Automated Detection of Substance-Use Status and Related Information from Clinical Text

This study aims to develop and evaluate an automated system for extracting information related to patient substance use (smoking, alcohol, and drugs) from unstructured clinical text (medical discharge records). The authors propose a four-stage system for the extraction of the substance-use status and related attributes (type, frequency, amount, quit-time, and period). The first stage uses a keyword search technique to detect sentences related to substance use and to exclude unrelated records. In the second stage, an extension of the NegEx negation detection algorithm is developed and employed for detecting the negated records. The third stage involves identifying the temporal status of the substance use by applying windowing and chunking methodologies. Finally, in the fourth stage, regular expressions, syntactic patterns, and keyword search techniques are used in order to extract the substance-use attributes. The proposed system achieves an F1-score of up to 0.99 for identifying substance-use-related records, 0.98 for detecting the negation status, and 0.94 for identifying temporal status. Moreover, F1-scores of up to 0.98, 0.98, 1.00, 0.92, and 0.98 are achieved for the extraction of the amount, frequency, type, quit-time, and period attributes, respectively. Natural Language Processing (NLP) and rule-based techniques are employed efficiently for extracting substance-use status and attributes, with the proposed system being able to detect substance-use status and attributes over both sentence-level and document-level data. Results show that the proposed system outperforms the compared state-of-the-art substance-use identification system on an unseen dataset, demonstrating its generalisability

Syntactic methods for negation detection in radiology reports in Spanish

Identification of the certainty of events is an important text mining problem. In particular, biomedical texts report medical conditions or findings that might be factual, hedged or negated. Identification of negation and its scope over a term of interest determines whether a finding is reported and is a challenging task. Not much work has been performed for Spanish in this domain. In this work we introduce different algorithms developed to determine if a term of interest is under the scope of negation in radiology reports written in Spanish. The methods include syntactic techniques based in rules derived from PoS tagging patterns, constituent tree patterns and dependency tree patterns, and an adaption of NegEx, a well known rule-based negation detection algorithm (Chapman et al., 2001a). All methods outperform a simple dictionary lookup algorithm developed as baseline. NegEx and the PoS tagging pattern method obtain the best results with 0.92 F1.Peer ReviewedPostprint (published version

Multi-domain clinical natural language processing with MedCAT: The Medical Concept Annotation Toolkit

Electronic health records (EHR) contain large volumes of unstructured text, requiring the application of information extraction (IE) technologies to enable clinical analysis. We present the open source Medical Concept Annotation Toolkit (MedCAT) that provides: (a) a novel self-supervised machine learning algorithm for extracting concepts using any concept vocabulary including UMLS/SNOMED-CT; (b) a feature-rich annotation interface for customizing and training IE models; and (c) integrations to the broader CogStack ecosystem for vendor-agnostic health system deployment. We show improved performance in extracting UMLS concepts from open datasets (F1:0.448-0.738 vs 0.429-0.650). Further real-world validation demonstrates SNOMED-CT extraction at 3 large London hospitals with self-supervised training over ∼8.8B words from ∼17M clinical records and further fine-tuning with ∼6K clinician annotated examples. We show strong transferability (F1 > 0.94) between hospitals, datasets and concept types indicating cross-domain EHR-agnostic utility for accelerated clinical and research use cases