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Register a new userProgressive Transformer-Based Generation of Radiology Reports
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Added by
Farhad Nooralahzadeh
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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No Arabic abstract
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.
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Pretrained using large amount of data, autoregressive language models are able to generate high quality sequences. However, these models do not perform well under hard lexical constraints as they lack fine control of content generation process. Progressive insertion-based transformers can overcome the above limitation and efficiently generate a sequence in parallel given some input tokens as constraint. These transformers however may fail to support hard lexical constraints as their generation process is more likely to terminate prematurely. The paper analyses such early termination problems and proposes the Entity-constrained insertion transformer (ENCONTER), a new insertion transformer that addresses the above pitfall without compromising much generation efficiency. We introduce a new training strategy that considers predefined hard lexical constraints (e.g., entities to be included in the generated sequence). Our experiments show that ENCONTER outperforms other baseline models in several performance metrics rendering it more suitable in practical applications. Our code is available at https://github.com/LARC-CMU-SMU/Enconter
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.
Extracting structured clinical information from free-text radiology reports can enable the use of radiology report information for a variety of critical healthcare applications. In our work, we present RadGraph, a dataset of entities and relations in full-text chest X-ray radiology reports based on a novel information extraction schema we designed to structure radiology reports. We release a development dataset, which contains board-certified radiologist annotations for 500 radiology reports from the MIMIC-CXR dataset (14,579 entities and 10,889 relations), and a test dataset, which contains two independent sets of board-certified radiologist annotations for 100 radiology reports split equally across the MIMIC-CXR and CheXpert datasets. Using these datasets, we train and test a deep learning model, RadGraph Benchmark, that achieves a micro F1 of 0.82 and 0.73 on relation extraction on the MIMIC-CXR and CheXpert test sets respectively. Additionally, we release an inference dataset, which contains annotations automatically generated by RadGraph Benchmark across 220,763 MIMIC-CXR reports (around 6 million entities and 4 million relations) and 500 CheXpert reports (13,783 entities and 9,908 relations) with mappings to associated chest radiographs. Our freely available dataset can facilitate a wide range of research in medical natural language processing, as well as computer vision and multi-modal learning when linked to chest radiographs.
This paper explores a variant of automatic headline generation methods, where a generated headline is required to include a given phrase such as a company or a product name. Previous methods using Transformer-based models generate a headline including a given phrase by providing the encoder with additional information corresponding to the given phrase. However, these methods cannot always include the phrase in the generated headline. Inspired by previous RNN-based methods generating token sequences in backward and forward directions from the given phrase, we propose a simple Transformer-based method that guarantees to include the given phrase in the high-quality generated headline. We also consider a new headline generation strategy that takes advantage of the controllable generation order of Transformer. Our experiments with the Japanese News Corpus demonstrate that our methods, which are guaranteed to include the phrase in the generated headline, achieve ROUGE scores comparable to previous Transformer-based methods. We also show that our generation strategy performs better than previous strategies.
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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