William G Dixon

Warren Del-Pinto, George Demetriou, Meghna Jani et al.

Coding of unstructured clinical free-text to produce interoperable structured data is essential to improve direct care, support clinical communication and to enable clinical research.However, manual clinical coding is difficult and time consuming, which motivates the development and use of natural language processing for automated coding. This work evaluates the quality and consistency of both manual and automated clinical coding of diagnoses from hospital outpatient letters. Using 100 randomly selected letters, two human clinicians performed coding of diagnosis lists to SNOMED CT. Automated coding was also performed using IMO's Concept Tagger. A gold standard was constructed by a panel of clinicians from a subset of the annotated diagnoses. This was used to evaluate the quality and consistency of both manual and automated coding via (1) a distance-based metric, treating SNOMED CT as a graph, and (2) a qualitative metric agreed upon by the panel of clinicians. Correlation between the two metrics was also evaluated. Comparing human and computer-generated codes to the gold standard, the results indicate that humans slightly out-performed automated coding, while both performed notably better when there was only a single diagnosis contained in the free-text description. Automated coding was considered acceptable by the panel of clinicians in approximately 90% of cases.

Maksim Belousov, Nikola Milosevic, William Dixon et al.

Adverse drug reactions (ADRs) are unwanted or harmful effects experienced after the administration of a certain drug or a combination of drugs, presenting a challenge for drug development and drug administration. In this paper, we present a set of taggers for extracting adverse drug reactions and related entities, including factors, severity, negations, drug class and animal. The systems used a mix of rule-based, machine learning (CRF) and deep learning (BLSTM with word2vec embeddings) methodologies in order to annotate the data. The systems were submitted to adverse drug reaction shared task, organised during Text Analytics Conference in 2017 by National Institute for Standards and Technology, archiving F1-scores of 76.00 and 75.61 respectively.