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GHS-NET:一种用于多标签生物医学文本分类的通用混合浅层神经网络。

GHS-NET a generic hybridized shallow neural network for multi-label biomedical text classification.

机构信息

Intelligent Criminology Research Lab, National Center of Artificial Intelligence, Al-Khawarizmi Institute of Computer Science, UET, Lahore, Pakistan; German Research Center for Artificial Intelligence (DFKI), 67663 Kaiserslautern, Germany.

Intelligent Criminology Research Lab, National Center of Artificial Intelligence, Al-Khawarizmi Institute of Computer Science, UET, Lahore, Pakistan; Department of Computer Science, University of Engineering and Technology (UET), Lahore, Pakistan.

出版信息

J Biomed Inform. 2021 Apr;116:103699. doi: 10.1016/j.jbi.2021.103699. Epub 2021 Feb 15.

Abstract

Exponential growth of biomedical literature and clinical data demands more robust yet precise computational methodologies to extract useful insights from biomedical literature and to perform accurate assignment of disease-specific codes. Such approaches can largely enhance the effectiveness of diverse biomedicine and bioinformatics applications. State-of-the-art computational biomedical text classification methodologies either solely leverage discrimintaive features extracted through convolution operations performed by deep convolutional neural network or contextual information extracted by recurrent neural network. However, none of the methodology takes advantage of both convolutional and recurrent neural networks. Further, existing methodologies lack to produce decent performance for the classification of different genre biomedical text such as biomedical literature or clinical notes. We, for the very first time, present a generic deep learning based hybrid multi-label classification methodology namely GHS-NET which can be utilized to accurately classify biomedical text of diverse genre. GHS-NET makes use of convolutional neural network to extract most discriminative features and bi-directional Long Short-Term Memory to acquire contextual information. GHS-NET effectiveness is evaluated for extreme multi-label biomedical literature classification and assignment of ICD-9 codes to clinical notes. For the task of extreme multi-label biomedical literature classification, performance comparison of GHS-Net and state-of-the-art deep learning based methodology reveals that GHS-Net marks the increment of 1%, 6%, and 1% for hallmarks of cancer dataset, 10%, 16%, and 11% for chemical exposure dataset in terms of precision, recall, and F1-score. For the task of clinical notes classification, GHS-Net outperforms previous best deep learning based methodology over Medical Information Mart for Intensive Care dataset (MIMIC-III) by the significant margin of 6%, 8% in terms of recall and F1-score. GHS-NET is available as a web service at and potentially can be used to accurately classify multi-variate disease and chemical exposure specific text.

摘要

生物医学文献和临床数据呈指数级增长,这就需要更强大、更精确的计算方法,以便从生物医学文献中提取有用的见解,并准确分配特定疾病的代码。这些方法可以大大提高各种生物医学和生物信息学应用的效果。最先进的计算生物医学文本分类方法要么仅利用通过深度卷积神经网络执行的卷积操作提取的判别特征,要么利用递归神经网络提取的上下文信息。然而,这些方法都没有利用卷积神经网络和递归神经网络。此外,现有的方法在对不同类型的生物医学文本(如生物医学文献或临床记录)进行分类时,性能不佳。我们首次提出了一种通用的深度学习混合多标签分类方法,即 GHS-NET,它可以用于准确地对不同类型的生物医学文本进行分类。GHS-NET 利用卷积神经网络提取最具判别力的特征,利用双向长短时记忆网络获取上下文信息。我们评估了 GHS-NET 在极端多标签生物医学文献分类和 ICD-9 代码分配到临床记录中的有效性。在极端多标签生物医学文献分类任务中,GHS-Net 与最先进的深度学习方法的性能比较表明,在癌症标志数据集方面,GHS-Net 的精度、召回率和 F1 得分分别提高了 1%、6%和 1%,在化学暴露数据集方面,分别提高了 10%、16%和 11%。在临床记录分类任务中,GHS-Net 在 MIMIC-III 数据集上的表现优于以前最好的基于深度学习的方法,在召回率和 F1 得分方面分别高出 6%和 8%。GHS-NET 可作为网络服务使用,并有可能用于准确分类多变量疾病和化学暴露特定文本。

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