ConBERT: A Concatenation of Bidirectional Transformers for Standardization of Operative Reports from Electronic Medical Records
Abstract
:1. Introduction
2. Materials and Methods
2.1. Clinical Data
2.2. Preprocessing
2.3. Methods
2.3.1. Embedding
2.3.2. BERT
2.3.3. Character BERT
2.3.4. Model Aggregation
2.3.5. Training Details
2.3.6. Evaluation
3. Results
3.1. Input Comparison
3.2. Comparison of Pre-Trained Models
3.3. Comparison of Aggregated Models
3.4. Web-Based Application
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Conflicts of Interest
References
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ID | Date | Division | Postoperative Diagnosis | Operative Report (Original) | Operative Report (ICD-9) | Code (ICD-9) |
---|---|---|---|---|---|---|
1 | 6 August 2019 | Hepatobiliary | GB stone | lap. cholecystectomy | Cholecystectomy; laparoscopic | 51.23 |
2 | 21 May 2012 | Colorectal | rectal ca. (AV 4 cm) | ULAR | Resection; rectum, other anterior | 48.63 |
3 | 29 January 2020 | Colorectal | r/o appendiceal cancer | Lap. RHC | Hemicolectomy; right | 45.73 |
Laparoscopy | 54.21 | |||||
4 | 22 June 2018 | Endocrine and Breast | Rt. PTC | THYROIDECTOMY, TOTAL | Thyroidectomy; complete | 06.4 |
central LN dissection | dissection; neck, not otherwise specified, radical | 40.40 | ||||
5 | 19 August 2020 | Transplantation and Vascular | HBV LC with HCC | LDLT | Transplant; liver, other | 50.59 |
Model | Corpus |
---|---|
MedicalBERT [10] | MIMIC-III Clinical note, PMC OA biomedical paper abstract |
UmlsBERT [18] | Intensive Care III (MIMIC-III), MedNLi, i2b2 2006, i2b2 2010, i2b2 2012, i2b2 2014 |
BioBERT [19] | English Wikipedia, BooksCorpus, PubMed Abstracts, PMC Full-text articles |
MedicalCharacterBERT [10] | MIMIC-III Clinical note, PMC OA biomedical paper abstract |
Proposed Model | AP | F1 | AUC | |||
---|---|---|---|---|---|---|
Micro | Macro | Micro | Macro | Micro | Macro | |
Diagnosis | 0.4552 | 0.2347 | 0.4694 | 0.1736 | 0.9710 | 0.9282 |
Operative report | 0.7692 | 0.4574 | 0.7292 | 0.4037 | 0.9889 | 0.9692 |
Operative report + Diagnosis | 0.7647 | 0.4891 | 0.7509 | 0.4382 | 0.9812 | 0.9675 |
Model | AP | F1 | AUC | ||||
---|---|---|---|---|---|---|---|
Micro | Macro | Micro | Macro | Micro | Macro | ||
Single Model | * Base | 0.7854 | 0.5718 | 0.7570 | 0.3210 | 0.9860 | 0.7565 |
Umls | 0.7872 | 0.5815 | 0.7603 | 0.3383 | 0.9863 | 0.7575 | |
Medical | 0.7836 | 0.5786 | 0.7584 | 0.3333 | 0.9854 | 0.7564 | |
Bio | 0.7895 | 0.5815 | 0.7592 | 0.3369 | 0.9863 | 0.7557 | |
* MC | 0.7751 | 0.5445 | 0.7495 | 0.2965 | 0.9853 | 0.7566 | |
Aggregated Model | Medical + * MC | 0.7898 | 0.5891 | 0.7604 | 0.3578 | 0.9867 | 0.7580 |
Umls + * MC | 0.7937 | 0.5959 | 0.7622 | 0.3643 | 0.9876 | 0.7587 | |
Bio + * MC | 0.7922 | 0.5905 | 0.7593 | 0.3637 | 0.9877 | 0.7583 |
ICD-9 Code | F1 | Number of Data in Test Set | ||
---|---|---|---|---|
Umls | Character | |||
Majority labels | 51.23 | 0.9324 | 0.9245 | 628 |
06.4 | 0.9751 | 0.9638 | 264 | |
50.12 | 0.4096 | 0.3871 | 111 | |
Minority labels | 46.43 | 0.7059 | 0.7200 | 27 |
38.03 | 0.7600 | 0.8077 | 23 | |
45.52 | 0.7857 | 0.8148 | 12 | |
39.25 | 0.6000 | 0.6667 | 6 |
Model | AP | F1 | AUC | ||||
---|---|---|---|---|---|---|---|
Micro | Macro | Micro | Macro | Micro | Macro | ||
Proposed Model | Umls + * MC | 0.7672 | 0.4899 | 0.7415 | 0.3975 | 0.9842 | 0.9703 |
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Park, S.; Bong, J.-W.; Park, I.; Lee, H.; Choi, J.; Park, P.; Kim, Y.; Choi, H.-S.; Kang, S. ConBERT: A Concatenation of Bidirectional Transformers for Standardization of Operative Reports from Electronic Medical Records. Appl. Sci. 2022, 12, 11250. https://doi.org/10.3390/app122111250
Park S, Bong J-W, Park I, Lee H, Choi J, Park P, Kim Y, Choi H-S, Kang S. ConBERT: A Concatenation of Bidirectional Transformers for Standardization of Operative Reports from Electronic Medical Records. Applied Sciences. 2022; 12(21):11250. https://doi.org/10.3390/app122111250
Chicago/Turabian StylePark, Sangjee, Jun-Woo Bong, Inseo Park, Hwamin Lee, Jiyoun Choi, Pyoungjae Park, Yoon Kim, Hyun-Soo Choi, and Sanghee Kang. 2022. "ConBERT: A Concatenation of Bidirectional Transformers for Standardization of Operative Reports from Electronic Medical Records" Applied Sciences 12, no. 21: 11250. https://doi.org/10.3390/app122111250
APA StylePark, S., Bong, J.-W., Park, I., Lee, H., Choi, J., Park, P., Kim, Y., Choi, H.-S., & Kang, S. (2022). ConBERT: A Concatenation of Bidirectional Transformers for Standardization of Operative Reports from Electronic Medical Records. Applied Sciences, 12(21), 11250. https://doi.org/10.3390/app122111250