scholarly journals A Hybrid Deep Learning Model for Protein–Protein Interactions Extraction from Biomedical Literature

2020 ◽  
Vol 10 (8) ◽  
pp. 2690 ◽  
Author(s):  
Changqin Quan ◽  
Zhiwei Luo ◽  
Song Wang
Keyword(s):  
Deep Learning ◽  
Protein Interactions ◽  
Short Term Memory ◽  
Channel Model ◽  
Biomedical Literature ◽  
Hybrid Architecture ◽  
Protein Protein Interactions ◽  
Long Distance ◽  
Proposed Model ◽  
Bidirectional Lstm

The exponentially increasing size of biomedical literature and the limited ability of manual curators to discover protein–protein interactions (PPIs) in text has led to delays in keeping PPI databases updated with the current findings. The state-of-the-art text mining methods for PPI extraction are primarily based on deep learning (DL) models, and the performance of a DL-based method is mainly affected by the architecture of DL models and the feature embedding methods. In this study, we compared different architectures of DL models, including convolutional neural networks (CNN), long short-term memory (LSTM), and hybrid models, and proposed a hybrid architecture of a bidirectional LSTM+CNN model for PPI extraction. Pretrained word embedding and shortest dependency path (SDP) embedding are fed into a two-embedding channel model, such that the model is able to model long-distance contextual information and can capture the local features and structure information effectively. The experimental results showed that the proposed model is superior to the non-hybrid DL models, and the hybrid CNN+Bidirectional LSTM model works well for PPI extraction. The visualization and comparison of the hidden features learned by different DL models further confirmed the effectiveness of the proposed model.

scholarly journals Extraction of chemical–protein interactions from the literature using neural networks and narrow instance representation

Database ◽  
2019 ◽  
Vol 2019 ◽  
Author(s):  
Rui Antunes ◽  
Sérgio Matos
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Protein Interactions ◽  
Short Term Memory ◽  
Relation Extraction ◽  
Knowledge Bases ◽  
Individual Variability ◽  
Biomedical Literature ◽  
Complex Sentence ◽  
The Individual

Abstract The scientific literature contains large amounts of information on genes, proteins, chemicals and their interactions. Extraction and integration of this information in curated knowledge bases help researchers support their experimental results, leading to new hypotheses and discoveries. This is especially relevant for precision medicine, which aims to understand the individual variability across patient groups in order to select the most appropriate treatments. Methods for improved retrieval and automatic relation extraction from biomedical literature are therefore required for collecting structured information from the growing number of published works. In this paper, we follow a deep learning approach for extracting mentions of chemical–protein interactions from biomedical articles, based on various enhancements over our participation in the BioCreative VI CHEMPROT task. A significant aspect of our best method is the use of a simple deep learning model together with a very narrow representation of the relation instances, using only up to 10 words from the shortest dependency path and the respective dependency edges. Bidirectional long short-term memory recurrent networks or convolutional neural networks are used to build the deep learning models. We report the results of several experiments and show that our best model is competitive with more complex sentence representations or network structures, achieving an F1-score of 0.6306 on the test set. The source code of our work, along with detailed statistics, is publicly available.

Construction of an Ensemble Scheme for Stock Price Prediction Using Deep Learning Techniques

2021 ◽  
Vol 17 (2) ◽  
pp. 72-95
Author(s):  
Justice Kwame Appati ◽  
Ismail Wafaa Denwar ◽  
Ebenezer Owusu ◽  
Michael Agbo Tettey Soli
Keyword(s):  
Deep Learning ◽  
Stock Price ◽  
Short Term Memory ◽  
Absolute Error ◽  
Stock Price Prediction ◽  
Price Prediction ◽  
Learning Techniques ◽  
Proposed Model ◽  
Bidirectional Lstm ◽  
Gated Recurrent Unit

This study proposes a deep learning approach for stock price prediction by bridging the long short-term memory with gated recurrent unit. In its evaluation, the mean absolute error and mean square error were used. The model proposed is an extension of the study of Hossain et al. established in 2018 with an MSE of 0.00098 as its lowest error. The current proposed model is a mix of the bidirectional LSTM and bidirectional GRU resulting in 0.00000008 MSE as the lowest error recorded. The LSTM model recorded 0.00000025 MSE, the GRU model recorded 0.00000077 MSE, and the LSTM + GRU model recorded 0.00000023 MSE. Other combinations of the existing models such as the bi-directional LSTM model recorded 0.00000019 MSE, bi-directional GRU recorded 0.00000011 MSE, bidirectional LSTM + GRU recorded 0.00000027 MSE, LSTM and bi-directional GRU recorded 0.00000020 MSE.

Deep Learning in the Study of Protein-Related Interactions

2020 ◽  
Vol 27 (5) ◽  
pp. 359-369 ◽  
Author(s):  
Cheng Shi ◽  
Jiaxing Chen ◽  
Xinyue Kang ◽  
Guiling Zhao ◽  
Xingzhen Lao ◽  
...  
Keyword(s):  
Deep Learning ◽  
Protein Interactions ◽  
Physiological Data ◽  
Great Promise ◽  
Complex Data ◽  
Protein Protein Interactions ◽  
Learning Patterns ◽  
Introductory Overview ◽  
Protein Research ◽  
Neural Network Theory

: Protein-related interaction prediction is critical to understanding life processes, biological functions, and mechanisms of drug action. Experimental methods used to determine proteinrelated interactions have always been costly and inefficient. In recent years, advances in biological and medical technology have provided us with explosive biological and physiological data, and deep learning-based algorithms have shown great promise in extracting features and learning patterns from complex data. At present, deep learning in protein research has emerged. In this review, we provide an introductory overview of the deep neural network theory and its unique properties. Mainly focused on the application of this technology in protein-related interactions prediction over the past five years, including protein-protein interactions prediction, protein-RNA\DNA, Protein– drug interactions prediction, and others. Finally, we discuss some of the challenges that deep learning currently faces.

Human Activity Recognition using Fourier Transform Inspired Deep Learning Combination Model

2019 ◽  
Vol 9 (1) ◽  
pp. 16-31
Author(s):  
Kyungkoo Jun
Keyword(s):  
Fourier Transform ◽  
Deep Learning ◽  
Short Term Memory ◽  
Window Size ◽  
Sensor Data ◽  
Data Sets ◽  
Data Set ◽  
Proposed Model ◽  
Testing Data ◽  
Labeling Scheme

Background & Objective: This paper proposes a Fourier transform inspired method to classify human activities from time series sensor data. Methods: Our method begins by decomposing 1D input signal into 2D patterns, which is motivated by the Fourier conversion. The decomposition is helped by Long Short-Term Memory (LSTM) which captures the temporal dependency from the signal and then produces encoded sequences. The sequences, once arranged into the 2D array, can represent the fingerprints of the signals. The benefit of such transformation is that we can exploit the recent advances of the deep learning models for the image classification such as Convolutional Neural Network (CNN). Results: The proposed model, as a result, is the combination of LSTM and CNN. We evaluate the model over two data sets. For the first data set, which is more standardized than the other, our model outperforms previous works or at least equal. In the case of the second data set, we devise the schemes to generate training and testing data by changing the parameters of the window size, the sliding size, and the labeling scheme. Conclusion: The evaluation results show that the accuracy is over 95% for some cases. We also analyze the effect of the parameters on the performance.

scholarly journals A Single-Terminal Fault Location Method for HVDC Transmission Lines Based on a Hybrid Deep Network

Electronics ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 255
Author(s):  
Lei Wang ◽  
Yigang He ◽  
Lie Li
Keyword(s):  
Deep Learning ◽  
Transmission Lines ◽  
Fault Location ◽  
Short Term Memory ◽  
Engineering Application ◽  
Energy Operator ◽  
Sampling Frequency ◽  
Learning Technology ◽  
Long Distance ◽  
Hvdc Transmission

High voltage direct current (HVDC) transmission systems play an increasingly important role in long-distance power transmission. Realizing accurate and timely fault location of transmission lines is extremely important for the safe operation of power systems. With the development of modern data acquisition and deep learning technology, deep learning methods have the feasibility of engineering application in fault location. The traditional single-terminal traveling wave method is used for fault location in HVDC systems. However, many challenges exist when a high impedance fault occurs including high sampling frequency dependence and difficulty to determine wave velocity and identify wave heads. In order to resolve these problems, this work proposed a deep hybrid convolutional neural network (CNN) and long short-term memory (LSTM) network model for single-terminal fault location of an HVDC system containing mixed cables and overhead line segments. Simultaneously, a variational mode decomposition–Teager energy operator is used in feature engineering to improve the effect of model training. 2D-CNN was employed as a classifier to identify fault segments, and LSTM as a regressor integrated the fault segment information of the classifier to achieve precise fault location. The experimental results demonstrate that the proposed method has high accuracy of fault location, with the effects of fault types, noise, sampling frequency, and different HVDC topologies in consideration.

scholarly journals A Hybrid Optimized LSTM Models for Human Activity Recognition with IOT Devices

2021 ◽  
pp. 182-189
Author(s):  
S. Arokiaraj ◽  
Dr. N. Viswanathan
Keyword(s):  
Deep Learning ◽  
Internet Of Things ◽  
Short Term Memory ◽  
The Other ◽  
Learning Models ◽  
Computational Overhead ◽  
Temporal Features ◽  
Human Movements ◽  
Proposed Model ◽  
Iot Devices

With the advent of Internet of things(IoT),HA (HA) recognition has contributed the more application in health care in terms of diagnosis and Clinical process. These devices must be aware of human movements to provide better aid in the clinical applications as well as user’s daily activity.Also , In addition to machine and deep learning algorithms, HA recognition systems has significantly improved in terms of high accurate recognition. However, the most of the existing models designed needs improvisation in terms of accuracy and computational overhead. In this research paper, we proposed a BAT optimized Long Short term Memory (BAT-LSTM) for an effective recognition of human activities using real time IoT systems. The data are collected by implanting the Internet of things) devices invasively. Then, proposed BAT-LSTM is deployed to extract the temporal features which are then used for classification to HA. Nearly 10,0000 dataset were collected and used for evaluating the proposed model. For the validation of proposed framework, accuracy, precision, recall, specificity and F1-score parameters are chosen and comparison is done with the other state-of-art deep learning models. The finding shows the proposed model outperforms the other learning models and finds its suitability for the HA recognition.

scholarly journals Stock Pattern Classification from Charts using Deep Learning Algorithms

2020 ◽  
Vol 3 (1) ◽  
pp. 445-454
Author(s):  
Celal Buğra Kaya ◽  
Alperen Yılmaz ◽  
Gizem Nur Uzun ◽  
Zeynep Hilal Kilimci
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Networks ◽  
Pattern Classification ◽  
Short Term Memory ◽  
Stock Exchange ◽  
Learning Techniques ◽  
Proposed Model ◽  
Istanbul Stock Exchange

Pattern classification is related with the automatic finding of regularities in dataset through the utilization of various learning techniques. Thus, the classification of the objects into a set of categories or classes is provided. This study is undertaken to evaluate deep learning methodologies to the classification of stock patterns. In order to classify patterns that are obtained from stock charts, convolutional neural networks (CNNs), recurrent neural networks (RNNs), and long-short term memory networks (LSTMs) are employed. To demonstrate the efficiency of proposed model in categorizing patterns, hand-crafted image dataset is constructed from stock charts in Istanbul Stock Exchange and NASDAQ Stock Exchange. Experimental results show that the usage of convolutional neural networks exhibits superior classification success in recognizing patterns compared to the other deep learning methodologies.

scholarly journals Nonintrusive Load Monitoring Based on Advanced Deep Learning and Novel Signature

2017 ◽  
Vol 2017 ◽  
pp. 1-22 ◽  
Author(s):  
Jihyun Kim ◽  
Thi-Thu-Huong Le ◽  
Howon Kim
Keyword(s):  
Deep Learning ◽  
Power Consumption ◽  
Distribution System ◽  
Short Term Memory ◽  
Electrical Power ◽  
Electricity Consumption ◽  
Classification Performance ◽  
Robust Solution ◽  
Proposed Model ◽  
Load Monitoring

Monitoring electricity consumption in the home is an important way to help reduce energy usage. Nonintrusive Load Monitoring (NILM) is existing technique which helps us monitor electricity consumption effectively and costly. NILM is a promising approach to obtain estimates of the electrical power consumption of individual appliances from aggregate measurements of voltage and/or current in the distribution system. Among the previous studies, Hidden Markov Model (HMM) based models have been studied very much. However, increasing appliances, multistate of appliances, and similar power consumption of appliances are three big issues in NILM recently. In this paper, we address these problems through providing our contributions as follows. First, we proposed state-of-the-art energy disaggregation based on Long Short-Term Memory Recurrent Neural Network (LSTM-RNN) model and additional advanced deep learning. Second, we proposed a novel signature to improve classification performance of the proposed model in multistate appliance case. We applied the proposed model on two datasets such as UK-DALE and REDD. Via our experimental results, we have confirmed that our model outperforms the advanced model. Thus, we show that our combination between advanced deep learning and novel signature can be a robust solution to overcome NILM’s issues and improve the performance of load identification.

Sign in / Sign up

Export Citation Format

Share Document