Key publications

Some key recent publications from our research group.

• Davidson EM, Poon MTC, Casey A, Grivas A, Duma D, Dong H, Suárez-Paniagua V, Grover C, Tobin R, Whalley H, Wu H, Alex B, Whiteley W. The reporting quality of natural language processing studies: systematic review of studies of radiology reports. BMC Medical Imaging. 2021 Oct 2;21(1):142. doi: 10.1186/s12880-021-00671-8

• Falis M, Dong H, Birch A, Alex B. CoPHE: A Count-Preserving Hierarchical Evaluation Metric in Large-Scale Multi-Label Text Classification. Accepted for Proceedings of the 2021 Conference on Empirical Methods in Natural Language Processing (EMNLP 2021), Association for Computational Linguistics, 2021 Nov 7-11. p. 1-6. arXiv preprint arXiv:2109.04853

• Dong H, Suárez-Paniagua V, Zhang H, Wang M, Whitfield E, Wu H. Rare Disease Identification from Clinical Notes with Ontologies and Weak Supervision. 2021 43rd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), 2021 Nov 1-5, p. 2294-2298. doi: 10.1109/EMBC46164.2021.9630043. arXiv preprint arXiv:2105.01995

• Suárez-Paniagua V, Casey A. BERT and Approximate String Matching for Automatic Recognition and Normalization of Professions in Spanish Medical Documents. Proceedings of the Iberian Languages Evaluation Forum (IberLEF 2021) co-located with the Conference of the Spanish Society for Natural Language Processing (SEPLN 2021). Málaga, Spain, 2021 Sep. p. 803-813. CEUR Workshop Proceedings. Pre-recorded presentation on Youtube

• Suárez-Paniagua V, Dong H, Casey A. A multi-BERT hybrid system for Named Entity Recognition in Spanish radiology reports. Proceedings of the Working Notes of CLEF 2021 - Conference and Labs of the Evaluation Forum (CLEF 2021). Bucharest, Romania, 2021 Sep 21-24. p. 846-856. CEUR Workshop Proceedings

• Rannikmäe K, Wu H, Tominey S, Whiteley W, Allen N, Sudlow C, and the UK Biobank. Developing automated methods for disease subtyping in UK Biobank: an exemplar study on stroke. BMC Medical Informatics and Decision Making. 2021 Jun 15;21(1):191. doi: 10.1186/s12911-021-01556-0

• Casey A, Davidson EM, Poon MTC, Dong H, Duma D, Grivas A, Grover C, Suárez-Paniagua V, Tobin R, Whiteley W, Wu H, Alex B. A Systematic Review of Natural Language Processing Applied to Radiology Reports. BMC Medical Informatics and Decision Making.  2021 June 3;21(1):179. doi: 10.1186/s12911-021-01533-7. arXiv preprint arXiv:2102.09553

• Dong H, Suárez-Paniagua V, Whiteley W, Wu H. Explainable Automated Coding of Clinical Notes using Hierarchical Label-wise Attention Networks and Label Embedding Initialisation. Journal of Biomedical Informatics. 2021 Mar 9;1-20. doi:10.1016/j.jbi.2021.103728. arXiv preprint arXiv:2010.15728

• Sykes D, Grivas A, Grover C, Tobin R, Sudlow C, Whiteley W, Mcintosh A, Whalley H, Alex B. Comparison of Rule-Based and Neural Network Models for Negation Detection in Radiology Reports. Natural Language Engineering. 2020 Nov 18;1-22. doi: 10.1017/S1351324920000509

• Grivas A, Alex B, Grover C, Tobin R, Whiteley W. Not a cute stroke: Analysis of Rule- and Neural Network-based Information Extraction Systems for Brain Radiology Reports. Proceedings of the 11th International Workshop on Health Text Mining and Information Analysis, Association for Computational Linguistics, 2020 Nov 20. p. 24–37. Anthology ID: 2020.louhi-1.4. Pre-recorded presentation on SlidesLive

• Wheater E, Mair G, Sudlow C, Alex B, Grover C, Whiteley W. A validated natural language processing algorithm for brain imaging phenotypes from radiology reports in UK electronic health records. BMC Medical Informatics and Decision Making. 2019 Dec 1;19(1):184. doi: 10.1186/s12911-019-0908-7

• Kugathasan P, Wu H, Gaughran F, Nielsen RE, Pritchard M, Dobson R, Stewart R, Stubbs B. Association of physical health multimorbidity with mortality in people with schizophrenia spectrum disorders: Using a novel semantic search system that captures physical diseases in electronic patient records. Schizophrenia Research. 2019 Nov 28. doi: 10.1016/j.schres.2019.10.061

• Alex B, Grover C, Tobin R, Sudlow C, Mair G, Whiteley W. Text mining brain imaging reports. Journal of Biomedical Semantics. 2019 Nov 1;10(1):23. doi: 10.1186/s13326-019-0211-7

• Gorinski PJ, Wu H, Grover C, Tobin R, Talbot C, Whalley H, Sudlow C, Whiteley W, Alex B. Named entity recognition for electronic health records: a comparison of rule-based and machine learning approaches, presented at HealTAC 2019 Conference, 2019 April 24-25. arXiv preprint arXiv:1903.03985

• Wu H, Hodgson K, Dyson S, Morley KI, Ibrahim ZM, Iqbal E, Stewart R, Dobson RJ, Sudlow C. Efficient reuse of natural language processing models for phenotype-mention identification in free-text electronic medical records: a phenotype embedding approach. JMIR Medical Informatics. 2019;7(4):e14782. doi: 10.2196/14782

• Bean DM, Teo J, Wu H, Oliveira R, Patel R, Bendayan R, Shah AM, Dobson RJ, Scott PA. Semantic computational analysis of anticoagulation use in atrial fibrillation from real world data. PloS one. 2019;14(11). doi:10.1371/journal.pone.0225625

• Wu H, Toti G, Morley KI, Ibrahim ZM, Folarin A, Jackson R, Kartoglu I, Agrawal A, Stringer C, Gale D, Gorrell G. SemEHR: A general-purpose semantic search system to surface semantic data from clinical notes for tailored care, trial recruitment, and clinical research. Journal of the American Medical Informatics Association. 2018 May;25(5):530-7. doi: 10.1093/jamia/ocx160

• Wu H, Toti G, Morley KI, Ibrahim Z, Folarin A, Kartoglu I, Jackson R, Agrawal A, Stringer C, Gale D, Gorrell GM. SemEHR: surfacing semantic data from clinical notes in electronic health records for tailored care, trial recruitment, and clinical research. The Lancet. 2017 Nov 1;390:S97. doi: 10.1016/S0140-6736(17)33032-5