Prediction of Drug-Disease Associations Based on Long Short-Term Memory Network and Gaussian Interaction Profile Kernel

Author(s):  
Han-Jing Jiang ◽  
Yan-Bin Wang ◽  
Yabing Huang
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yesol Park ◽  
Joohong Lee ◽  
Heesang Moon ◽  
Yong Suk Choi ◽  
Mina Rho

AbstractWith recent advances in biotechnology and sequencing technology, the microbial community has been intensively studied and discovered to be associated with many chronic as well as acute diseases. Even though a tremendous number of studies describing the association between microbes and diseases have been published, text mining methods that focus on such associations have been rarely studied. We propose a framework that combines machine learning and natural language processing methods to analyze the association between microbes and diseases. A hierarchical long short-term memory network was used to detect sentences that describe the association. For the sentences determined, two different parse tree-based search methods were combined to find the relation-describing word. The ensemble model of constituency parsing for structural pattern matching and dependency-based relation extraction improved the prediction accuracy. By combining deep learning and parse tree-based extractions, our proposed framework could extract the microbe-disease association with higher accuracy. The evaluation results showed that our system achieved an F-score of 0.8764 and 0.8524 in binary decisions and extracting relation words, respectively. As a case study, we performed a large-scale analysis of the association between microbes and diseases. Additionally, a set of common microbes shared by multiple diseases were also identified in this study. This study could provide valuable information for the major microbes that were studied for a specific disease. The code and data are available at https://github.com/DMnBI/mdi_predictor.


2021 ◽  
Vol 9 (6) ◽  
pp. 651
Author(s):  
Yan Yan ◽  
Hongyan Xing

In order for the detection ability of floating small targets in sea clutter to be improved, on the basis of the complete ensemble empirical mode decomposition (CEEMD) algorithm, the high-frequency parts and low-frequency parts are determined by the energy proportion of the intrinsic mode function (IMF); the high-frequency part is denoised by wavelet packet transform (WPT), whereas the denoised high-frequency IMFs and low-frequency IMFs reconstruct the pure sea clutter signal together. According to the chaotic characteristics of sea clutter, we proposed an adaptive training timesteps strategy. The training timesteps of network were determined by the width of embedded window, and the chaotic long short-term memory network detection was designed. The sea clutter signals after denoising were predicted by chaotic long short-term memory (LSTM) network, and small target signals were detected from the prediction errors. The experimental results showed that the CEEMD-WPT algorithm was consistent with the target distribution characteristics of sea clutter, and the denoising performance was improved by 33.6% on average. The proposed chaotic long- and short-term memory network, which determines the training step length according to the width of embedded window, is a new detection method that can accurately detect small targets submerged in the background of sea clutter.


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