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- Computational text phenotyping is the practice of identifying patients with certain disorders and traits from clinical notes. Rare diseases are challenging to be identified due to few cases available for machine learning and the need for data annotation from domain experts. We propose a method using ontologies and weak supervision, with recent pre-trained contextual representations from Bi-directional Transformers (e.g. BERT). The ontology-driven framework includes two steps: (i) Text-to-UMLS, extracting phenotypes by contextually linking mentions to concepts in Unified Medical Language System (UMLS), with a Named Entity Recognition and Linking (NER+L) tool, SemEHR, and weak supervision with customised rules and contextual mention representation; (ii) UMLS-to-ORDO, matching UMLS concepts to rare diseases in Orphanet Rare Disease Ontology (ORDO). The weakly supervised approach is proposed to learn a phenotype confirmation model to improve Text-to-UMLS linking, without annotated data from domain experts. We evaluated the approach on three clinical datasets, MIMIC-III discharge summaries, MIMIC-III radiology reports, and NHS Tayside brain imaging reports from two institutions in the US and the UK, with annotations. The improvements in the precision were pronounced (by over 30% to 50% absolute score for Text-to-UMLS linking), with almost no loss of recall compared to the existing NER+L tool, SemEHR. Results on radiology reports from MIMIC-III and NHS Tayside were consistent with the discharge summaries. The overall pipeline processing clinical notes can extract rare disease cases, mostly uncaptured in structured data (manually assigned ICD codes). The study provides empirical evidence for the task by applying a weakly supervised NLP pipeline on clinical notes. The proposed weak supervised deep learning approach requires no human annotation except for validation and testing, by leveraging ontologies, NER+L tools, and contextual representations. The study also demonstrates that Natural Language Processing (NLP) can complement traditional ICD-based approaches to better estimate rare diseases in clinical notes. We discuss the usefulness and limitations of the weak supervision approach and propose directions for future studies.
- Artificial intelligence (AI) and natural language processing (NLP) have found a highly promising application in automated clinical coding (ACC), an innovation that will have profound impacts on the clinical coding industry, billing and revenue management, and potentially clinical care itself. Dong et al. recently analyzed the technical challenges of ACC and proposed future directions. Primary challenges for ACC exist at the technological and implementation levels; clinical documents are redundant and complex, code sets like the ICD-10 are rapidly evolving, training sets are not comprehensive of codes, and ACC models have yet to fully capture the logic and rules of coding decisions. Next steps include interdisciplinary collaboration with clinical coders, accessibility and transparency of datasets, and tailoring models to specific use cases.
- Much of the knowledge and information needed for enabling high-quality clinical research is stored in free-text format. Natural language processing (NLP) has been used to extract information from these sources at scale for several decades. This paper aims to present a comprehensive review of clinical NLP for the past 15 years in the UK to identify the community, depict its evolution, analyse methodologies and applications, and identify the main barriers. We collect a dataset of clinical NLP projects (n = 94; £ = 41.97 m) funded by UK funders or the European Union’s funding programmes. Additionally, we extract details on 9 funders, 137 organisations, 139 persons and 431 research papers. Networks are created from timestamped data interlinking all entities, and network analysis is subsequently applied to generate insights. 431 publications are identified as part of a literature review, of which 107 are eligible for final analysis. Results show, not surprisingly, clinical NLP in the UK has increased substantially in the last 15 years: the total budget in the period of 2019–2022 was 80 times that of 2007–2010. However, the effort is required to deepen areas such as disease (sub-)phenotyping and broaden application domains. There is also a need to improve links between academia and industry and enable deployments in real-world settings for the realisation of clinical NLP’s great potential in care delivery. The major barriers include research and development access to hospital data, lack of capable computational resources in the right places, the scarcity of labelled data and barriers to sharing of pretrained models.
- The purpose of these datasets is to support equivalence and subsumption ontology matching. There are five ontology pairs extracted from MONDO and UMLS: Source Ontology Pair Category MONDO OMIM-ORDO Disease MONDO NCIT-DOID Disease UMLS SNOMED-FMA Body UMLS SNOMED-NCIT Pharm UMLS SNOMED-NCIT Neoplas Each pair is associated with three folders: "raw_data", "equiv_match", and "subs_match", corresponding to the downloaded source ontologies, the package for equivalence matching, and the package for subsumption matching. See detailed documentation at: https://krr-oxford.github.io/DeepOnto/#/om_resources. See the incoming OAEI Bio-ML track at: https://www.cs.ox.ac.uk/isg/projects/ConCur/oaei/. See our resource paper at: https://arxiv.org/abs/2205.03447.
- HEALTHCARE TEXT ANALYTICS CONFERENCE 2022
publications (hide)99
- BMC Medical Informatics and Decision Making, 24 (1): 289 (Oct 8, 2024)
- (2024)
- (2023)
- (2023)cite arxiv:2309.17255Comment: 32 pages, 1 figure, accepted for Transactions on Graph Data and Knowledge (TGDK).
- (2023)cite arxiv:2309.07172Comment: Accepted at ISWC 2023 (Posters and Demos).
- (August 2023)
- (August 2023)
- The Semantic Web, page 244--261. Cham, Springer Nature Switzerland, (2023)
- World Wide Web, (May 2, 2023)
- (2023)cite arxiv:2302.06761.
- (2023)cite arxiv:2302.07189.
- npj Digital Medicine, (October 2022)
- The Semantic Web -- ISWC 2022, page 575--591. Cham, Springer International Publishing, (2022)
- (2021)cite arxiv:2109.11406Comment: 39 pages.
- (2022)cite arxiv:2205.05656Comment: 20 pages, 5 figures, submitted to Journal of Biomedical Informatics.
- Proceedings of the 21st Workshop on Biomedical Language Processing, page 389--401. Dublin, Ireland, Association for Computational Linguistics, (May 2022)
- (2022)cite arxiv:2205.03447.
- (2022)cite arxiv:2204.09781.
- (2022)cite arxiv:2203.11092.
- (2022)cite arxiv:2202.09791Comment: Short paper (5 pages).
