Systematic evaluation of common natural language processing techniques to codify clinical notes.
Proper codification of medical diagnoses and procedures is essential for optimized health care management, quality improvement, research, and reimbursement tasks within large healthcare systems. Assignment of diagnostic or procedure codes is a tedious manual process, often prone to human error. Natu...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2024-01-01
|
| Series: | PLoS ONE |
| Online Access: | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0298892&type=printable |
| _version_ | 1797263535773843456 |
|---|---|
| author | Nazgol Tavabi Mallika Singh James Pruneski Ata M Kiapour |
| author_facet | Nazgol Tavabi Mallika Singh James Pruneski Ata M Kiapour |
| author_sort | Nazgol Tavabi |
| collection | DOAJ |
| description | Proper codification of medical diagnoses and procedures is essential for optimized health care management, quality improvement, research, and reimbursement tasks within large healthcare systems. Assignment of diagnostic or procedure codes is a tedious manual process, often prone to human error. Natural Language Processing (NLP) has been suggested to facilitate this manual codification process. Yet, little is known on best practices to utilize NLP for such applications. With Large Language Models (LLMs) becoming more ubiquitous in daily life, it is critical to remember, not every task requires that level of resource and effort. Here we comprehensively assessed the performance of common NLP techniques to predict current procedural terminology (CPT) from operative notes. CPT codes are commonly used to track surgical procedures and interventions and are the primary means for reimbursement. Our analysis of 100 most common musculoskeletal CPT codes suggest that traditional approaches can outperform more resource intensive approaches like BERT significantly (P-value = 4.4e-17) with average AUROC of 0.96 and accuracy of 0.97, in addition to providing interpretability which can be very helpful and even crucial in the clinical domain. We also proposed a complexity measure to quantify the complexity of a classification task and how this measure could influence the effect of dataset size on model's performance. Finally, we provide preliminary evidence that NLP can help minimize the codification error, including mislabeling due to human error. |
| first_indexed | 2024-04-25T00:14:33Z |
| format | Article |
| id | doaj.art-6ffd10c5216f4bc79c6d425c2950013c |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-25T00:14:33Z |
| publishDate | 2024-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-6ffd10c5216f4bc79c6d425c2950013c2024-03-13T05:31:35ZengPublic Library of Science (PLoS)PLoS ONE1932-62032024-01-01193e029889210.1371/journal.pone.0298892Systematic evaluation of common natural language processing techniques to codify clinical notes.Nazgol TavabiMallika SinghJames PruneskiAta M KiapourProper codification of medical diagnoses and procedures is essential for optimized health care management, quality improvement, research, and reimbursement tasks within large healthcare systems. Assignment of diagnostic or procedure codes is a tedious manual process, often prone to human error. Natural Language Processing (NLP) has been suggested to facilitate this manual codification process. Yet, little is known on best practices to utilize NLP for such applications. With Large Language Models (LLMs) becoming more ubiquitous in daily life, it is critical to remember, not every task requires that level of resource and effort. Here we comprehensively assessed the performance of common NLP techniques to predict current procedural terminology (CPT) from operative notes. CPT codes are commonly used to track surgical procedures and interventions and are the primary means for reimbursement. Our analysis of 100 most common musculoskeletal CPT codes suggest that traditional approaches can outperform more resource intensive approaches like BERT significantly (P-value = 4.4e-17) with average AUROC of 0.96 and accuracy of 0.97, in addition to providing interpretability which can be very helpful and even crucial in the clinical domain. We also proposed a complexity measure to quantify the complexity of a classification task and how this measure could influence the effect of dataset size on model's performance. Finally, we provide preliminary evidence that NLP can help minimize the codification error, including mislabeling due to human error.https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0298892&type=printable |
| spellingShingle | Nazgol Tavabi Mallika Singh James Pruneski Ata M Kiapour Systematic evaluation of common natural language processing techniques to codify clinical notes. PLoS ONE |
| title | Systematic evaluation of common natural language processing techniques to codify clinical notes. |
| title_full | Systematic evaluation of common natural language processing techniques to codify clinical notes. |
| title_fullStr | Systematic evaluation of common natural language processing techniques to codify clinical notes. |
| title_full_unstemmed | Systematic evaluation of common natural language processing techniques to codify clinical notes. |
| title_short | Systematic evaluation of common natural language processing techniques to codify clinical notes. |
| title_sort | systematic evaluation of common natural language processing techniques to codify clinical notes |
| url | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0298892&type=printable |
| work_keys_str_mv | AT nazgoltavabi systematicevaluationofcommonnaturallanguageprocessingtechniquestocodifyclinicalnotes AT mallikasingh systematicevaluationofcommonnaturallanguageprocessingtechniquestocodifyclinicalnotes AT jamespruneski systematicevaluationofcommonnaturallanguageprocessingtechniquestocodifyclinicalnotes AT atamkiapour systematicevaluationofcommonnaturallanguageprocessingtechniquestocodifyclinicalnotes |