scholarly journals A Hybrid Deep Learning Model for Predicting Protein Hydroxylation Sites

2018 ◽  
Vol 19 (9) ◽  
pp. 2817 ◽  
Author(s):  
Haixia Long ◽  
Bo Liao ◽  
Xingyu Xu ◽  
Jialiang Yang
Keyword(s):  
Deep Learning ◽  
Short Term Memory ◽  
Learning Model ◽  
New Drugs ◽  
Post Translational Modifications ◽  
Novel Approach ◽  
Benchmark Datasets ◽  
Memory Network ◽  
Scoring Matrix ◽  
Deep Learning Model

Protein hydroxylation is one type of post-translational modifications (PTMs) playing critical roles in human diseases. It is known that protein sequence contains many uncharacterized residues of proline and lysine. The question that needs to be answered is: which residue can be hydroxylated, and which one cannot. The answer will not only help understand the mechanism of hydroxylation but can also benefit the development of new drugs. In this paper, we proposed a novel approach for predicting hydroxylation using a hybrid deep learning model integrating the convolutional neural network (CNN) and long short-term memory network (LSTM). We employed a pseudo amino acid composition (PseAAC) method to construct valid benchmark datasets based on a sliding window strategy and used the position-specific scoring matrix (PSSM) to represent samples as inputs to the deep learning model. In addition, we compared our method with popular predictors including CNN, iHyd-PseAAC, and iHyd-PseCp. The results for 5-fold cross-validations all demonstrated that our method significantly outperforms the other methods in prediction accuracy.

scholarly journals Advancing PICO element detection in biomedical text via deep neural networks

2020 ◽  
Vol 36 (12) ◽  
pp. 3856-3862
Author(s):  
Di Jin ◽  
Peter Szolovits
Keyword(s):  
Deep Learning ◽  
Short Term Memory ◽  
Conditional Random Field ◽  
Contextual Information ◽  
Learning Model ◽  
Detection Accuracy ◽  
Clinical Question ◽  
Specific Patient ◽  
Benchmark Datasets ◽  
Deep Learning Model

Abstract Motivation In evidence-based medicine, defining a clinical question in terms of the specific patient problem aids the physicians to efficiently identify appropriate resources and search for the best available evidence for medical treatment. In order to formulate a well-defined, focused clinical question, a framework called PICO is widely used, which identifies the sentences in a given medical text that belong to the four components typically reported in clinical trials: Participants/Problem (P), Intervention (I), Comparison (C) and Outcome (O). In this work, we propose a novel deep learning model for recognizing PICO elements in biomedical abstracts. Based on the previous state-of-the-art bidirectional long-short-term memory (bi-LSTM) plus conditional random field architecture, we add another layer of bi-LSTM upon the sentence representation vectors so that the contextual information from surrounding sentences can be gathered to help infer the interpretation of the current one. In addition, we propose two methods to further generalize and improve the model: adversarial training and unsupervised pre-training over large corpora. Results We tested our proposed approach over two benchmark datasets. One is the PubMed-PICO dataset, where our best results outperform the previous best by 5.5%, 7.9% and 5.8% for P, I and O elements in terms of F1 score, respectively. And for the other dataset named NICTA-PIBOSO, the improvements for P/I/O elements are 3.9%, 15.6% and 1.3% in F1 score, respectively. Overall, our proposed deep learning model can obtain unprecedented PICO element detection accuracy while avoiding the need for any manual feature selection. Availability and implementation Code is available at https://github.com/jind11/Deep-PICO-Detection.

scholarly journals Predicting subcellular location of protein with evolution information and sequence-based deep learning

2021 ◽  
Vol 22 (S10) ◽  
Author(s):  
Zhijun Liao ◽  
Gaofeng Pan ◽  
Chao Sun ◽  
Jijun Tang
Keyword(s):  
Deep Learning ◽  
Short Term Memory ◽  
Protein Sequences ◽  
Subcellular Location ◽  
Protein Subcellular Location ◽  
Benchmark Datasets ◽  
Memory Network ◽  
Scoring Matrix ◽  
Protein Subcellular Locations ◽  
Protein Subcellular Localization Prediction

Abstract Background Protein subcellular localization prediction plays an important role in biology research. Since traditional methods are laborious and time-consuming, many machine learning-based prediction methods have been proposed. However, most of the proposed methods ignore the evolution information of proteins. In order to improve the prediction accuracy, we present a deep learning-based method to predict protein subcellular locations. Results Our method utilizes not only amino acid compositions sequence but also evolution matrices of proteins. Our method uses a bidirectional long short-term memory network that processes the entire protein sequence and a convolutional neural network that extracts features from protein sequences. The position specific scoring matrix is used as a supplement to protein sequences. Our method was trained and tested on two benchmark datasets. The experiment results show that our method yields accurate results on the two datasets with an average precision of 0.7901, ranking loss of 0.0758 and coverage of 1.2848. Conclusion The experiment results show that our method outperforms five methods currently available. According to those experiments, we can see that our method is an acceptable alternative to predict protein subcellular location.

Improving Sentiment Analysis using Hybrid Deep Learning Model

2020 ◽  
Vol 13 (4) ◽  
pp. 627-640 ◽  
Author(s):  
Avinash Chandra Pandey ◽  
Dharmveer Singh Rajpoot
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Sentiment Analysis ◽  
Classification Accuracy ◽  
Short Term Memory ◽  
Computational Cost ◽  
Extraction Process ◽  
Learning Model ◽  
Sentiment Classification ◽  
Deep Learning Model

Background: Sentiment analysis is a contextual mining of text which determines viewpoint of users with respect to some sentimental topics commonly present at social networking websites. Twitter is one of the social sites where people express their opinion about any topic in the form of tweets. These tweets can be examined using various sentiment classification methods to find the opinion of users. Traditional sentiment analysis methods use manually extracted features for opinion classification. The manual feature extraction process is a complicated task since it requires predefined sentiment lexicons. On the other hand, deep learning methods automatically extract relevant features from data hence; they provide better performance and richer representation competency than the traditional methods. Objective: The main aim of this paper is to enhance the sentiment classification accuracy and to reduce the computational cost. Method: To achieve the objective, a hybrid deep learning model, based on convolution neural network and bi-directional long-short term memory neural network has been introduced. Results: The proposed sentiment classification method achieves the highest accuracy for the most of the datasets. Further, from the statistical analysis efficacy of the proposed method has been validated. Conclusion: Sentiment classification accuracy can be improved by creating veracious hybrid models. Moreover, performance can also be enhanced by tuning the hyper parameters of deep leaning models.

scholarly journals Application of Rough and Fuzzy Set Theory for Prediction of Stochastic Wind Speed Data Using Long Short-Term Memory

Atmosphere ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 924
Author(s):  
Moslem Imani ◽  
Hoda Fakour ◽  
Wen-Hau Lan ◽  
Huan-Chin Kao ◽  
Chi Ming Lee ◽  
...  
Keyword(s):  
Deep Learning ◽  
Wind Speed ◽  
Set Theory ◽  
Rough Set ◽  
Fuzzy Set Theory ◽  
Short Term Memory ◽  
Learning Model ◽  
Short Term ◽  
Long Short Term Memory ◽  
Deep Learning Model

Despite the great significance of precisely forecasting the wind speed for development of the new and clean energy technology and stable grid operators, the stochasticity of wind speed makes the prediction a complex and challenging task. For improving the security and economic performance of power grids, accurate short-term wind power forecasting is crucial. In this paper, a deep learning model (Long Short-term Memory (LSTM)) has been proposed for wind speed prediction. Knowing that wind speed time series is nonlinear stochastic, the mutual information (MI) approach was used to find the best subset from the data by maximizing the joint MI between subset and target output. To enhance the accuracy and reduce input characteristics and data uncertainties, rough set and interval type-2 fuzzy set theory are combined in the proposed deep learning model. Wind speed data from an international airport station in the southern coast of Iran Bandar-Abbas City was used as the original input dataset for the optimized deep learning model. Based on the statistical results, the rough set LSTM (RST-LSTM) model showed better prediction accuracy than fuzzy and original LSTM, as well as traditional neural networks, with the lowest error for training and testing datasets in different time horizons. The suggested model can support the optimization of the control approach and the smooth procedure of power system. The results confirm the superior capabilities of deep learning techniques for wind speed forecasting, which could also inspire new applications in meteorology assessment.

AOHDL: Archimedes Optimization Based Hybrid Deep Learning Model for Soybean Plant Disease Classification

2021 ◽  
Author(s):  
J. Annrose ◽  
N. Herald Anantha Rufus ◽  
C. R. Edwin Selva Rex ◽  
D. Godwin Immanuel
Keyword(s):  
Deep Learning ◽  
Optimization Algorithm ◽  
Short Term Memory ◽  
Learning Model ◽  
Disease Classification ◽  
Training Data ◽  
Machine Learning Techniques ◽  
Soybean Plant ◽  
Lower Accuracy ◽  
Deep Learning Model

Abstract Bean which is botanically called Phaseolus vulgaris L belongs to the Fabaceae family.During bean disease identification, unnecessary economical losses occur due to the delay of the treatment period, incorrect treatment, and lack of knowledge. The existing deep learning and machine learning techniques met few issues such as high computational complexity, higher cost associated with the training data, more execution time, noise, feature dimensionality, lower accuracy, low speed, etc. To tackle these problems, we have proposed a hybrid deep learning model with an Archimedes optimization algorithm (HDL-AOA) for bean disease classification. In this work, there are five bean classes of which one is a healthy class whereas the remaining four classes indicate different diseases such as Bean halo blight, Pythium diseases, Rhizoctonia root rot, and Anthracnose abnormalities acquired from the Soybean (Large) Data Set.The hybrid deep learning technique is the combination of wavelet packet decomposition (WPD) and long short term memory (LSTM). Initially, the WPD decomposes the input images into four sub-series. For these sub-series, four LSTM networks were developed. During bean disease classification, an Archimedes optimization algorithm (AOA) enhances the classification accuracy for multiple single LSTM networks. MATLAB software implements the HDL-AOA model for bean disease classification. The proposed model accomplishes lower MAPE than other exiting methods. Finally, the proposed HDL-AOA model outperforms excellent classification results using different evaluation measures such as accuracy, specificity, sensitivity, precision, recall, and F-score.

scholarly journals Soybean Plant Disease Classification using Archimedes Optimization Algorithm based Hybrid Deep Learning Model

2021 ◽  
Author(s):  
J. Annrose ◽  
N. Herald Anantha Rufus ◽  
C. R. Edwin Selva Rex ◽  
D. Godwin Immanuel
Keyword(s):  
Deep Learning ◽  
Optimization Algorithm ◽  
Short Term Memory ◽  
Learning Model ◽  
Disease Classification ◽  
Training Data ◽  
Machine Learning Techniques ◽  
Soybean Plant ◽  
Lower Accuracy ◽  
Deep Learning Model

Abstract Bean which is botanically called Phaseolus vulgaris L belongs to the Fabaceae family.During bean disease identification, unnecessary economical losses occur due to the delay of the treatment period, incorrect treatment, and lack of knowledge. The existing deep learning and machine learning techniques met few issues such as high computational complexity, higher cost associated with the training data, more execution time, noise, feature dimensionality, lower accuracy, low speed, etc. To tackle these problems, we have proposed a hybrid deep learning model with an Archimedes optimization algorithm (HDL-AOA) for bean disease classification. In this work, there are five bean classes of which one is a healthy class whereas the remaining four classes indicate different diseases such as Bean halo blight, Pythium diseases, Rhizoctonia root rot, and Anthracnose abnormalities acquired from the Soybean (Large) Data Set.The hybrid deep learning technique is the combination of wavelet packet decomposition (WPD) and long short term memory (LSTM). Initially, the WPD decomposes the input images into four sub-series. For these sub-series, four LSTM networks were developed. During bean disease classification, an Archimedes optimization algorithm (AOA) enhances the classification accuracy for multiple single LSTM networks. MATLAB software implements the HDL-AOA model for bean disease classification. The proposed model accomplishes lower MAPE than other exiting methods. Finally, the proposed HDL-AOA model outperforms excellent classification results using different evaluation measures such as accuracy, specificity, sensitivity, precision, recall, and F-score.

scholarly journals Spatio-temporal deep learning model for distortion classification in laparoscopic video

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 1010
Author(s):  
Nouar AlDahoul ◽  
Hezerul Abdul Karim ◽  
Abdulaziz Saleh Ba Wazir ◽  
Myles Joshua Toledo Tan ◽  
Mohammad Faizal Ahmad Fauzi
Keyword(s):  
Deep Learning ◽  
Large Scale ◽  
Spatial Information ◽  
Short Term Memory ◽  
Learning Model ◽  
Motion Blur ◽  
Video Frame ◽  
Video Enhancement ◽  
Deep Learning Model ◽  
Laparoscopic Videos

Background: Laparoscopy is a surgery performed in the abdomen without making large incisions in the skin and with the aid of a video camera, resulting in laparoscopic videos. The laparoscopic video is prone to various distortions such as noise, smoke, uneven illumination, defocus blur, and motion blur. One of the main components in the feedback loop of video enhancement systems is distortion identification, which automatically classifies the distortions affecting the videos and selects the video enhancement algorithm accordingly. This paper aims to address the laparoscopic video distortion identification problem by developing fast and accurate multi-label distortion classification using a deep learning model. Current deep learning solutions based on convolutional neural networks (CNNs) can address laparoscopic video distortion classification, but they learn only spatial information. Methods: In this paper, utilization of both spatial and temporal features in a CNN-long short-term memory (CNN-LSTM) model is proposed as a novel solution to enhance the classification. First, pre-trained ResNet50 CNN was used to extract spatial features from each video frame by transferring representation from large-scale natural images to laparoscopic images. Next, LSTM was utilized to consider the temporal relation between the features extracted from the laparoscopic video frames to produce multi-label categories. A novel laparoscopic video dataset proposed in the ICIP2020 challenge was used for training and evaluation of the proposed method. Results: The experiments conducted show that the proposed CNN-LSTM outperforms the existing solutions in terms of accuracy (85%), and F1-score (94.2%). Additionally, the proposed distortion identification model is able to run in real-time with low inference time (0.15 sec). Conclusions: The proposed CNN-LSTM model is a feasible solution to be utilized in laparoscopic videos for distortion identification.

scholarly journals Prediction of synoptic-scale sea level pressure over the Indian monsoon region using deep learning

2021 ◽  
Author(s):  
Aryaman Sinha ◽  
Mayuna Gupta ◽  
K S S Sai Srujan ◽  
Hariprasad Kodamana ◽  
Sandeep Sukumaran
Keyword(s):  
Deep Learning ◽  
Sea Level ◽  
Short Term Memory ◽  
Weather Forecasting ◽  
Weather Prediction ◽  
Learning Model ◽  
Synoptic Scale ◽  
Sea Level Pressure ◽  
Level Pressure ◽  
Deep Learning Model

<div><div><div><p>The synoptic-scale (3 - 7 days) variability is a dominant contributor to the Indian summer monsoon (ISM) seasonal precipitation. An accurate prediction of ISM precipitation by dynamical or statistical models remains a challenge. Here we show that the sea level pressure (SLP) can be used as a proxy to predict the active-break cycle as well as the genesis of low- pressure-systems (LPS), using a deep learning model, namely, convolutional long short-term memory (ConvLSTM) networks. The deep learning model is able to reliably predict the daily SLP anomalies over Central India and the Bay of Bengal at a lead time of 7 days. As the fluctuations in SLP drive the changes in the strength of the atmospheric circulation, the prediction of SLP anomalies is useful in predicting the intensity of ISM. It is demonstrated that the ConvLSTM possesses better prediction skill compared to a conventional numerical weather prediction model, indicating the usefulness of a physics guided deep learning model in medium range weather forecasting.</p></div></div></div>

scholarly journals Which Attributes Matter the Most for Loan Origination? A Neural Attention Approach

2020 ◽  
Author(s):  
Antonios Alexos ◽  
Sotirios Chatzis
Keyword(s):  
Deep Learning ◽  
Real World ◽  
Individual Case ◽  
Learning Model ◽  
Attention Mechanism ◽  
Novel Approach ◽  
Specific Individual ◽  
Real World Datasets ◽  
Deep Learning Model

In this paper we address the understanding of the problem, of why a deep learning model decides that an individual is eligible for a loan or not. Here we propose a novel approach for inferring, which attributes matter the most, for making a decision in each specific individual case. Specifically we leverage concepts from neural attention to devise a novel feature wise attention mechanism. As we show, using real world datasets, our approach offers unique insights into the importance of various features, by producing a decision explanation for each specific loan case. At the same time, we observe that our novel mechanism, generates decisions which are much closer to the decisions generated by human experts, compared to the existent competitors.

scholarly journals Hybrid deep learning model using recurrent neural network and gated recurrent unit for heart disease prediction

2021 ◽  
Vol 11 (6) ◽  
pp. 5467
Author(s):  
Surenthiran Krishnan ◽  
Pritheega Magalingam ◽  
Roslina Ibrahim
Keyword(s):  
Neural Network ◽  
Heart Disease ◽  
Deep Learning ◽  
Recurrent Neural Network ◽  
Short Term Memory ◽  
Learning Model ◽  
Disease Prediction ◽  
The Neural Network ◽  
Proposed Model ◽  
Deep Learning Model

<span>This paper proposes a new hybrid deep learning model for heart disease prediction using recurrent neural network (RNN) with the combination of multiple gated recurrent units (GRU), long short-term memory (LSTM) and Adam optimizer. This proposed model resulted in an outstanding accuracy of 98.6876% which is the highest in the existing model of RNN. The model was developed in Python 3.7 by integrating RNN in multiple GRU that operates in Keras and Tensorflow as the backend for deep learning process, supported by various Python libraries. The recent existing models using RNN have reached an accuracy of 98.23% and deep neural network (DNN) has reached 98.5%. The common drawbacks of the existing models are low accuracy due to the complex build-up of the neural network, high number of neurons with redundancy in the neural network model and imbalance datasets of Cleveland. Experiments were conducted with various customized model, where results showed that the proposed model using RNN and multiple GRU with synthetic minority oversampling technique (SMOTe) has reached the best performance level. This is the highest accuracy result for RNN using Cleveland datasets and much promising for making an early heart disease prediction for the patients.</span>

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