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Register a new userAn Empirical Study of UMLS Concept Extraction from Clinical Notes using Boolean Combination Ensembles
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Michael Heinz
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Our objective in this study is to investigate the behavior of Boolean operators on combining annotation output from multiple Natural Language Processing (NLP) systems across multiple corpora and to assess how filtering by aggregation of Unified Medical Language System (UMLS) Metathesaurus concepts affects system performance for Named Entity Recognition (NER) of UMLS concepts. We used three corpora annotated for UMLS concepts: 2010 i2b2 VA challenge set (31,161 annotations), Multi-source Integrated Platform for Answering Clinical Questions (MiPACQ) corpus (17,457 annotations including UMLS concept unique identifiers), and Fairview Health Services corpus (44,530 annotations). Our results showed that for UMLS concept matching, Boolean ensembling of the MiPACQ corpus trended towards higher performance over individual systems. Use of an approximate grid-search can help optimize the precision-recall tradeoff and can provide a set of heuristics for choosing an optimal set of ensembles.
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Background and Objective: Code assignment is of paramount importance in many levels in modern hospitals, from ensuring accurate billing process to creating a valid record of patient care history. However, the coding process is tedious and subjective, and it requires medical coders with extensive training. This study aims to evaluate the performance of deep-learning-based systems to automatically map clinical notes to ICD-9 medical codes. Methods: The evaluations of this research are focused on end-to-end learning methods without manually defined rules. Traditional machine learning algorithms, as well as state-of-the-art deep learning methods such as Recurrent Neural Networks and Convolution Neural Networks, were applied to the Medical Information Mart for Intensive Care (MIMIC-III) dataset. An extensive number of experiments was applied to different settings of the tested algorithm. Results: Findings showed that the deep learning-based methods outperformed other conventional machine learning methods. From our assessment, the best models could predict the top 10 ICD-9 codes with 0.6957 F1 and 0.8967 accuracy and could estimate the top 10 ICD-9 categories with 0.7233 F1 and 0.8588 accuracy. Our implementation also outperformed existing work under certain evaluation metrics. Conclusion: A set of standard metrics was utilized in assessing the performance of ICD-9 code assignment on MIMIC-III dataset. All the developed evaluation tools and resources are available online, which can be used as a baseline for further research.
Neural models have achieved remarkable success on relation extraction (RE) benchmarks. However, there is no clear understanding which type of information affects existing RE models to make decisions and how to further improve the performance of these models. To this end, we empirically study the effect of two main information sources in text: textual context and entity mentions (names). We find that (i) while context is the main source to support the predictions, RE models also heavily rely on the information from entity mentions, most of which is type information, and (ii) existing datasets may leak shallow heuristics via entity mentions and thus contribute to the high performance on RE benchmarks. Based on the analyses, we propose an entity-masked contrastive pre-training framework for RE to gain a deeper understanding on both textual context and type information while avoiding rote memorization of entities or use of superficial cues in mentions. We carry out extensive experiments to support our views, and show that our framework can improve the effectiveness and robustness of neural models in different RE scenarios. All the code and datasets are released at https://github.com/thunlp/RE-Context-or-Names.
Multilingual pre-trained Transformers, such as mBERT (Devlin et al., 2019) and XLM-RoBERTa (Conneau et al., 2020a), have been shown to enable the effective cross-lingual zero-shot transfer. However, their performance on Arabic information extraction (IE) tasks is not very well studied. In this paper, we pre-train a customized bilingual BERT, dubbed GigaBERT, that is designed specifically for Arabic NLP and English-to-Arabic zero-shot transfer learning. We study GigaBERTs effectiveness on zero-short transfer across four IE tasks: named entity recognition, part-of-speech tagging, argument role labeling, and relation extraction. Our best model significantly outperforms mBERT, XLM-RoBERTa, and AraBERT (Antoun et al., 2020) in both the supervised and zero-shot transfer settings. We have made our pre-trained models publicly available at https://github.com/lanwuwei/GigaBERT.
The newly emerged transformer technology has a tremendous impact on NLP research. In the general English domain, transformer-based models have achieved state-of-the-art performances on various NLP benchmarks. In the clinical domain, researchers also have investigated transformer models for clinical applications. The goal of this study is to systematically explore three widely used transformer-based models (i.e., BERT, RoBERTa, and XLNet) for clinical relation extraction and develop an open-source package with clinical pre-trained transformer-based models to facilitate information extraction in the clinical domain. We developed a series of clinical RE models based on three transformer architectures, namely BERT, RoBERTa, and XLNet. We evaluated these models using 2 publicly available datasets from 2018 MADE1.0 and 2018 n2c2 challenges. We compared two classification strategies (binary vs. multi-class classification) and investigated two approaches to generate candidate relations in different experimental settings. In this study, we compared three transformer-based (BERT, RoBERTa, and XLNet) models for relation extraction. We demonstrated that the RoBERTa-clinical RE model achieved the best performance on the 2018 MADE1.0 dataset with an F1-score of 0.8958. On the 2018 n2c2 dataset, the XLNet-clinical model achieved the best F1-score of 0.9610. Our results indicated that the binary classification strategy consistently outperformed the multi-class classification strategy for clinical relation extraction. Our methods and models are publicly available at https://github.com/uf-hobi-informatics-lab/ClinicalTransformerRelationExtraction. We believe this work will improve current practice on clinical relation extraction and other related NLP tasks in the biomedical domain.
The recognition and normalization of clinical information, such as tumor morphology mentions, is an important, but complex process consisting of multiple subtasks. In this paper, we describe our system for the CANTEMIST shared task, which is able to extract, normalize and rank ICD codes from Spanish electronic health records using neural sequence labeling and parsing approaches with context-aware embeddings. Our best system achieves 85.3 F1, 76.7 F1, and 77.0 MAP for the three tasks, respectively.
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