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Register a new userExplainable CNN-attention Networks (C-Attention Network) for Automated Detection of Alzheimers Disease
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Added by
Ning Wang
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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In this work, we propose three explainable deep learning architectures to automatically detect patients with Alzheimer`s disease based on their language abilities. The architectures use: (1) only the part-of-speech features; (2) only language embedding features and (3) both of these feature classes via a unified architecture. We use self-attention mechanisms and interpretable 1-dimensional ConvolutionalNeural Network (CNN) to generate two types of explanations of the model`s action: intra-class explanation and inter-class explanation. The inter-class explanation captures the relative importance of each of the different features in that class, while the inter-class explanation captures the relative importance between the classes. Note that although we have considered two classes of features in this paper, the architecture is easily expandable to more classes because of its modularity. Extensive experimentation and comparison with several recent models show that our method outperforms these methods with an accuracy of 92.2% and F1 score of 0.952on the DementiaBank dataset while being able to generate explanations. We show by examples, how to generate these explanations using attention values.
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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.
Recent years, the approaches based on neural networks have shown remarkable potential for sentence modeling. There are two main neural network structures: recurrent neural network (RNN) and convolution neural network (CNN). RNN can capture long term dependencies and store the semantics of the previous information in a fixed-sized vector. However, RNN is a biased model and its ability to extract global semantics is restricted by the fixed-sized vector. Alternatively, CNN is able to capture n-gram features of texts by utilizing convolutional filters. But the width of convolutional filters restricts its performance. In order to combine the strengths of the two kinds of networks and alleviate their shortcomings, this paper proposes Attention-based Multichannel Convolutional Neural Network (AMCNN) for text classification. AMCNN utilizes a bi-directional long short-term memory to encode the history and future information of words into high dimensional representations, so that the information of both the front and back of the sentence can be fully expressed. Then the scalar attention and vectorial attention are applied to obtain multichannel representations. The scalar attention can calculate the word-level importance and the vectorial attention can calculate the feature-level importance. In the classification task, AMCNN uses a CNN structure to cpture word relations on the representations generated by the scalar and vectorial attention mechanism instead of calculating the weighted sums. It can effectively extract the n-gram features of the text. The experimental results on the benchmark datasets demonstrate that AMCNN achieves better performance than state-of-the-art methods. In addition, the visualization results verify the semantic richness of multichannel representations.
In longitudinal electronic health records (EHRs), the event records of a patient are distributed over a long period of time and the temporal relations between the events reflect sufficient domain knowledge to benefit prediction tasks such as the rate of inpatient mortality. Medical concept embedding as a feature extraction method that transforms a set of medical concepts with a specific time stamp into a vector, which will be fed into a supervised learning algorithm. The quality of the embedding significantly determines the learning performance over the medical data. In this paper, we propose a medical concept embedding method based on applying a self-attention mechanism to represent each medical concept. We propose a novel attention mechanism which captures the contextual information and temporal relationships between medical concepts. A light-weight neural net, Temporal Self-Attention Network (TeSAN), is then proposed to learn medical concept embedding based solely on the proposed attention mechanism. To test the effectiveness of our proposed methods, we have conducted clustering and prediction tasks on two public EHRs datasets comparing TeSAN against five state-of-the-art embedding methods. The experimental results demonstrate that the proposed TeSAN model is superior to all the compared methods. To the best of our knowledge, this work is the first to exploit temporal self-attentive relations between medical events.
The massive growth of digital biomedical data is making biomedical text indexing and classification increasingly important. Accordingly, previous research has devised numerous deep learning techniques focused on using feedforward, convolutional or recurrent neural architectures. More recently, fine-tuned transformers-based pretrained models (PTMs) have demonstrated superior performance compared to such models in many natural language processing tasks. However, the direct use of PTMs in the biomedical domain is only limited to the target documents, ignoring the rich semantic information in the label descriptions. In this paper, we develop an improved label attention-based architecture to inject semantic label description into the fine-tuning process of PTMs. Results on two public medical datasets show that the proposed fine-tuning scheme outperforms the conventionally fine-tuned PTMs and prior state-of-the-art models. Furthermore, we show that fine-tuning with the label attention mechanism is interpretable in the interpretability study.
This paper introduces and evaluates two novel Hierarchical Attention Network models [Yang et al., 2016] - i) Hierarchical Pruned Attention Networks, which remove the irrelevant words and sentences from the classification process in order to reduce potential noise in the document classification accuracy and ii) Hierarchical Sparsemax Attention Networks, which replace the Softmax function used in the attention mechanism with the Sparsemax [Martins and Astudillo, 2016], capable of better handling importance distributions where a lot of words or sentences have very low probabilities. Our empirical evaluation on the IMDB Review for sentiment analysis datasets shows both approaches to be able to match the results obtained by the current state-of-the-art (without, however, any significant benefits). All our source code is made available athttps://github.com/jmribeiro/dsl-project.
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