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Register a new userA Pseudo Label-wise Attention Network for Automatic ICD Coding
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Yifan Wu
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Automatic International Classification of Diseases (ICD) coding is defined as a kind of text multi-label classification problem, which is difficult because the number of labels is very large and the distribution of labels is unbalanced. The label-wise attention mechanism is widely used in automatic ICD coding because it can assign weights to every word in full Electronic Medical Records (EMR) for different ICD codes. However, the label-wise attention mechanism is computational redundant and costly. In this paper, we propose a pseudo label-wise attention mechanism to tackle the problem. Instead of computing different attention modes for different ICD codes, the pseudo label-wise attention mechanism automatically merges similar ICD codes and computes only one attention mode for the similar ICD codes, which greatly compresses the number of attention modes and improves the predicted accuracy. In addition, we apply a more convenient and effective way to obtain the ICD vectors, and thus our model can predict new ICD codes by calculating the similarities between EMR vectors and ICD vectors. Extensive experiments show the superior performance of our model. On the public MIMIC-III dataset and private Xiangya dataset, our model achieves micro f1 of 0.583 and 0.806, respectively, which outperforms other competing models. Furthermore, we verify the ability of our model in predicting new ICD codes. The case study shows how pseudo label-wise attention works, and demonstrates the effectiveness of pseudo label-wise attention mechanism.
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Given the clinical notes written in electronic health records (EHRs), it is challenging to predict the diagnostic codes which is formulated as a multi-label classification task. The large set of labels, the hierarchical dependency, and the imbalanced data make this prediction task extremely hard. Most existing work built a binary prediction for each label independently, ignoring the dependencies between labels. To address this problem, we propose a two-stage framework to improve automatic ICD coding by capturing the label correlation. Specifically, we train a label set distribution estimator to rescore the probability of each label set candidate generated by a base predictor. This paper is the first attempt at learning the label set distribution as a reranking module for medical code prediction. In the experiments, our proposed framework is able to improve upon best-performing predictors on the benchmark MIMIC datasets. The source code of this project is available at https://github.com/MiuLab/ICD-Correlation.
Diagnostic or procedural coding of clinical notes aims to derive a coded summary of disease-related information about patients. Such coding is usually done manually in hospitals but could potentially be automated to improve the efficiency and accuracy of medical coding. Recent studies on deep learning for automated medical coding achieved promising performances. However, the explainability of these models is usually poor, preventing them to be used confidently in supporting clinical practice. Another limitation is that these models mostly assume independence among labels, ignoring the complex correlation among medical codes which can potentially be exploited to improve the performance. We propose a Hierarchical Label-wise Attention Network (HLAN), which aimed to interpret the model by quantifying importance (as attention weights) of words and sentences related to each of the labels. Secondly, we propose to enhance the major deep learning models with a label embedding (LE) initialisation approach, which learns a dense, continuous vector representation and then injects the representation into the final layers and the label-wise attention layers in the models. We evaluated the methods using three settings on the MIMIC-III discharge summaries: full codes, top-50 codes, and the UK NHS COVID-19 shielding codes. Experiments were conducted to compare HLAN and LE initialisation to the state-of-the-art neural network based methods. HLAN achieved the best Micro-level AUC and $F_1$ on the top-50 code prediction and comparable results on the NHS COVID-19 shielding code prediction to other models. By highlighting the most salient words and sentences for each label, HLAN showed more meaningful and comprehensive model interpretation compared to its downgraded baselines and the CNN-based models. LE initialisation consistently boosted most deep learning models for automated medical coding.
Hierarchical multi-label text classification (HMTC) has been gaining popularity in recent years thanks to its applicability to a plethora of real-world applications. The existing HMTC algorithms largely focus on the design of classifiers, such as the local, global, or a combination of them. However, very few studies have focused on hierarchical feature extraction and explore the association between the hierarchical labels and the text. In this paper, we propose a Label-based Attention for Hierarchical Mutlti-label Text Classification Neural Network (LA-HCN), where the novel label-based attention module is designed to hierarchically extract important information from the text based on the labels from different hierarchy levels. Besides, hierarchical information is shared across levels while preserving the hierarchical label-based information. Separate local and global document embeddings are obtained and used to facilitate the respective local and global classifications. In our experiments, LA-HCN outperforms other state-of-the-art neural network-based HMTC algorithms on four public HMTC datasets. The ablation study also demonstrates the effectiveness of the proposed label-based attention module as well as the novel local and global embeddings and classifications. By visualizing the learned attention (words), we find that LA-HCN is able to extract meaningful information corresponding to the different labels which provides explainability that may be helpful for the human analyst.
A major challenge of multi-label text classification (MLTC) is to stimulatingly exploit possible label differences and label correlations. In this paper, we tackle this challenge by developing Label-Wise Pre-Training (LW-PT) method to get a document representation with label-aware information. The basic idea is that, a multi-label document can be represented as a combination of multiple label-wise representations, and that, correlated labels always cooccur in the same or similar documents. LW-PT implements this idea by constructing label-wise document classification tasks and trains label-wise document encoders. Finally, the pre-trained label-wise encoder is fine-tuned with the downstream MLTC task. Extensive experimental results validate that the proposed method has significant advantages over the previous state-of-the-art models and is able to discover reasonable label relationship. The code is released to facilitate other researchers.
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