Published on in Vol 7 , No 3 (2019) :Jul-Sep

Fine-Tuning Bidirectional Encoder Representations From Transformers (BERT)–Based Models on Large-Scale Electronic Health Record Notes: An Empirical Study

Fine-Tuning Bidirectional Encoder Representations From Transformers (BERT)–Based Models on Large-Scale Electronic Health Record Notes: An Empirical Study

Fine-Tuning Bidirectional Encoder Representations From Transformers (BERT)–Based Models on Large-Scale Electronic Health Record Notes: An Empirical Study

Journals

  1. Xu D, Gopale M, Zhang J, Brown K, Begoli E, Bethard S. Unified Medical Language System resources improve sieve-based generation and Bidirectional Encoder Representations from Transformers (BERT)–based ranking for concept normalization. Journal of the American Medical Informatics Association 2020;27(10):1510 View
  2. Park B, Afzal M, Hussain J, Abbas A, Lee S. Automatic Identification of High Impact Relevant Articles to Support Clinical Decision Making Using Attention-Based Deep Learning. Electronics 2020;9(9):1364 View
  3. Li L, Wang P, Yan J, Wang Y, Li S, Jiang J, Sun Z, Tang B, Chang T, Wang S, Liu Y. Real-world data medical knowledge graph: construction and applications. Artificial Intelligence in Medicine 2020;103:101817 View
  4. Colicchio T, Dissanayake P, Cimino J. Formal representation of patients’ care context data: the path to improving the electronic health record. Journal of the American Medical Informatics Association 2020;27(11):1648 View
  5. Kang H, Li J, Wu M, Shen L, Hou L. Building a Pharmacogenomics Knowledge Model Toward Precision Medicine: Case Study in Melanoma. JMIR Medical Informatics 2020;8(10):e20291 View
  6. Jim H, Hoogland A, Brownstein N, Barata A, Dicker A, Knoop H, Gonzalez B, Perkins R, Rollison D, Gilbert S, Nanda R, Berglund A, Mitchell R, Johnstone P. Innovations in research and clinical care using patient‐generated health data. CA: A Cancer Journal for Clinicians 2020;70(3):182 View
  7. Kersloot M, van Putten F, Abu-Hanna A, Cornet R, Arts D. Natural language processing algorithms for mapping clinical text fragments onto ontology concepts: a systematic review and recommendations for future studies. Journal of Biomedical Semantics 2020;11(1) View
  8. Qin Q, Zhao S, Liu C, Hassanien A. A BERT-BiGRU-CRF Model for Entity Recognition of Chinese Electronic Medical Records. Complexity 2021;2021:1 View
  9. Tahayori B, Chini‐Foroush N, Akhlaghi H. Advanced natural language processing technique to predict patient disposition based on emergency triage notes. Emergency Medicine Australasia 2021;33(3):480 View
  10. Kim Y, Lee J, Choi S, Lee J, Kim J, Seok J, Joo H. Validation of deep learning natural language processing algorithm for keyword extraction from pathology reports in electronic health records. Scientific Reports 2020;10(1) View
  11. Ji Y, Zhou Z, Liu H, Davuluri R, Kelso J. DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome. Bioinformatics 2021;37(15):2112 View
  12. Lu Z, Wang J, Li X. Revealing Opinions for COVID-19 Questions Using a Context Retriever, Opinion Aggregator, and Question-Answering Model: Model Development Study. Journal of Medical Internet Research 2021;23(3):e22860 View
  13. Lee H, Kang J, Yeo J. Medical Specialty Recommendations by an Artificial Intelligence Chatbot on a Smartphone: Development and Deployment. Journal of Medical Internet Research 2021;23(5):e27460 View
  14. Mitra A, Rawat B, McManus D, Yu H. Relation Classification for Bleeding Events From Electronic Health Records Using Deep Learning Systems: An Empirical Study. JMIR Medical Informatics 2021;9(7):e27527 View
  15. Emmert-Streib F. Grand Challenges for Artificial Intelligence in Molecular Medicine. Frontiers in Molecular Medicine 2021;1 View
  16. Percha B. Modern Clinical Text Mining: A Guide and Review. Annual Review of Biomedical Data Science 2021;4(1):165 View
  17. Miftahutdinov Z, Kadurin A, Kudrin R, Tutubalina E, Wren J. Medical concept normalization in clinical trials with drug and disease representation learning. Bioinformatics 2021;37(21):3856 View
  18. Kumar V, Reforgiato Recupero D, Helaoui R, Riboni D. K-LM: Knowledge Augmenting in Language Models Within the Scholarly Domain. IEEE Access 2022;10:91802 View
  19. Tamine L, Goeuriot L. Semantic Information Retrieval on Medical Texts. ACM Computing Surveys 2022;54(7):1 View
  20. Krishnan R, Rajpurkar P, Topol E. Self-supervised learning in medicine and healthcare. Nature Biomedical Engineering 2022;6(12):1346 View
  21. Mitchell J, Szepietowski P, Howard R, Reisman P, Jones J, Lewis P, Fridley B, Rollison D. A Question-and-Answer System to Extract Data From Free-Text Oncological Pathology Reports (CancerBERT Network): Development Study. Journal of Medical Internet Research 2022;24(3):e27210 View
  22. Caskey J, McConnell I, Oguss M, Dligach D, Kulikoff R, Grogan B, Gibson C, Wimmer E, DeSalvo T, Nyakoe-Nyasani E, Churpek M, Afshar M. Identifying COVID-19 Outbreaks From Contact-Tracing Interview Forms for Public Health Departments: Development of a Natural Language Processing Pipeline. JMIR Public Health and Surveillance 2022;8(3):e36119 View
  23. Nair L, Shivani M, Jo Cheriyan S. Enabling Remote School Education using Knowledge Graphs and Deep Learning Techniques. Procedia Computer Science 2022;215:618 View
  24. Park W, Siddiqui I, Chakraborty C, Qureshi N, Shin D. Scarcity-aware spam detection technique for big data ecosystem. Pattern Recognition Letters 2022;157:67 View
  25. Guo S, Yang W, Han L, Song X, Wang G. A multi-layer soft lattice based model for Chinese clinical named entity recognition. BMC Medical Informatics and Decision Making 2022;22(1) View
  26. Kariampuzha W, Alyea G, Qu S, Sanjak J, Mathé E, Sid E, Chatelaine H, Yadaw A, Xu Y, Zhu Q. Precision information extraction for rare disease epidemiology at scale. Journal of Translational Medicine 2023;21(1) View
  27. Kanaparthi V. Examining Natural Language Processing Techniques in the Education and Healthcare Fields. International Journal of Engineering and Advanced Technology 2022;12(2):8 View
  28. Li L, Zhai Y, Gao J, Wang L, Hou L, Zhao J. Stacking-BERT model for Chinese medical procedure entity normalization. Mathematical Biosciences and Engineering 2022;20(1):1018 View
  29. Kawazoe Y, Shimamoto K, Shibata D, Shinohara E, Kawaguchi H, Yamamoto T. Impact of a Clinical Text–Based Fall Prediction Model on Preventing Extended Hospital Stays for Elderly Inpatients: Model Development and Performance Evaluation. JMIR Medical Informatics 2022;10(7):e37913 View
  30. Brisk R, Bond R, Finlay D, McLaughlin J, Piadlo A, McEneaney D. WaSP-ECG: A Wave Segmentation Pretraining Toolkit for Electrocardiogram Analysis. Frontiers in Physiology 2022;13 View
  31. Olthof A, van Ooijen P, Cornelissen L. Deep Learning-Based Natural Language Processing in Radiology: The Impact of Report Complexity, Disease Prevalence, Dataset Size, and Algorithm Type on Model Performance. Journal of Medical Systems 2021;45(10) View
  32. Wan C, Ge X, Wang J, Zhang X, Yu Y, Hu J, Liu Y, Ma H. Identification and Impact Analysis of Family History of Psychiatric Disorder in Mood Disorder Patients With Pretrained Language Model. Frontiers in Psychiatry 2022;13 View
  33. Wang K, Wang Z, Usman M. Deep Learning Models and Social Governance Guided by Fair Policies. Scientific Programming 2022;2022:1 View
  34. Nassiri K, Akhloufi M. Transformer models used for text-based question answering systems. Applied Intelligence 2022 View
  35. Li I, Pan J, Goldwasser J, Verma N, Wong W, Nuzumlalı M, Rosand B, Li Y, Zhang M, Chang D, Taylor R, Krumholz H, Radev D. Neural Natural Language Processing for unstructured data in electronic health records: A review. Computer Science Review 2022;46:100511 View
  36. Segura-Bedmar I, Camino-Perdones D, Guerrero-Aspizua S. Exploring deep learning methods for recognizing rare diseases and their clinical manifestations from texts. BMC Bioinformatics 2022;23(1) View
  37. Piao C, Lv M, Wang S, Zhou R, Wang Y, Wei J, Liu J. Multi-objective data enhancement for deep learning-based ultrasound analysis. BMC Bioinformatics 2022;23(1) View
  38. Colicchio T, Liang W, Dissanayake P, Do Rosario C, Cimino J. Physicians' perceptions about a semantically integrated display for chart review: A Multi-Specialty survey. International Journal of Medical Informatics 2022;163:104788 View
  39. Bannour N, Wajsbürt P, Rance B, Tannier X, Névéol A. Privacy-preserving mimic models for clinical named entity recognition in French. Journal of Biomedical Informatics 2022;130:104073 View
  40. Frei J, Soto-Rey I, Kramer F, Banerjee I. DrNote: An open medical annotation service. PLOS Digital Health 2022;1(8):e0000086 View
  41. Richter-Pechanski P, Geis N, Kiriakou C, Schwab D, Dieterich C. Automatic extraction of 12 cardiovascular concepts from German discharge letters using pre-trained language models. DIGITAL HEALTH 2021;7:205520762110576 View
  42. Lin C, Hsu K, Liang C, Lee T, Liou C, Lee J, Peng T, Shih C, Fann Y. A disease-specific language representation model for cerebrovascular disease research. Computer Methods and Programs in Biomedicine 2021;211:106446 View
  43. Vyas S, Shabaz M, Pandit P, Parvathy L, Ofori I, AL-Farga A. Integration of Artificial Intelligence and Blockchain Technology in Healthcare and Agriculture. Journal of Food Quality 2022;2022:1 View
  44. Khurshid S, Reeder C, Harrington L, Singh P, Sarma G, Friedman S, Di Achille P, Diamant N, Cunningham J, Turner A, Lau E, Haimovich J, Al-Alusi M, Wang X, Klarqvist M, Ashburner J, Diedrich C, Ghadessi M, Mielke J, Eilken H, McElhinney A, Derix A, Atlas S, Ellinor P, Philippakis A, Anderson C, Ho J, Batra P, Lubitz S. Cohort design and natural language processing to reduce bias in electronic health records research. npj Digital Medicine 2022;5(1) View
  45. Li S, Hickey G, Lander M, Kanwar M. Artificial Intelligence and Mechanical Circulatory Support. Heart Failure Clinics 2022;18(2):301 View
  46. Frei J, Kramer F. German Medical Named Entity Recognition Model and Data Set Creation Using Machine Translation and Word Alignment: Algorithm Development and Validation. JMIR Formative Research 2023;7:e39077 View
  47. López-García G, Jerez J, Ribelles N, Alba E, Veredas F. Explainable clinical coding with in-domain adapted transformers. Journal of Biomedical Informatics 2023;139:104323 View
  48. Roitero K, Portelli B, Popescu M, Mea V. DiLBERT: Cheap Embeddings for Disease Related Medical NLP. IEEE Access 2021;9:159714 View
  49. Shoeibi A, Moridian P, Khodatars M, Ghassemi N, Jafari M, Alizadehsani R, Kong Y, Gorriz J, Ramírez J, Khosravi A, Nahavandi S, Acharya U. An overview of deep learning techniques for epileptic seizures detection and prediction based on neuroimaging modalities: Methods, challenges, and future works. Computers in Biology and Medicine 2022;149:106053 View
  50. Zhang A, Xing L, Zou J, Wu J. Shifting machine learning for healthcare from development to deployment and from models to data. Nature Biomedical Engineering 2022;6(12):1330 View
  51. Alzubi R, Alzoubi H, Katsigiannis S, West D, Ramzan N. Automated Detection of Substance-Use Status and Related Information from Clinical Text. Sensors 2022;22(24):9609 View
  52. Wu X, Duan J, Pan Y, Li M. Medical Knowledge Graph: Data Sources, Construction, Reasoning, and Applications. Big Data Mining and Analytics 2023;6(2):201 View
  53. Park C, Yi P, Al Yousif H, Wang K. Machine vs. Radiologist-Based Translations of RadLex: Implications for Multi-language Report Interoperability. Journal of Digital Imaging 2022;35(3):660 View
  54. Jupin-Delevaux É, Djahnine A, Talbot F, Richard A, Gouttard S, Mansuy A, Douek P, Si-Mohamed S, Boussel L. BERT-based natural language processing analysis of French CT reports: Application to the measurement of the positivity rate for pulmonary embolism. Research in Diagnostic and Interventional Imaging 2023;6:100027 View

Books/Policy Documents

  1. Blinov P, Avetisian M, Kokh V, Umerenkov D, Tuzhilin A. Artificial Intelligence in Medicine. View
  2. Zhu R, Tu X, Huang J. Data Analytics in Biomedical Engineering and Healthcare. View
  3. Lin H, Yang L, Wang P. Trends and Applications in Information Systems and Technologies. View
  4. Jia G, Zhu W, Tang J, Zhang W. HCI in Business, Government and Organizations. View