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Register a new userDoes the Magic of BERT Apply to Medical Code Assignment? A Quantitative Study
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Added by
Shaoxiong Ji
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Unsupervised pretraining is an integral part of many natural language processing systems, and transfer learning with language models has achieved remarkable results in many downstream tasks. In the clinical application of medical code assignment, diagnosis and procedure codes are inferred from lengthy clinical notes such as hospital discharge summaries. However, it is not clear if pretrained models are useful for medical code prediction without further architecture engineering. This paper conducts a comprehensive quantitative analysis of various contextualized language models performance, pretrained in different domains, for medical code assignment from clinical notes. We propose a hierarchical fine-tuning architecture to capture interactions between distant words and adopt label-wise attention to exploit label information. Contrary to current trends, we demonstrate that a carefully trained classical CNN outperforms attention-based models on a MIMIC-III subset with frequent codes. Our empirical findings suggest directions for improving the medical code assignment application.
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Medical code assignment from clinical text is a fundamental task in clinical information system management. As medical notes are typically lengthy and the medical coding systems code space is large, this task is a long-standing challenge. Recent work applies deep neural network models to encode the medical notes and assign medical codes to clinical documents. However, these methods are still ineffective as they do not fully encode and capture the lengthy and rich semantic information of medical notes nor explicitly exploit the interactions between the notes and codes. We propose a novel method, gated convolutional neural networks, and a note-code interaction (GatedCNN-NCI), for automatic medical code assignment to overcome these challenges. Our methods capture the rich semantic information of the lengthy clinical text for better representation by utilizing embedding injection and gated information propagation in the medical note encoding module. With a novel note-code interaction design and a graph message passing mechanism, we explicitly capture the underlying dependency between notes and codes, enabling effective code prediction. A weight sharing scheme is further designed to decrease the number of trainable parameters. Empirical experiments on real-world clinical datasets show that our proposed model outperforms state-of-the-art models in most cases, and our model size is on par with light-weighted baselines.
Medical code assignment, which predicts medical codes from clinical texts, is a fundamental task of intelligent medical information systems. The emergence of deep models in natural language processing has boosted the development of automatic assignment methods. However, recent advanced neural architectures with flat convolutions or multi-channel feature concatenation ignore the sequential causal constraint within a text sequence and may not learn meaningful clinical text representations, especially for lengthy clinical notes with long-term sequential dependency. This paper proposes a Dilated Convolutional Attention Network (DCAN), integrating dilated convolutions, residual connections, and label attention, for medical code assignment. It adopts dilated convolutions to capture complex medical patterns with a receptive field which increases exponentially with dilation size. Experiments on a real-world clinical dataset empirically show that our model improves the state of the art.
Contextualized representations give significantly improved results for a wide range of NLP tasks. Much work has been dedicated to analyzing the features captured by representative models such as BERT. Existing work finds that syntactic, semantic and word sense knowledge are encoded in BERT. However, little work has investigated word features for character-based languages such as Chinese. We investigate Chinese BERT using both attention weight distribution statistics and probing tasks, finding that (1) word information is captured by BERT; (2) word-level features are mostly in the middle representation layers; (3) downstream tasks make different use of word features in BERT, with POS tagging and chunking relying the most on word features, and natural language inference relying the least on such features.
Can quantum-mechanical particles propagating on a fixed spacetime background be approximated as test bodies satisfying the weak equivalence principle? We ultimately answer the question in the negative but find that, when universality of free-fall is assessed locally, a nontrivial agreement between quantum mechanics and the weak equivalence principle exists. Implications for mass sensing by quantum probes are discussed in some details.
Large Transformers pretrained over clinical notes from Electronic Health Records (EHR) have afforded substantial gains in performance on predictive clinical tasks. The cost of training such models (and the necessity of data access to do so) coupled with their utility motivates parameter sharing, i.e., the release of pretrained models such as ClinicalBERT. While most efforts have used deidentified EHR, many researchers have access to large sets of sensitive, non-deidentified EHR with which they might train a BERT model (or similar). Would it be safe to release the weights of such a model if they did? In this work, we design a battery of approaches intended to recover Personal Health Information (PHI) from a trained BERT. Specifically, we attempt to recover patient names and conditions with which they are associated. We find that simple probing methods are not able to meaningfully extract sensitive information from BERT trained over the MIMIC-III corpus of EHR. However, more sophisticated attacks may succeed in doing so: To facilitate such research, we make our experimental setup and baseline probing models available at https://github.com/elehman16/exposing_patient_data_release
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