Learning from medical data streams: an introduction

Clinical practice and research are facing a new challenge created by the rapid growth of health information science and technology, and the complexity and volume of biomedical data. Machine learning from medical data streams is a recent area of research that aims to provide better knowledge extraction and evidence-based clinical decision support in scenarios where data are produced as a continuous flow. This year's edition of AIME, the Conference on Artificial Intelligence in Medicine, enabled the sound discussion of this area of research, mainly by the inclusion of a dedicated workshop. This paper is an introduction to LEMEDS, the Learning from Medical Data Streams workshop, which highlights the contributed papers, the invited talk and expert panel discussion, as well as related papers accepted to the main conference

A tool for enhancing MetaMap performance when annotating clinical guideline documents with UMLS concepts

We developed a tool that integrates the National Library of Medicine's MetaMap software with GATE, an open-source text an- alytics framework. The tool allows non-ASCII encoded documents of numerous formats to be annotated with UMLS concepts. We created a GATE pipeline to chunk cardiovascular disease guideline text into default segments (blank-line delimited), XML element content, sentences and phrases, which were sequentially submitted to MetaMap for annotation. XML element, sentence and phrase chunking allowed term extraction and mapping to be completed in around 1/3 of the time taken with de- fault chunking, although with slight loss of accuracy (F1.0s=0.94-0.99). However, phrase chunking allows more complex input to be processed in real time, which is not possible with the other approaches. We discuss the results in relation to use of MetaMap's --term processing option for generating pre- and post-coordinated mappings from composite phrases

A context-aware adaptive feedback agent for activity monitoring and coaching

A focus in treatment of chronic diseases is optimizing levels of physical activity. At Roessingh Research and Development, a system was developed, consisting of a Smartphone and an activity sensor, that can measure a patient’s daily activity behavior and provide motivational feedback messages. We are currently looking into ways of increasing the effectiveness of motivational messages that aim to stimulate sustainable behavioral change, by adapting its timing and content to individual patients in their current context of use

Thirty years of artificial intelligence in medicine (AIME) conferences: A review of research themes

Over the past 30 years, the international conference on Artificial Intelligence in MEdicine (AIME) has been organized at different venues across Europe every 2 years, establishing a forum for scientific exchange and creating an active research community. The Artificial Intelligence in Medicine journal has published theme issues with extended versions of selected AIME papers since 1998

D-WISE: Diabetes Web-Centric Information and Support Environment: Conceptual Specification and Proposed Evaluation

AbstractObjectiveTo develop and evaluate Diabetes Web-Centric Information and Support Environment (D-WISE) that offers 1) a computerized decision-support system to assist physicians to A) use the Canadian Diabetes Association clinical practice guidelines (CDA CPGs) to recommend evidence-informed interventions; B) offer a computerized readiness assessment strategy to help physicians administer behaviour-change strategies to help patients adhere to disease self-management programs; and 2) a patient-specific diabetes self-management application, accessible through smart mobile devices, that offers behaviour-change interventions to engage patients in self-management.MethodsThe above-mentioned objectives were pursued through a knowledge management approach that involved 1) Translation of paper-based CDA CPGs and behaviour-change models as computerized decision-support tools that will assist physicians to offer evidence-informed and personalized diabetes management and behaviour-change strategies; 2) Engagement of patients in their diabetes care by generating a diabetes self-management program that takes into account their preferences, challenges and needs; 3) Empowering patients to self-manage their condition by providing them with personalized educational and motivational messages through a mobile self-management application. The theoretical foundation of our research is grounded in behaviour-change models and healthcare knowledge management.We used 1) knowledge modelling to computerize the paper-based CDA CPGs and behaviour-change models, in particular, the behaviour-change strategy elements of A) readiness-to-change assessments; B) motivation-enhancement interventions categorized along the lines of patients' being ready, ambivalent or not ready; and C) self-efficacy enhancement. The CDA CPGs and the behaviour-change models are modelled and computerized in terms of A) a diabetes management ontology that serves as the knowledge resource for all the services offered by D-WISE; B) decision support services that use logic-based reasoning algorithms to utilize the knowledge encoded within the diabetes management ontology to assist physicians by recommending patient-specific diabetes-management interventions and behaviour-change strategies; C) a mobile diabetes self-management application to engage and educate diabetes patients to self-manage their condition in a home-based setting while working in concert with their family physicians.ResultsWe have been successful in creating and conducting a usability assessment of the physician decision support tool. These results will be published once the patient self- management application has been evaluated.ConclusionsD-WISE will be evaluated through pilot studies measuring 1) the usability of the e-Health interventions; and 2) the impact of the interventions on patients' behaviour changes and diabetes control

Proceedings of the Tenth International Workshop on Health Text Mining and Information Analysis (LOUHI 2019)

International audienc

High Throughput Neurological Phenotyping with MetaMap

The phenotyping of neurological patients involves the conversion of signs and symptoms into machine readable codes selected from an appropriate ontology. The phenotyping of neurological patients is manual and laborious. MetaMap is used for high throughput mapping of the medical literature to concepts in the Unified Medical Language System Metathesaurus (UMLS). MetaMap was evaluated as a tool for the high throughput phenotyping of neurological patients. Based on 15 patient histories from electronic health records, 30 patient histories from neurology textbooks, and 20 clinical summaries from the Online Mendelian Inheritance in Man repository, MetaMap showed a recall of 61-89%, a precision of 84-93%, and an accuracy of 56-84% for the identification of phenotype concepts. The most common cause of false negatives (failure to recognize a phenotype concept) was an inability of MetaMap to find concepts that were represented as a description or a definition of the concept. The most common cause of false positives (incorrect identification of a concept in the text) was a failure to recognize that a concept was negated. MetaMap shows potential for high throughput phenotyping of neurological patients if the problems of false negatives and false positives can be solved

Automating the Calibration of a Neonatal Condition Monitoring System

Abstract. Condition monitoring of premature babies in intensive care can be carried out using a Factorial Switching Linear Dynamical System (FSLDS) [15]. A crucial part of training the FSLDS is the manual calibration stage, where an interval of normality must be identified for each baby that is monitored. In this paper we replace this manual step by using a classifier to predict whether an interval is normal or not. We show that the monitoring results obtained using automated calibration are almost as good as those using manual calibration

Interpreting streaming biosignals:in search of best approaches to augmenting mobile health monitoring with machine learning for adaptive clinical decision support

We investigate Body Area Networks for ambulant patient monitoring. As well as sensing physiological parameters, BAN applications may provide feedback to patients. Automating formulation of feedback requires realtime analysis and interpretation of streaming biosignals and other context and knowledge sources. We illustrate with two prototype applications: the first is designed to detect epileptic seizures and support appropriate intervention. The second is a decision support application aiding weight management; the goal is to promote health and prevent chronic illnesses associated with overweight/obesity. We begin to explore extending these and other m-health applications with generic AI-based decision support and machine learning. Monitoring success of different behavioural change strategies could provide a basis for machine learning, enabling adaptive clinical decision support by personalising and adapting strategies to individuals and their changing needs. Data mining applied to BAN data aggregated from large numbers of patients opens up possibilities for discovery of new clinical knowledge