Automatic Adverse Drug Reaction Extraction from Electronic Health Records

Patients' electronic health records convey crucial information. The application of natural language processing techniques to these records may be an effective means of extracting information that may improve clinical decision making, clinical documentation and billing, disease prediction and the detection of adverse drug reactions. Adverse drug reactions are a major health problem, resulting in hospital re-admissions and even the death of thousands of patients. An automatic detection system can highlight said reactions in a document, summarise them and automatically report them.

In this context, the Basurto University Hospital and the Galdakao Hospital 'were interested in creating a system that would use natural language processing techniques to analyse patient health records in order to automatically identify any adverse effects' explains the engineer Sara Santiso, who also holds a PhD in Computer Science. After the hospitals contacted the IXA group at the UPV/EHU, several researchers started working to build a robust model with which to extract adverse drug reactions from electronic health records written in Spanish, based on clinical text mining.

To this end 'not only have we used techniques based on traditional machine learning algorithms, we have also explored deep learning techniques, reaching the conclusion that these are better able to detect adverse reactions' explains Santiso, one of the authors of the study. Machine learning and deep learning imitate the way the human brain learns, although they use different types of algorithms to do so.

Difficulties finding a corpus in Spanish

Santiso underscores the difficulties the team encountered when trying to find a large enough corpus with which to work: 'At first, we started with only a few health records, because they are difficult to obtain due to privacy issues; you have to sign confidentiality agreements in order to work with them' she explains. The research team has found that 'having a larger corpus helps the system learn the examples contained in it more effectively, thereby giving rise to better results'.

Through this study, which was carried out with health records written in Spanish, 'we are contributing to closing the gap between clinical text mining in English and that carried out in other languages, which accounts for less than 5% of all papers published in the field. Indeed, the extraction of clinical information is not yet fully developed due (among other things) to the potential for extracting information from other hospitals and in other languages' claims the researcher.

Although natural language processing has been of inestimable help in the computer-aided detection of adverse drug reactions, there is still room for improvement: 'To date, systems have tended to focus on detecting drug-disease pairs located in the same sentence.

However, health records contain implicit information that might reveal underlying relations (for example, information about antecedents might be relevant for determining the causes of an adverse event). In other words, future research should strive to detect both explicitly and implicitly-stated inter-sentence relationships'. Moreover, another issue that should be the subject of future research is the lack of electronic health records written in Spanish.

Sara Santiso, Alicia Pérez, Arantza Casillas.
Adverse Drug Reaction extraction: Tolerance to entity recognition errors and sub-domain variants.
Computer Methods and Programs in Biomedicine, Volume 199, 2021. doi: 10.1016/j.cmpb.2020.105891

Most Popular Now

FDA Authorizes Software that Can Help Id…

Today, the U.S. Food and Drug Administration authorized marketing of software to assist medical professionals who examine body tissues (pathologists) in the detection of areas that are suspicious for cancer...

Orion Health Supports Professional Recor…

Orion Health is supporting the Professional Record Standards Body's partnership scheme by applying to become a 'quality partner'. The company, which is one of the UK’s leading providers of shared care...

Roche Opens Access to Pathology Imaging …

Roche (SIX: RO, ROG; OTCQX: RHHBY) announced the introduction of the Roche Digital Pathology Open Environment that allows software developers to easily integrate their image analysis tools for tumour tissue...

App Launched in Multiple Languages to He…

An app is being launched to help patients with long term conditions manage their health via care plans accessed on their phone. Unity, by mobile health provider, Health Fabric, will...

Northumbria Healthcare Picks CliniSys to…

Pathologists at one of England's most innovative trusts have chosen the CliniSys laboratory information system (LIMS) as part of a digital strategy to support its drive to continually improve patient...

A Computer Algorithm Called 'Eva' May Ha…

A prescriptive computer program developed by the USC Marshall School of Business and Wharton School of Business of the University of Pennsylvania for Greece to identify asymptomatic, infected travelers...

Contact-Tracing Apps could Improve Vacci…

Mathematical modeling of disease spread suggests that herd immunity could be achieved with fewer vaccine doses by using Bluetooth-based contact-tracing apps to identify people who have more exposure to others...

University of Oxford and Oracle Cloud Sy…

The fast spread of the highly infectious Delta variant underscores the need for faster identification of COVID-19 mutations. Uniting governments and medical communities in this challenge, the University of Oxford...

Study Finds Telemedicine Appointments Re…

Telemedicine appointments combined with in-person visits significantly reduced the risk of further illness for children with medically complex cases, according to results of a new study by researchers with The...

AI Tool Improves Accuracy of Breast Canc…

A computer program trained to see patterns among thousands of breast ultrasound images can aid physicians in accurately diagnosing breast cancer, a new study shows. When tested separately on 44,755 already...

Using Internet in Retirement Boosts Cogn…

Using the internet during your retirement years can boost your cognitive function, a new study has found. Researchers from Lancaster University Management School, the Norwegian University Science and Technology and...

FDA Clears First Major Imaging Device Ad…

Today, the U.S. Food and Drug Administration cleared the first new major technological improvement for Computed Tomography (CT) imaging in nearly a decade. "Computed tomography is an important medical imaging tool...