Yu Deng, Yunzhao Xing, Jason Quach, Xiaotian Chen, Xiaoqiang Wu, Yafei Zhang, Charlotte Moureaud, Mengjia Yu, Yujie Zhao, Li Wang, Sheng Zhong
{"title":"开发大型语言模型,检测 x 上帖子中的药物不良事件。","authors":"Yu Deng, Yunzhao Xing, Jason Quach, Xiaotian Chen, Xiaoqiang Wu, Yafei Zhang, Charlotte Moureaud, Mengjia Yu, Yujie Zhao, Li Wang, Sheng Zhong","doi":"10.1080/10543406.2024.2403442","DOIUrl":null,"url":null,"abstract":"<p><p>Adverse drug events (ADEs) are one of the major causes of hospital admissions and are associated with increased morbidity and mortality. Post-marketing ADE identification is one of the most important phases of drug safety surveillance. Traditionally, data sources for post-marketing surveillance mainly come from spontaneous reporting system such as the Food and Drug Administration Adverse Event Reporting System (FAERS). Social media data such as posts on X (formerly Twitter) contain rich patient and medication information and could potentially accelerate drug surveillance research. However, ADE information in social media data is usually locked in the text, making it difficult to be employed by traditional statistical approaches. In recent years, large language models (LLMs) have shown promise in many natural language processing tasks. In this study, we developed several LLMs to perform ADE classification on X data. We fine-tuned various LLMs including BERT-base, Bio_ClinicalBERT, RoBERTa, and RoBERTa-large. We also experimented ChatGPT few-shot prompting and ChatGPT fine-tuned on the whole training data. We then evaluated the model performance based on sensitivity, specificity, negative predictive value, positive predictive value, accuracy, F1-measure, and area under the ROC curve. Our results showed that RoBERTa-large achieved the best F1-measure (0.8) among all models followed by ChatGPT fine-tuned model with F1-measure of 0.75. Our feature importance analysis based on 1200 random samples and RoBERTa-Large showed the most important features are as follows: \"withdrawals\"/\"withdrawal\", \"dry\", \"dealing\", \"mouth\", and \"paralysis\". The good model performance and clinically relevant features show the potential of LLMs in augmenting ADE detection for post-marketing drug safety surveillance.</p>","PeriodicalId":54870,"journal":{"name":"Journal of Biopharmaceutical Statistics","volume":" ","pages":"1-12"},"PeriodicalIF":1.2000,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Developing large language models to detect adverse drug events in posts on x.\",\"authors\":\"Yu Deng, Yunzhao Xing, Jason Quach, Xiaotian Chen, Xiaoqiang Wu, Yafei Zhang, Charlotte Moureaud, Mengjia Yu, Yujie Zhao, Li Wang, Sheng Zhong\",\"doi\":\"10.1080/10543406.2024.2403442\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Adverse drug events (ADEs) are one of the major causes of hospital admissions and are associated with increased morbidity and mortality. Post-marketing ADE identification is one of the most important phases of drug safety surveillance. Traditionally, data sources for post-marketing surveillance mainly come from spontaneous reporting system such as the Food and Drug Administration Adverse Event Reporting System (FAERS). Social media data such as posts on X (formerly Twitter) contain rich patient and medication information and could potentially accelerate drug surveillance research. However, ADE information in social media data is usually locked in the text, making it difficult to be employed by traditional statistical approaches. In recent years, large language models (LLMs) have shown promise in many natural language processing tasks. In this study, we developed several LLMs to perform ADE classification on X data. We fine-tuned various LLMs including BERT-base, Bio_ClinicalBERT, RoBERTa, and RoBERTa-large. We also experimented ChatGPT few-shot prompting and ChatGPT fine-tuned on the whole training data. We then evaluated the model performance based on sensitivity, specificity, negative predictive value, positive predictive value, accuracy, F1-measure, and area under the ROC curve. Our results showed that RoBERTa-large achieved the best F1-measure (0.8) among all models followed by ChatGPT fine-tuned model with F1-measure of 0.75. Our feature importance analysis based on 1200 random samples and RoBERTa-Large showed the most important features are as follows: \\\"withdrawals\\\"/\\\"withdrawal\\\", \\\"dry\\\", \\\"dealing\\\", \\\"mouth\\\", and \\\"paralysis\\\". The good model performance and clinically relevant features show the potential of LLMs in augmenting ADE detection for post-marketing drug safety surveillance.</p>\",\"PeriodicalId\":54870,\"journal\":{\"name\":\"Journal of Biopharmaceutical Statistics\",\"volume\":\" \",\"pages\":\"1-12\"},\"PeriodicalIF\":1.2000,\"publicationDate\":\"2024-09-20\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Biopharmaceutical Statistics\",\"FirstCategoryId\":\"3\",\"ListUrlMain\":\"https://doi.org/10.1080/10543406.2024.2403442\",\"RegionNum\":4,\"RegionCategory\":\"医学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q4\",\"JCRName\":\"PHARMACOLOGY & PHARMACY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Biopharmaceutical Statistics","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.1080/10543406.2024.2403442","RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"PHARMACOLOGY & PHARMACY","Score":null,"Total":0}
Developing large language models to detect adverse drug events in posts on x.
Adverse drug events (ADEs) are one of the major causes of hospital admissions and are associated with increased morbidity and mortality. Post-marketing ADE identification is one of the most important phases of drug safety surveillance. Traditionally, data sources for post-marketing surveillance mainly come from spontaneous reporting system such as the Food and Drug Administration Adverse Event Reporting System (FAERS). Social media data such as posts on X (formerly Twitter) contain rich patient and medication information and could potentially accelerate drug surveillance research. However, ADE information in social media data is usually locked in the text, making it difficult to be employed by traditional statistical approaches. In recent years, large language models (LLMs) have shown promise in many natural language processing tasks. In this study, we developed several LLMs to perform ADE classification on X data. We fine-tuned various LLMs including BERT-base, Bio_ClinicalBERT, RoBERTa, and RoBERTa-large. We also experimented ChatGPT few-shot prompting and ChatGPT fine-tuned on the whole training data. We then evaluated the model performance based on sensitivity, specificity, negative predictive value, positive predictive value, accuracy, F1-measure, and area under the ROC curve. Our results showed that RoBERTa-large achieved the best F1-measure (0.8) among all models followed by ChatGPT fine-tuned model with F1-measure of 0.75. Our feature importance analysis based on 1200 random samples and RoBERTa-Large showed the most important features are as follows: "withdrawals"/"withdrawal", "dry", "dealing", "mouth", and "paralysis". The good model performance and clinically relevant features show the potential of LLMs in augmenting ADE detection for post-marketing drug safety surveillance.
期刊介绍:
The Journal of Biopharmaceutical Statistics, a rapid publication journal, discusses quality applications of statistics in biopharmaceutical research and development. Now publishing six times per year, it includes expositions of statistical methodology with immediate applicability to biopharmaceutical research in the form of full-length and short manuscripts, review articles, selected/invited conference papers, short articles, and letters to the editor. Addressing timely and provocative topics important to the biostatistical profession, the journal covers:
Drug, device, and biological research and development;
Drug screening and drug design;
Assessment of pharmacological activity;
Pharmaceutical formulation and scale-up;
Preclinical safety assessment;
Bioavailability, bioequivalence, and pharmacokinetics;
Phase, I, II, and III clinical development including complex innovative designs;
Premarket approval assessment of clinical safety;
Postmarketing surveillance;
Big data and artificial intelligence and applications.