search tool for use in distributed diagnostic applications

We describe a high performance Grid based signal search tool for distributed diagnostic applications developed in conjunction with Rolls-Royce plc for civil aero engine condition monitoring applications. With the introduction of advanced monitoring technology into engineering systems, healthcare, etc., the associated diagnostic processes are increasingly required to handle and consider vast amounts of data. An exemplar of such a diagnosis process was developed during the DAME project, which built a proof of concept demonstrator to assist in the enhanced diagnosis and prognosis of aero-engine conditions. In particular it has shown the utility of an interactive viewing and high performance distributed search tool (the Signal Data Explorer) in the aero-engine diagnostic process. The viewing and search techniques are equally applicable to other domains. The Signal Data Explorer and search services have been demonstrated on the Worldwide Universities Network to search distributed databases of electrocardiograph data

A Convolutional Neural Network for the Automatic Diagnosis of Collagen VI related Muscular Dystrophies

The development of machine learning systems for the diagnosis of rare diseases is challenging mainly due the lack of data to study them. Despite this challenge, this paper proposes a system for the Computer Aided Diagnosis (CAD) of low-prevalence, congenital muscular dystrophies from confocal microscopy images. The proposed CAD system relies on a Convolutional Neural Network (CNN) which performs an independent classification for non-overlapping patches tiling the input image, and generates an overall decision summarizing the individual decisions for the patches on the query image. This decision scheme points to the possibly problematic areas in the input images and provides a global quantitative evaluation of the state of the patients, which is fundamental for diagnosis and to monitor the efficiency of therapies.Comment: Submitted for review to Expert Systems With Application

DPVis: Visual Analytics with Hidden Markov Models for Disease Progression Pathways

Clinical researchers use disease progression models to understand patient status and characterize progression patterns from longitudinal health records. One approach for disease progression modeling is to describe patient status using a small number of states that represent distinctive distributions over a set of observed measures. Hidden Markov models (HMMs) and its variants are a class of models that both discover these states and make inferences of health states for patients. Despite the advantages of using the algorithms for discovering interesting patterns, it still remains challenging for medical experts to interpret model outputs, understand complex modeling parameters, and clinically make sense of the patterns. To tackle these problems, we conducted a design study with clinical scientists, statisticians, and visualization experts, with the goal to investigate disease progression pathways of chronic diseases, namely type 1 diabetes (T1D), Huntington's disease, Parkinson's disease, and chronic obstructive pulmonary disease (COPD). As a result, we introduce DPVis which seamlessly integrates model parameters and outcomes of HMMs into interpretable and interactive visualizations. In this study, we demonstrate that DPVis is successful in evaluating disease progression models, visually summarizing disease states, interactively exploring disease progression patterns, and building, analyzing, and comparing clinically relevant patient subgroups.Comment: to appear at IEEE Transactions on Visualization and Computer Graphic