Systematic Comparative Analysis of Large Pretrained Language Models on Contextualized Medication Event Extraction
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arXiv
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| Format: | Preprint |
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2025
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| _version_ | 1866911175380303872 |
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| author | Abdul-Quddoos, Tariq Dong, Xishuang Qian, Lijun |
| author_facet | Abdul-Quddoos, Tariq Dong, Xishuang Qian, Lijun |
| contents | Attention-based models have become the leading approach in modeling medical language for Natural Language Processing (NLP) in clinical notes. These models outperform traditional techniques by effectively capturing contextual representations of language. In this research a comparative analysis is done amongst pre-trained attention based models namely Bert Base, BioBert, two variations of Bio+Clinical Bert, RoBerta, and Clinical Longformer on task related to Electronic Health Record (EHR) information extraction. The tasks from Track 1 of Harvard Medical School's 2022 National Clinical NLP Challenges (n2c2) are considered for this comparison, with the Contextualized Medication Event Dataset (CMED) given for these task. CMED is a dataset of unstructured EHRs and annotated notes that contain task relevant information about the EHRs. The goal of the challenge is to develop effective solutions for extracting contextual information related to patient medication events from EHRs using data driven methods. Each pre-trained model is fine-tuned and applied on CMED to perform medication extraction, medical event detection, and multi-dimensional medication event context classification. Processing methods are also detailed for breaking down EHRs for compatibility with the applied models. Performance analysis has been carried out using a script based on constructing medical terms from the evaluation portion of CMED with metrics including recall, precision, and F1-Score. The results demonstrate that models pre-trained on clinical data are more effective in detecting medication and medication events, but Bert Base, pre-trained on general domain data showed to be the most effective for classifying the context of events related to medications. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2509_19224 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Systematic Comparative Analysis of Large Pretrained Language Models on Contextualized Medication Event Extraction Abdul-Quddoos, Tariq Dong, Xishuang Qian, Lijun Computation and Language Artificial Intelligence Attention-based models have become the leading approach in modeling medical language for Natural Language Processing (NLP) in clinical notes. These models outperform traditional techniques by effectively capturing contextual representations of language. In this research a comparative analysis is done amongst pre-trained attention based models namely Bert Base, BioBert, two variations of Bio+Clinical Bert, RoBerta, and Clinical Longformer on task related to Electronic Health Record (EHR) information extraction. The tasks from Track 1 of Harvard Medical School's 2022 National Clinical NLP Challenges (n2c2) are considered for this comparison, with the Contextualized Medication Event Dataset (CMED) given for these task. CMED is a dataset of unstructured EHRs and annotated notes that contain task relevant information about the EHRs. The goal of the challenge is to develop effective solutions for extracting contextual information related to patient medication events from EHRs using data driven methods. Each pre-trained model is fine-tuned and applied on CMED to perform medication extraction, medical event detection, and multi-dimensional medication event context classification. Processing methods are also detailed for breaking down EHRs for compatibility with the applied models. Performance analysis has been carried out using a script based on constructing medical terms from the evaluation portion of CMED with metrics including recall, precision, and F1-Score. The results demonstrate that models pre-trained on clinical data are more effective in detecting medication and medication events, but Bert Base, pre-trained on general domain data showed to be the most effective for classifying the context of events related to medications. |
| title | Systematic Comparative Analysis of Large Pretrained Language Models on Contextualized Medication Event Extraction |
| topic | Computation and Language Artificial Intelligence |
| url | https://arxiv.org/abs/2509.19224 |