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Register a new userAn Ensemble Approach for Automatic Structuring of Radiology Reports
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Added by
Morteza Pourreza Shahri
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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Automatic structuring of electronic medical records is of high demand for clinical workflow solutions to facilitate extraction, storage, and querying of patient care information. However, developing a scalable solution is extremely challenging, specifically for radiology reports, as most healthcare institutes use either no template or department/institute specific templates. Moreover, radiologists reporting style varies from one to another as sentences are telegraphic and do not follow general English grammar rules. We present an ensemble method that consolidates the predictions of three models, capturing various attributes of textual information for automatic labeling of sentences with section labels. These three models are: 1) Focus Sentence model, capturing context of the target sentence; 2) Surrounding Context model, capturing the neighboring context of the target sentence; and finally, 3) Formatting/Layout model, aimed at learning report formatting cues. We utilize Bi-directional LSTMs, followed by sentence encoders, to acquire the context. Furthermore, we define several features that incorporate the structure of reports. We compare our proposed approach against multiple baselines and state-of-the-art approaches on a proprietary dataset as well as 100 manually annotated radiology notes from the MIMIC-III dataset, which we are making publicly available. Our proposed approach significantly outperforms other approaches by achieving 97.1% accuracy.
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Inspired by Curriculum Learning, we propose a consecutive (i.e., image-to-text-to-text) generation framework where we divide the problem of radiology report generation into two steps. Contrary to generating the full radiology report from the image at once, the model generates global concepts from the image in the first step and then reforms them into finer and coherent texts using a transformer architecture. We follow the transformer-based sequence-to-sequence paradigm at each step. We improve upon the state-of-the-art on two benchmark datasets.
Ontologies have become the effective modeling for various applications and significantly in the semantic web. The difficulty of extracting information from the web, which was created mainly for visualising information, has driven the birth of the semantic web, which will contain much more resources than the web and will attach machine-readable semantic information to these resources. Ontological bootstrapping on a set of predefined sources, such as web services, must address the problem of multiple, largely unrelated concepts. The web services consist of basically two components, Web Services Description Language (WSDL) descriptors and free text descriptors. The WSDL descriptor is evaluated using two methods, namely Term Frequency/Inverse Document Frequency (TF/IDF) and web context generation. The proposed bootstrapping ontological process integrates TF/IDF and web context generation and applies validation using the free text descriptor service, so that, it offers more accurate definition of ontologies. This paper uses ranking adaption model which predicts the rank for a collection of web service documents which leads to the automatic construction, enrichment and adaptation of ontologies.
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Despite the rapid development of natural language processing (NLP) implementation in electronic medical records (EMRs), Chinese EMRs processing remains challenging due to the limited corpus and specific grammatical characteristics, especially for radiology reports. In this study, we designed an NLP pipeline for the direct extraction of clinically relevant features from Chinese radiology reports, which is the first key step in computer-aided radiologic diagnosis. The pipeline was comprised of named entity recognition, synonyms normalization, and relationship extraction to finally derive the radiological features composed of one or more terms. In named entity recognition, we incorporated lexicon into deep learning model bidirectional long short-term memory-conditional random field (BiLSTM-CRF), and the model finally achieved an F1 score of 93.00%. With the extracted radiological features, least absolute shrinkage and selection operator and machine learning methods (support vector machine, random forest, decision tree, and logistic regression) were used to build the classifiers for liver cancer prediction. For liver cancer diagnosis, random forest had the highest predictive performance in liver cancer diagnosis (F1 score 86.97%, precision 87.71%, and recall 86.25%). This work was a comprehensive NLP study focusing on Chinese radiology reports and the application of NLP in cancer risk prediction. The proposed NLP pipeline for the radiological feature extraction could be easily implemented in other kinds of Chinese clinical texts and other disease predictive tasks.
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