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Detecting Adverse Drug Events with Multiple Representations of Clinical Measurements
Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
2014 (English)In: 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM): Proceedings, IEEE Computer Society, 2014, 536-543 p.Conference paper, Published paper (Refereed)
Abstract [en]

Adverse drug events (ADEs) are grossly under-reported in electronic health records (EHRs). This could be mitigated by methods that are able to detect ADEs in EHRs, thereby allowing for missing ADE-specific diagnosis codes to be identified and added. A crucial aspect of constructing such systems is to find proper representations of the data in order to allow the predictive modeling to be as accurate as possible. One category of EHR data that can be used as indicators of ADEs are clinical measurements. However, using clinical measurements as features is not unproblematic due to the high rate of missing values and they can be repeated a variable number of times in each patient health record. In this study, five basic representations of clinical measurements are proposed and evaluated to handle these two problems. An empirical investigation using random forest on 27 datasets from a real EHR database with different ADE targets is presented, demonstrating that the predictive performance, in terms of accuracy and area under ROC curve, is higher when representing clinical measurements crudely as whether they were taken or how many times they were taken by a patient. Furthermore, a sixth alternative, combining all five basic representations, significantly outperforms using any of the basic representation except for one. A subsequent analysis of variable importance is also conducted with this fused feature set, showing that when clinical measurements have a high missing rate, the number of times they were taken by one patient is ranked as more informative than looking at their actual values. The observation from random forest is also confirmed empirically using other commonly employed classifiers. This study demonstrates that the way in which clinical measurements from EHRs are presented has a high impact for ADE detection, and that using multiple representations outperforms using a basic representation.

Place, publisher, year, edition, pages
IEEE Computer Society, 2014. 536-543 p.
National Category
Information Systems
Research subject
Computer and Systems Sciences
Identifiers
URN: urn:nbn:se:su:diva-110970DOI: 10.1109/BIBM.2014.6999216ISBN: 978-1-4799-5669-2 (electronic)OAI: oai:DiVA.org:su-110970DiVA: diva2:773744
Conference
Bioinformatics and Biomedicine (BIBM), 2014 IEEE International Conference, Belfast, UK, 2-5 November, 2014
Available from: 2014-12-19 Created: 2014-12-19 Last updated: 2017-01-30Bibliographically approved
In thesis
1. Learning Predictive Models from Electronic Health Records
Open this publication in new window or tab >>Learning Predictive Models from Electronic Health Records
2017 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The ongoing digitization of healthcare, which has been much accelerated by the widespread adoption of electronic health records, generates unprecedented amounts of clinical data in a readily computable form. This, in turn, affords great opportunities for making meaningful secondary use of clinical data in the endeavor to improve healthcare, as well as to support epidemiology and medical research. To that end, there is a need for techniques capable of effectively and efficiently analyzing large amounts of clinical data. While machine learning provides the necessary tools, learning effective predictive models from electronic health records comes with many challenges due to the complexity of the data. Electronic health records contain heterogeneous and longitudinal data that jointly provides a rich perspective of patient trajectories in the healthcare process. The diverse characteristics of the data need to be properly accounted for when learning predictive models from clinical data. However, how best to represent healthcare data for predictive modeling has been insufficiently studied. This thesis addresses several of the technical challenges involved in learning effective predictive models from electronic health records.

Methods are developed to address the challenges of (i) representing heterogeneous types of data, (ii) leveraging the concept hierarchy of clinical codes, and (iii) modeling the temporality of clinical events. The proposed methods are evaluated empirically in the context of detecting adverse drug events in electronic health records. Various representations of each type of data that account for its unique characteristics are investigated and it is shown that combining multiple representations yields improved predictive performance. It is also demonstrated how the information embedded in the concept hierarchy of clinical codes can be exploited, both for creating enriched feature spaces and for decomposing the predictive task. Moreover, incorporating temporal information leads to more effective predictive models by distinguishing between event occurrences in the patient history. Both single-point representations, using pre-assigned or learned temporal weights, and multivariate time series representations are shown to be more informative than representations in which temporality is ignored. Effective methods for representing heterogeneous and longitudinal data are key for enhancing and truly enabling meaningful secondary use of electronic health records through large-scale analysis of clinical data.

Place, publisher, year, edition, pages
Stockholm: Department of Computer and Systems Sciences, Stockholm University, 2017. 82 p.
Series
Report Series / Department of Computer & Systems Sciences, ISSN 1101-8526 ; 17-001
Keyword
Data Science, Machine Learning, Predictive Modeling, Data Representation, Health Informatics, Electronic Health Records
National Category
Computer Science
Research subject
Computer and Systems Sciences
Identifiers
urn:nbn:se:su:diva-137936 (URN)978-91-7649-682-4 (ISBN)978-91-7649-683-1 (ISBN)
Public defence
2017-03-02, Lilla hörsalen, NOD-huset, Borgarfjordsgatan 12, Kista, 13:00 (English)
Opponent
Supervisors
Available from: 2017-02-07 Created: 2017-01-13 Last updated: 2017-02-08Bibliographically approved

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