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Register a new userCheXbert: Combining Automatic Labelers and Expert Annotations for Accurate Radiology Report Labeling Using BERT
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Added by
Akshay Smit
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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The extraction of labels from radiology text reports enables large-scale training of medical imaging models. Existing approaches to report labeling typically rely either on sophisticated feature engineering based on medical domain knowledge or manual annotations by experts. In this work, we introduce a BERT-based approach to medical image report labeling that exploits both the scale of available rule-based systems and the quality of expert annotations. We demonstrate superior performance of a biomedically pretrained BERT model first trained on annotations of a rule-based labeler and then finetuned on a small set of expert annotations augmented with automated backtranslation. We find that our final model, CheXbert, is able to outperform the previous best rules-based labeler with statistical significance, setting a new SOTA for report labeling on one of the largest datasets of chest x-rays.
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In this paper, we focus on the classification of books using short descriptive texts (cover blurbs) and additional metadata. Building upon BERT, a deep neural language model, we demonstrate how to combine text representations with metadata and knowledge graph embeddings, which encode author information. Compared to the standard BERT approach we achieve considerably better results for the classification task. For a more coarse-grained classification using eight labels we achieve an F1- score of 87.20, while a detailed classification using 343 labels yields an F1-score of 64.70. We make the source code and trained models of our experiments publicly available
Recently, transformer-based language models such as BERT have shown tremendous performance improvement for a range of natural language processing tasks. However, these language models usually are computation expensive and memory intensive during inference. As a result, it is difficult to deploy them on resource-restricted devices. To improve the inference performance, as well as reduce the model size while maintaining the model accuracy, we propose a novel quantization method named KDLSQ-BERT that combines knowledge distillation (KD) with learned step size quantization (LSQ) for language model quantization. The main idea of our method is that the KD technique is leveraged to transfer the knowledge from a teacher model to a student model when exploiting LSQ to quantize that student model during the quantization training process. Extensive experiment results on GLUE benchmark and SQuAD demonstrate that our proposed KDLSQ-BERT not only performs effectively when doing different bit (e.g. 2-bit $sim$ 8-bit) quantization, but also outperforms the existing BERT quantization methods, and even achieves comparable performance as the full-precision base-line model while obtaining 14.9x compression ratio. Our code will be public available.
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.
Techniques for automatically extracting important content elements from business documents such as contracts, statements, and filings have the potential to make business operations more efficient. This problem can be formulated as a sequence labeling task, and we demonstrate the adaption of BERT to two types of business documents: regulatory filings and property lease agreements. There are aspects of this problem that make it easier than standard information extraction tasks and other aspects that make it more difficult, but on balance we find that modest amounts of annotated data (less than 100 documents) are sufficient to achieve reasonable accuracy. We integrate our models into an end-to-end cloud platform that provides both an easy-to-use annotation interface as well as an inference interface that allows users to upload documents and inspect model outputs.
Both performance and efficiency are crucial factors for sequence labeling tasks in many real-world scenarios. Although the pre-trained models (PTMs) have significantly improved the performance of various sequence labeling tasks, their computational cost is expensive. To alleviate this problem, we extend the recent successful early-exit mechanism to accelerate the inference of PTMs for sequence labeling tasks. However, existing early-exit mechanisms are specifically designed for sequence-level tasks, rather than sequence labeling. In this paper, we first propose a simple extension of sentence-level early-exit for sequence labeling tasks. To further reduce the computational cost, we also propose a token-level early-exit mechanism that allows partial tokens to exit early at different layers. Considering the local dependency inherent in sequence labeling, we employed a window-based criterion to decide for a token whether or not to exit. The token-level early-exit brings the gap between training and inference, so we introduce an extra self-sampling fine-tuning stage to alleviate it. The extensive experiments on three popular sequence labeling tasks show that our approach can save up to 66%-75% inference cost with minimal performance degradation. Compared with competitive compressed models such as DistilBERT, our approach can achieve better performance under the same speed-up ratios of 2X, 3X, and 4X.
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