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| Main Authors: | , , |
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| Format: | Preprint |
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2024
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| Online Access: | https://arxiv.org/abs/2404.16198 |
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| _version_ | 1866915727347286016 |
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| author | Rahmanian, Mojdeh Fakhrahmad, Seyed Mostafa Mousavi, Seyedeh Zahra |
| author_facet | Rahmanian, Mojdeh Fakhrahmad, Seyed Mostafa Mousavi, Seyedeh Zahra |
| contents | Objective: Clinical trials are essential for advancing pharmaceutical interventions, but they face a bottleneck in selecting eligible participants. Although leveraging electronic health records (EHR) for recruitment has gained popularity, the complex nature of unstructured medical texts presents challenges in efficiently identifying participants. Natural Language Processing (NLP) techniques have emerged as a solution with a recent focus on transformer models. In this study, we aimed to evaluate the performance of a prompt-based large language model for the cohort selection task from unstructured medical notes collected in the EHR. Methods: To process the medical records, we selected the most related sentences of the records to the eligibility criteria needed for the trial. The SNOMED CT concepts related to each eligibility criterion were collected. Medical records were also annotated with MedCAT based on the SNOMED CT ontology. Annotated sentences including concepts matched with the criteria-relevant terms were extracted. A prompt-based large language model (Generative Pre-trained Transformer (GPT) in this study) was then used with the extracted sentences as the training set. To assess its effectiveness, we evaluated the model's performance using the dataset from the 2018 n2c2 challenge, which aimed to classify medical records of 311 patients based on 13 eligibility criteria through NLP techniques. Results: Our proposed model showed the overall micro and macro F measures of 0.9061 and 0.8060 which were among the highest scores achieved by the experiments performed with this dataset. Conclusion: The application of a prompt-based large language model in this study to classify patients based on eligibility criteria received promising scores. Besides, we proposed a method of extractive summarization with the aid of SNOMED CT ontology that can be also applied to other medical texts. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2404_16198 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Towards Efficient Patient Recruitment for Clinical Trials: Application of a Prompt-Based Learning Model Rahmanian, Mojdeh Fakhrahmad, Seyed Mostafa Mousavi, Seyedeh Zahra Computation and Language I.7 Objective: Clinical trials are essential for advancing pharmaceutical interventions, but they face a bottleneck in selecting eligible participants. Although leveraging electronic health records (EHR) for recruitment has gained popularity, the complex nature of unstructured medical texts presents challenges in efficiently identifying participants. Natural Language Processing (NLP) techniques have emerged as a solution with a recent focus on transformer models. In this study, we aimed to evaluate the performance of a prompt-based large language model for the cohort selection task from unstructured medical notes collected in the EHR. Methods: To process the medical records, we selected the most related sentences of the records to the eligibility criteria needed for the trial. The SNOMED CT concepts related to each eligibility criterion were collected. Medical records were also annotated with MedCAT based on the SNOMED CT ontology. Annotated sentences including concepts matched with the criteria-relevant terms were extracted. A prompt-based large language model (Generative Pre-trained Transformer (GPT) in this study) was then used with the extracted sentences as the training set. To assess its effectiveness, we evaluated the model's performance using the dataset from the 2018 n2c2 challenge, which aimed to classify medical records of 311 patients based on 13 eligibility criteria through NLP techniques. Results: Our proposed model showed the overall micro and macro F measures of 0.9061 and 0.8060 which were among the highest scores achieved by the experiments performed with this dataset. Conclusion: The application of a prompt-based large language model in this study to classify patients based on eligibility criteria received promising scores. Besides, we proposed a method of extractive summarization with the aid of SNOMED CT ontology that can be also applied to other medical texts. |
| title | Towards Efficient Patient Recruitment for Clinical Trials: Application of a Prompt-Based Learning Model |
| topic | Computation and Language I.7 |
| url | https://arxiv.org/abs/2404.16198 |