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Jianfu Li Yujia Zhou Xiaoqian Jiang Karthik Natarajan Serguei Vs Pakhomov Hongfang Liu Hua Xu 《J Am Med Inform Assoc》2021,28(10):2193
Objective: Developing clinical natural language processing systems often requires access to many clinical documents, which are not widely available to the public due to privacy and security concerns. To address this challenge, we propose to develop methods to generate synthetic clinical notes and evaluate their utility in real clinical natural language processing tasks.Materials and Methods: We implemented 4 state-of-the-art text generation models, namely CharRNN, SegGAN, GPT-2, and CTRL, to generate clinical text for the History and Present Illness section. We then manually annotated clinical entities for randomly selected 500 History and Present Illness notes generated from the best-performing algorithm. To compare the utility of natural and synthetic corpora, we trained named entity recognition (NER) models from all 3 corpora and evaluated their performance on 2 independent natural corpora.Results: Our evaluation shows GPT-2 achieved the best BLEU (bilingual evaluation understudy) score (with a BLEU-2 of 0.92). NER models trained on synthetic corpus generated by GPT-2 showed slightly better performance on 2 independent corpora: strict F1 scores of 0.709 and 0.748, respectively, when compared with the NER models trained on natural corpus (F1 scores of 0.706 and 0.737, respectively), indicating the good utility of synthetic corpora in clinical NER model development. In addition, we also demonstrated that an augmented method that combines both natural and synthetic corpora achieved better performance than that uses the natural corpus only.Conclusions: Recent advances in text generation have made it possible to generate synthetic clinical notes that could be useful for training NER models for information extraction from natural clinical notes, thus lowering the privacy concern and increasing data availability. Further investigation is needed to apply this technology to practice. 相似文献
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ObjectiveThe goal of this study is to explore transformer-based models (eg, Bidirectional Encoder Representations from Transformers [BERT]) for clinical concept extraction and develop an open-source package with pretrained clinical models to facilitate concept extraction and other downstream natural language processing (NLP) tasks in the medical domain.MethodsWe systematically explored 4 widely used transformer-based architectures, including BERT, RoBERTa, ALBERT, and ELECTRA, for extracting various types of clinical concepts using 3 public datasets from the 2010 and 2012 i2b2 challenges and the 2018 n2c2 challenge. We examined general transformer models pretrained using general English corpora as well as clinical transformer models pretrained using a clinical corpus and compared them with a long short-term memory conditional random fields (LSTM-CRFs) mode as a baseline. Furthermore, we integrated the 4 clinical transformer-based models into an open-source package.Results and ConclusionThe RoBERTa-MIMIC model achieved state-of-the-art performance on 3 public clinical concept extraction datasets with F1-scores of 0.8994, 0.8053, and 0.8907, respectively. Compared to the baseline LSTM-CRFs model, RoBERTa-MIMIC remarkably improved the F1-score by approximately 4% and 6% on the 2010 and 2012 i2b2 datasets. This study demonstrated the efficiency of transformer-based models for clinical concept extraction. Our methods and systems can be applied to other clinical tasks. The clinical transformer package with 4 pretrained clinical models is publicly available at https://github.com/uf-hobi-informatics-lab/ClinicalTransformerNER. We believe this package will improve current practice on clinical concept extraction and other tasks in the medical domain. 相似文献
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系统介绍了生物医学文本挖掘的具体流程和文本挖掘技术在生物医学领域中的应用情况,并着重从自然语言处理和本体、命名实体识别、关系抽取、文本分类与聚类、共现分析、系统工具及评价、可视化等方面分别做了阐述. 相似文献
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目的/意义 探讨人工智能技术应用于淋巴水肿患者电子病历非结构化文本数据的关键实体识别问题。方法/过程 阐述样本稀缺背景下模型微调训练的解决方案,选取首都医科大学附属北京世纪坛医院淋巴外科既往收治患者594例为研究对象,依据临床医生标注的15种关键实体类别,微调GlobalPointer模型的预测层,借助其全局指针识别嵌套和非嵌套的关键实体。分析实验结果的准确性和临床应用可行性。结果/结论 微调后模型总体精准率、召回率和 Macro_F1均值分别为0.795、0.641和0.697,为淋巴水肿电子病历数据精准挖掘奠定基础。 相似文献
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目的 针对缺血性脑卒中这一发病率高、预后差的疾病,应用自然语言处理技术从患者出院小结中进行文本数据挖掘,并通过Python编程语言将非结构化的文本数据转换成供后续统计分析的结构化数据库.方法 利用缺血性脑卒中患者出院小结资料,构建基于知识增强的语义表示模型(ERNIE)+神经网络+条件随机场的命名实体识别模型,进行疾病、药物、手术、影像学检查、症状5种医疗命名实体的识别,提取实体构建半结构化数据库.为了进一步从半结构化数据库中提取出结构化数据,构建基于ERNIE的孪生文本相似度匹配模型,评价指标为准确率,采用最优模型构建协变量提取器.结果 命名实体识别模型总体F1值为90.27％,其中疾病F1值为88.41％,药物F1值为91.03％,影像学检查F1值为87.71％,手术F1值为87.07％,症状F1值为96.59％.文本相似度匹配模型的总体准确率为99.11％.结论 通过自然语言处理技术,实现了从完全的非结构化数据到半结构化数据再到结构化数据的构建流程,与人工阅读病历并手动提取病历信息相比,极大提高了数据库构建的效率. 相似文献
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ObjectiveThe study sought to develop and evaluate a knowledge-based data augmentation method to improve the performance of deep learning models for biomedical natural language processing by overcoming training data scarcity.Materials and MethodsWe extended the easy data augmentation (EDA) method for biomedical named entity recognition (NER) by incorporating the Unified Medical Language System (UMLS) knowledge and called this method UMLS-EDA. We designed experiments to systematically evaluate the effect of UMLS-EDA on popular deep learning architectures for both NER and classification. We also compared UMLS-EDA to BERT.ResultsUMLS-EDA enables substantial improvement for NER tasks from the original long short-term memory conditional random fields (LSTM-CRF) model (micro-F1 score: +5%, + 17%, and +15%), helps the LSTM-CRF model (micro-F1 score: 0.66) outperform LSTM-CRF with transfer learning by BERT (0.63), and improves the performance of the state-of-the-art sentence classification model. The largest gain on micro-F1 score is 9%, from 0.75 to 0.84, better than classifiers with BERT pretraining (0.82).ConclusionsThis study presents a UMLS-based data augmentation method, UMLS-EDA. It is effective at improving deep learning models for both NER and sentence classification, and contributes original insights for designing new, superior deep learning approaches for low-resource biomedical domains. 相似文献
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Objective Semantic role labeling (SRL), which extracts a shallow semantic relation representation from different surface textual forms of free text sentences, is important for understanding natural language. Few studies in SRL have been conducted in the medical domain, primarily due to lack of annotated clinical SRL corpora, which are time-consuming and costly to build. The goal of this study is to investigate domain adaptation techniques for clinical SRL leveraging resources built from newswire and biomedical literature to improve performance and save annotation costs.Materials and Methods Multisource Integrated Platform for Answering Clinical Questions (MiPACQ), a manually annotated SRL clinical corpus, was used as the target domain dataset. PropBank and NomBank from newswire and BioProp from biomedical literature were used as source domain datasets. Three state-of-the-art domain adaptation algorithms were employed: instance pruning, transfer self-training, and feature augmentation. The SRL performance using different domain adaptation algorithms was evaluated by using 10-fold cross-validation on the MiPACQ corpus. Learning curves for the different methods were generated to assess the effect of sample size.Results and Conclusion When all three source domain corpora were used, the feature augmentation algorithm achieved statistically significant higher F-measure (83.18%), compared to the baseline with MiPACQ dataset alone (F-measure, 81.53%), indicating that domain adaptation algorithms may improve SRL performance on clinical text. To achieve a comparable performance to the baseline method that used 90% of MiPACQ training samples, the feature augmentation algorithm required <50% of training samples in MiPACQ, demonstrating that annotation costs of clinical SRL can be reduced significantly by leveraging existing SRL resources from other domains. 相似文献
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针对医学数据专业性强、结构复杂等特点,解析了构建医学知识图谱的关键技术,介绍了利用机器学习和深度学习的方法识别医学命名实体、实体链接和抽取语义关系,以及医学知识图谱在医院智能导诊、疾病筛查和预测、辅助临床诊断、医疗保险风险预测和医学知识科普方面的应用。结合当前我国医学知识图谱构建在数据和技术层面临的问题和挑战,提出了相应的对策和建议。 相似文献
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Jingcheng Du Yang Xiang Madhuri Sankaranarayanapillai Meng Zhang Jingqi Wang Yuqi Si Huy Anh Pham Hua Xu Yong Chen Cui Tao 《J Am Med Inform Assoc》2021,28(7):1393
ObjectiveAutomated analysis of vaccine postmarketing surveillance narrative reports is important to understand the progression of rare but severe vaccine adverse events (AEs). This study implemented and evaluated state-of-the-art deep learning algorithms for named entity recognition to extract nervous system disorder-related events from vaccine safety reports.Materials and MethodsWe collected Guillain-Barré syndrome (GBS) related influenza vaccine safety reports from the Vaccine Adverse Event Reporting System (VAERS) from 1990 to 2016. VAERS reports were selected and manually annotated with major entities related to nervous system disorders, including, investigation, nervous_AE, other_AE, procedure, social_circumstance, and temporal_expression. A variety of conventional machine learning and deep learning algorithms were then evaluated for the extraction of the above entities. We further pretrained domain-specific BERT (Bidirectional Encoder Representations from Transformers) using VAERS reports (VAERS BERT) and compared its performance with existing models.Results and ConclusionsNinety-one VAERS reports were annotated, resulting in 2512 entities. The corpus was made publicly available to promote community efforts on vaccine AEs identification. Deep learning-based methods (eg, bi-long short-term memory and BERT models) outperformed conventional machine learning-based methods (ie, conditional random fields with extensive features). The BioBERT large model achieved the highest exact match F-1 scores on nervous_AE, procedure, social_circumstance, and temporal_expression; while VAERS BERT large models achieved the highest exact match F-1 scores on investigation and other_AE. An ensemble of these 2 models achieved the highest exact match microaveraged F-1 score at 0.6802 and the second highest lenient match microaveraged F-1 score at 0.8078 among peer models. 相似文献
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目的/意义 构建中医古籍医案命名实体语料库,提升通用领域命名实体识别模型在中医古籍医案领域的识别精度与适用性。方法/过程 制定中医古籍医案命名实体标注规范,并据此对2 384则新安医案进行人工标注。构建RoBERTa-BiLSTM-CRF中医古籍医案命名实体识别模型,利用RoBERTa预训练语言模型生成具有语义特征的字向量,利用BiLSTM-CRF模型学习序列全局语义特征并解码输出最佳标签序列。引入词典和规则特征,增强模型对实体边界和类别的感知能力。结果/结论 模型在所建立的新安医案命名实体语料库上展现了良好的识别效果。融合领域术语词典与规则特征后,模型的综合F1值提升至72.8%。 相似文献
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ObjectiveAccurate extraction of breast cancer patients’ phenotypes is important for clinical decision support and clinical research. This study developed and evaluated cancer domain pretrained CancerBERT models for extracting breast cancer phenotypes from clinical texts. We also investigated the effect of customized cancer-related vocabulary on the performance of CancerBERT models.Materials and MethodsA cancer-related corpus of breast cancer patients was extracted from the electronic health records of a local hospital. We annotated named entities in 200 pathology reports and 50 clinical notes for 8 cancer phenotypes for fine-tuning and evaluation. We kept pretraining the BlueBERT model on the cancer corpus with expanded vocabularies (using both term frequency-based and manually reviewed methods) to obtain CancerBERT models. The CancerBERT models were evaluated and compared with other baseline models on the cancer phenotype extraction task.ResultsAll CancerBERT models outperformed all other models on the cancer phenotyping NER task. Both CancerBERT models with customized vocabularies outperformed the CancerBERT with the original BERT vocabulary. The CancerBERT model with manually reviewed customized vocabulary achieved the best performance with macro F1 scores equal to 0.876 (95% CI, 0.873–0.879) and 0.904 (95% CI, 0.902–0.906) for exact match and lenient match, respectively.ConclusionsThe CancerBERT models were developed to extract the cancer phenotypes in clinical notes and pathology reports. The results validated that using customized vocabulary may further improve the performances of domain specific BERT models in clinical NLP tasks. The CancerBERT models developed in the study would further help clinical decision support. 相似文献
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Objective
An analysis of the timing of events is critical for a deeper understanding of the course of events within a patient record. The 2012 i2b2 NLP challenge focused on the extraction of temporal relationships between concepts within textual hospital discharge summaries.Materials and methods
The team from the National Research Council Canada (NRC) submitted three system runs to the second track of the challenge: typifying the time-relationship between pre-annotated entities. The NRC system was designed around four specialist modules containing statistical machine learning classifiers. Each specialist targeted distinct sets of relationships: local relationships, ‘sectime’-type relationships, non-local overlap-type relationships, and non-local causal relationships.Results
The best NRC submission achieved a precision of 0.7499, a recall of 0.6431, and an F1 score of 0.6924, resulting in a statistical tie for first place. Post hoc improvements led to a precision of 0.7537, a recall of 0.6455, and an F1 score of 0.6954, giving the highest scores reported on this task to date.Discussion and conclusions
Methods for general relation extraction extended well to temporal relations, and gave top-ranked state-of-the-art results. Careful ordering of predictions within result sets proved critical to this success. 相似文献14.
Jonnalagadda SR Li D Sohn S Wu ST Wagholikar K Torii M Liu H 《J Am Med Inform Assoc》2012,19(5):867-874
Objective
This paper describes the coreference resolution system submitted by Mayo Clinic for the 2011 i2b2/VA/Cincinnati shared task Track 1C. The goal of the task was to construct a system that links the markables corresponding to the same entity.Materials and methods
The task organizers provided progress notes and discharge summaries that were annotated with the markables of treatment, problem, test, person, and pronoun. We used a multi-pass sieve algorithm that applies deterministic rules in the order of preciseness and simultaneously gathers information about the entities in the documents. Our system, MedCoref, also uses a state-of-the-art machine learning framework as an alternative to the final, rule-based pronoun resolution sieve.Results
The best system that uses a multi-pass sieve has an overall score of 0.836 (average of B3, MUC, Blanc, and CEAF F score) for the training set and 0.843 for the test set.Discussion
A supervised machine learning system that typically uses a single function to find coreferents cannot accommodate irregularities encountered in data especially given the insufficient number of examples. On the other hand, a completely deterministic system could lead to a decrease in recall (sensitivity) when the rules are not exhaustive. The sieve-based framework allows one to combine reliable machine learning components with rules designed by experts.Conclusion
Using relatively simple rules, part-of-speech information, and semantic type properties, an effective coreference resolution system could be designed. The source code of the system described is available at https://sourceforge.net/projects/ohnlp/files/MedCoref. 相似文献15.
知识图谱技术促进了新药研发的进展,但国内研究起点晚且领域知识多以文本形式存储,图谱重用率低。因此,本研究基于多源异构的医药文本,设计了以Bert-wwm-ext预训练模型为基础,并融合级联思想的中文命名实体识别模型,从而减少了传统单次分类的复杂度,进一步提高了文本识别的效率。实验结果显示,该模型在自建的训练语料上的F1分数达0.903,精确率达89.2%,召回率达91.5%。同时,将模型应用于公开数据集CCKS2019上,结果显示该模型能够更好地识别中文文本中的医疗实体。最后,利用此模型构建了一个中文医药知识图谱,图谱包含13 530个实体,10 939个属性,以及39 247个相关关系。本研究所提出的中文医药实体识别与图谱构建方法,有望助力研究者加快医药知识新发现,从而缩短新药研发进程。 相似文献
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Objective Many tasks in natural language processing utilize lexical pattern-matching techniques, including information extraction (IE), negation identification, and syntactic parsing. However, it is generally difficult to derive patterns that achieve acceptable levels of recall while also remaining highly precise.Materials and Methods We present a multiple sequence alignment (MSA)-based technique that automatically generates patterns, thereby leveraging language usage to determine the context of words that influence a given target. MSAs capture the commonalities among word sequences and are able to reveal areas of linguistic stability and variation. In this way, MSAs provide a systemic approach to generating lexical patterns that are generalizable, which will both increase recall levels and maintain high levels of precision.Results The MSA-generated patterns exhibited consistent F1-, F.5-, and F2- scores compared to two baseline techniques for IE across four different tasks. Both baseline techniques performed well for some tasks and less well for others, but MSA was found to consistently perform at a high level for all four tasks.Discussion The performance of MSA on the four extraction tasks indicates the method’s versatility. The results show that the MSA-based patterns are able to handle the extraction of individual data elements as well as relations between two concepts without the need for large amounts of manual intervention.Conclusion We presented an MSA-based framework for generating lexical patterns that showed consistently high levels of both performance and recall over four different extraction tasks when compared to baseline methods. 相似文献
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Kenneth Jung Paea LePendu Srinivasan Iyer Anna Bauer-Mehren Bethany Percha Nigam H Shah 《J Am Med Inform Assoc》2015,22(1):121-131
Objective The trade-off between the speed and simplicity of dictionary-based term recognition and the richer linguistic information provided by more advanced natural language processing (NLP) is an area of active discussion in clinical informatics. In this paper, we quantify this trade-off among text processing systems that make different trade-offs between speed and linguistic understanding. We tested both types of systems in three clinical research tasks: phase IV safety profiling of a drug, learning adverse drug–drug interactions, and learning used-to-treat relationships between drugs and indications.Materials We first benchmarked the accuracy of the NCBO Annotator and REVEAL in a manually annotated, publically available dataset from the 2008 i2b2 Obesity Challenge. We then applied the NCBO Annotator and REVEAL to 9 million clinical notes from the Stanford Translational Research Integrated Database Environment (STRIDE) and used the resulting data for three research tasks.Results There is no significant difference between using the NCBO Annotator and REVEAL in the results of the three research tasks when using large datasets. In one subtask, REVEAL achieved higher sensitivity with smaller datasets.Conclusions For a variety of tasks, employing simple term recognition methods instead of advanced NLP methods results in little or no impact on accuracy when using large datasets. Simpler dictionary-based methods have the advantage of scaling well to very large datasets. Promoting the use of simple, dictionary-based methods for population level analyses can advance adoption of NLP in practice. 相似文献
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