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Recognition of pulmonary diseases from lung sounds using convolutional neural networks and long short-term memory.

ABSTRACT: In this paper, a study is conducted to explore the ability of deep learning in recognizing pulmonary diseases from electronically recorded lung sounds. The selected data-set included a total of 103 patients obtained from locally recorded stethoscope lung sounds acquired at King Abdullah University Hospital, Jordan University of Science and Technology, Jordan. In addition, 110 patients data were added to the data-set from the Int. Conf. on Biomedical Health Informatics publicly available challenge database. Initially, all signals were checked to have a sampling frequency of 4 kHz and segmented into 5 s segments. Then, several preprocessing steps were undertaken to ensure smoother and less noisy signals. These steps included wavelet smoothing, displacement artifact removal, and z-score normalization. The deep learning network architecture consisted of two stages; convolutional neural networks and bidirectional long short-term memory units. The training of the model was evaluated based on a k-fold cross-validation scheme of tenfolds using several performance evaluation metrics including Cohen's kappa, accuracy, sensitivity, specificity, precision, and F1-score. The developed algorithm achieved the highest average accuracy of 99.62% with a precision of 98.85% in classifying patients based on the pulmonary disease types using CNN + BDLSTM. Furthermore, a total agreement of 98.26% was obtained between the predictions and original classes within the training scheme. This study paves the way towards implementing deep learning models in clinical settings to assist clinicians in decision making related to the recognition of pulmonary diseases.

Supplementary information

The online version supplementary material available at 10.1007/s12652-021-03184-y.

SUBMITTER: Fraiwan M

PROVIDER: S-EPMC8019351 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Experimental techniques for measuring chromatin accessibility are expensive and time consuming, appealing for the development of computational approaches to predict open chromatin regions from DNA sequences. Along this direction, existing methods fall into two classes: one based on handcrafted k -mer features and the other based on convolutional neural networks. Although both categories have shown good performance in specific applications thus far, there still lacks a comprehensive framework to integrate useful k -mer co-occurrence information with recent advances in deep learning.We fill this gap by addressing the problem of chromatin accessibility prediction with a convolutional Long Short-Term Memory (LSTM) network with k -mer embedding. We first split DNA sequences into k -mers and pre-train k -mer embedding vectors based on the co-occurrence matrix of k -mers by using an unsupervised representation learning approach. We then construct a supervised deep learning architecture comprised of an embedding layer, three convolutional layers and a Bidirectional LSTM (BLSTM) layer for feature learning and classification. We demonstrate that our method gains high-quality fixed-length features from variable-length sequences and consistently outperforms baseline methods. We show that k -mer embedding can effectively enhance model performance by exploring different embedding strategies. We also prove the efficacy of both the convolution and the BLSTM layers by comparing two variations of the network architecture. We confirm the robustness of our model to hyper-parameters by performing sensitivity analysis. We hope our method can eventually reinforce our understanding of employing deep learning in genomic studies and shed light on research regarding mechanisms of chromatin accessibility.The source code can be downloaded from https://github.com/minxueric/ismb2017_lstm .tingchen@tsinghua.edu.cn or ruijiang@tsinghua.edu.cn.Supplementary materials are available at Bioinformatics online.

Dataset Information

Recognition of pulmonary diseases from lung sounds using convolutional neural networks and long short-term memory.

Supplementary information

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