Prediction of Long Non-Coding RNAs Based on Deep Learning

With the rapid development of high-throughput sequencing technology, a large number of transcript sequences have been discovered, and how to identify long non-coding RNAs (lncRNAs) from transcripts is a challenging task. The identification and inclusion of lncRNAs not only can more clearly help us to understand life activities themselves, but can also help humans further explore and study the disease at the molecular level. At present, the detection of lncRNAs mainly includes two forms of calculation and experiment. Due to the limitations of bio sequencing technology and ineluctable errors in sequencing processes, the detection effect of these methods is not very satisfactory. In this paper, we constructed a deep-learning model to effectively distinguish lncRNAs from mRNAs. We used k-mer embedding vectors obtained through training the GloVe algorithm as input features and set up the deep learning framework to include a bidirectional long short-term memory model (BLSTM) layer and a convolutional neural network (CNN) layer with three additional hidden layers. By testing our model, we have found that it obtained the best values of 97.9%, 96.4% and 99.0% in F1score, accuracy and auROC, respectively, which showed better classification performance than the traditional PLEK, CNCI and CPC methods for identifying lncRNAs. We hope that our model will provide effective help in distinguishing mature mRNAs from lncRNAs, and become a potential tool to help humans understand and detect the diseases associated with lncRNAs.

Download Full-text

HADLN: Hybrid Attention-Based Deep Learning Network for Automated Arrhythmia Classification

Frontiers in Physiology ◽

10.3389/fphys.2021.683025 ◽

2021 ◽

Vol 12 ◽

Author(s):

Mingfeng Jiang ◽

Jiayan Gu ◽

Yang Li ◽

Bo Wei ◽

Jucheng Zhang ◽

...

Keyword(s):

Atrial Fibrillation ◽

Deep Learning ◽

Short Term Memory ◽

Classification Performance ◽

Attention Mechanism ◽

Learning Network ◽

Deep Convolution Neural Network ◽

Deep Learning Network ◽

Deep Learning Model ◽

Fusion Features

In recent years, with the development of artificial intelligence, deep learning model has achieved initial success in ECG data analysis, especially the detection of atrial fibrillation. In order to solve the problems of ignoring the correlation between contexts and gradient dispersion in traditional deep convolution neural network model, the hybrid attention-based deep learning network (HADLN) method is proposed to implement arrhythmia classification. The HADLN can make full use of the advantages of residual network (ResNet) and bidirectional long–short-term memory (Bi-LSTM) architecture to obtain fusion features containing local and global information and improve the interpretability of the model through the attention mechanism. The method is trained and verified by using the PhysioNet 2017 challenge dataset. Without loss of generality, the ECG signal is classified into four categories, including atrial fibrillation, noise, other, and normal signals. By combining the fusion features and the attention mechanism, the learned model has a great improvement in classification performance and certain interpretability. The experimental results show that the proposed HADLN method can achieve precision of 0.866, recall of 0.859, accuracy of 0.867, and F1-score of 0.880 on 10-fold cross-validation.

Download Full-text

Improving Sentiment Analysis using Hybrid Deep Learning Model

Recent Advances in Computer Science and Communications ◽

10.2174/2213275912666190328200012 ◽

2020 ◽

Vol 13 (4) ◽

pp. 627-640 ◽

Cited By ~ 1

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.

Download Full-text

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

Atmosphere ◽

10.3390/atmos12070924 ◽

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.

Download Full-text

BEHRT-HF: an interpretable transformer-based, deep learning model for prediction of incident heart failure

European Heart Journal ◽

10.1093/ehjci/ehaa946.3553 ◽

2020 ◽

Vol 41 (Supplement_2) ◽

Author(s):

S Rao ◽

Y Li ◽

R Ramakrishnan ◽

A Hassaine ◽

D Canoy ◽

...

Keyword(s):

Heart Failure ◽

Deep Learning ◽

State Of The Art ◽

Failure Prediction ◽

Predictive Performance ◽

Learning Model ◽

Learning Framework ◽

Incident Heart Failure ◽

Ablation Study ◽

Deep Learning Model

Abstract Background/Introduction Predicting incident heart failure has been challenging. Deep learning models when applied to rich electronic health records (EHR) offer some theoretical advantages. However, empirical evidence for their superior performance is limited and they remain commonly uninterpretable, hampering their wider use in medical practice. Purpose We developed a deep learning framework for more accurate and yet interpretable prediction of incident heart failure. Methods We used longitudinally linked EHR from practices across England, involving 100,071 patients, 13% of whom had been diagnosed with incident heart failure during follow-up. We investigated the predictive performance of a novel transformer deep learning model, “Transformer for Heart Failure” (BEHRT-HF), and validated it using both an external held-out dataset and an internal five-fold cross-validation mechanism using area under receiver operating characteristic (AUROC) and area under the precision recall curve (AUPRC). Predictor groups included all outpatient and inpatient diagnoses within their temporal context, medications, age, and calendar year for each encounter. By treating diagnoses as anchors, we alternatively removed different modalities (ablation study) to understand the importance of individual modalities to the performance of incident heart failure prediction. Using perturbation-based techniques, we investigated the importance of associations between selected predictors and heart failure to improve model interpretability. Results BEHRT-HF achieved high accuracy with AUROC 0.932 and AUPRC 0.695 for external validation, and AUROC 0.933 (95% CI: 0.928, 0.938) and AUPRC 0.700 (95% CI: 0.682, 0.718) for internal validation. Compared to the state-of-the-art recurrent deep learning model, RETAIN-EX, BEHRT-HF outperformed it by 0.079 and 0.030 in terms of AUPRC and AUROC. Ablation study showed that medications were strong predictors, and calendar year was more important than age. Utilising perturbation, we identified and ranked the intensity of associations between diagnoses and heart failure. For instance, the method showed that established risk factors including myocardial infarction, atrial fibrillation and flutter, and hypertension all strongly associated with the heart failure prediction. Additionally, when population was stratified into different age groups, incident occurrence of a given disease had generally a higher contribution to heart failure prediction in younger ages than when diagnosed later in life. Conclusions Our state-of-the-art deep learning framework outperforms the predictive performance of existing models whilst enabling a data-driven way of exploring the relative contribution of a range of risk factors in the context of other temporal information. Funding Acknowledgement Type of funding source: Private grant(s) and/or Sponsorship. Main funding source(s): National Institute for Health Research, Oxford Martin School, Oxford Biomedical Research Centre

Download Full-text

PlncRNA-HDeep: plant long noncoding RNA prediction using hybrid deep learning based on two encoding styles

BMC Bioinformatics ◽

10.1186/s12859-020-03870-2 ◽

2021 ◽

Vol 22 (S3) ◽

Author(s):

Jun Meng ◽

Qiang Kang ◽

Zheng Chang ◽

Yushi Luan

Keyword(s):

Deep Learning ◽

Noncoding Rna ◽

Nearest Neighbor ◽

Short Term Memory ◽

Biological Activities ◽

Support Vector ◽

Multiple Perspectives ◽

K Nearest Neighbor ◽

Rna Sequences ◽

Deep Learning Model

Abstract Background Long noncoding RNAs (lncRNAs) play an important role in regulating biological activities and their prediction is significant for exploring biological processes. Long short-term memory (LSTM) and convolutional neural network (CNN) can automatically extract and learn the abstract information from the encoded RNA sequences to avoid complex feature engineering. An ensemble model learns the information from multiple perspectives and shows better performance than a single model. It is feasible and interesting that the RNA sequence is considered as sentence and image to train LSTM and CNN respectively, and then the trained models are hybridized to predict lncRNAs. Up to present, there are various predictors for lncRNAs, but few of them are proposed for plant. A reliable and powerful predictor for plant lncRNAs is necessary. Results To boost the performance of predicting lncRNAs, this paper proposes a hybrid deep learning model based on two encoding styles (PlncRNA-HDeep), which does not require prior knowledge and only uses RNA sequences to train the models for predicting plant lncRNAs. It not only learns the diversified information from RNA sequences encoded by p-nucleotide and one-hot encodings, but also takes advantages of lncRNA-LSTM proposed in our previous study and CNN. The parameters are adjusted and three hybrid strategies are tested to maximize its performance. Experiment results show that PlncRNA-HDeep is more effective than lncRNA-LSTM and CNN and obtains 97.9% sensitivity, 95.1% precision, 96.5% accuracy and 96.5% F1 score on Zea mays dataset which are better than those of several shallow machine learning methods (support vector machine, random forest, k-nearest neighbor, decision tree, naive Bayes and logistic regression) and some existing tools (CNCI, PLEK, CPC2, LncADeep and lncRNAnet). Conclusions PlncRNA-HDeep is feasible and obtains the credible predictive results. It may also provide valuable references for other related research.

Download Full-text

Surrounding Vehicles’ Contribution to Car-Following Models: Deep-Learning-Based Analysis

Transportation Research Record Journal of the Transportation Research Board ◽

10.1177/03611981211018693 ◽

2021 ◽

pp. 036119812110186

Author(s):

Saeed Vasebi ◽

Yeganeh M. Hayeri ◽

Peter J. Jin

Keyword(s):

Deep Learning ◽

Traffic Flow ◽

Short Term Memory ◽

Data Availability ◽

Car Following ◽

Preceding Vehicle ◽

Long Short Term Memory ◽

The Right ◽

Mean Square Errors ◽

Deep Learning Model

Relatively recent increased computational power and extensive traffic data availability have provided a unique opportunity to re-investigate drivers’ car-following (CF) behavior. Classic CF models assume drivers’ behavior is only influenced by their preceding vehicle. Recent studies have indicated that considering surrounding vehicles’ information (e.g., multiple preceding vehicles) could affect CF models’ performance. An in-depth investigation of surrounding vehicles’ contribution to CF modeling performance has not been reported in the literature. This study uses a deep-learning model with long short-term memory (LSTM) to investigate to what extent considering surrounding vehicles could improve CF models’ performance. This investigation helps to select the right inputs for traffic flow modeling. Five CF models are compared in this study (i.e., classic, multi-anticipative, adjacent-lanes, following-vehicle, and all-surrounding-vehicles CF models). Performance of the CF models is compared in relation to accuracy, stability, and smoothness of traffic flow. The CF models are trained, validated, and tested by a large publicly available dataset. The average mean square errors (MSEs) for the classic, multi-anticipative, adjacent-lanes, following-vehicle, and all-surrounding-vehicles CF models are 1.58 × 10−3, 1.54 × 10−3, 1.56 × 10−3, 1.61 × 10−3, and 1.73 × 10−3, respectively. However, the results show insignificant performance differences between the classic CF model and multi-anticipative model or adjacent-lanes model in relation to accuracy, stability, or smoothness. The following-vehicle CF model shows similar performance to the multi-anticipative model. The all-surrounding-vehicles CF model has underperformed all the other models.

Download Full-text

Sensory Descriptor Analysis of Whisky Lexicons through the Use of Deep Learning

Foods ◽

10.3390/foods10071633 ◽

2021 ◽

Vol 10 (7) ◽

pp. 1633

Author(s):

Chreston Miller ◽

Leah Hamilton ◽

Jacob Lahne

Keyword(s):

Deep Learning ◽

Short Term Memory ◽

Descriptive Analysis ◽

Food Products ◽

Training Dataset ◽

Test Accuracy ◽

Language Structure ◽

Deep Learning Model ◽

Descriptor Analysis ◽

Descriptive Language

This paper is concerned with extracting relevant terms from a text corpus on whisk(e)y. “Relevant” terms are usually contextually defined in their domain of use. Arguably, every domain has a specialized vocabulary used for describing things. For example, the field of Sensory Science, a sub-field of Food Science, investigates human responses to food products and differentiates “descriptive” terms for flavors from “ordinary”, non-descriptive language. Within the field, descriptors are generated through Descriptive Analysis, a method wherein a human panel of experts tastes multiple food products and defines descriptors. This process is both time-consuming and expensive. However, one could leverage existing data to identify and build a flavor language automatically. For example, there are thousands of professional and semi-professional reviews of whisk(e)y published on the internet, providing abundant descriptors interspersed with non-descriptive language. The aim, then, is to be able to automatically identify descriptive terms in unstructured reviews for later use in product flavor characterization. We created two systems to perform this task. The first is an interactive visual tool that can be used to tag examples of descriptive terms from thousands of whisky reviews. This creates a training dataset that we use to perform transfer learning using GloVe word embeddings and a Long Short-Term Memory deep learning model architecture. The result is a model that can accurately identify descriptors within a corpus of whisky review texts with a train/test accuracy of 99% and precision, recall, and F1-scores of 0.99. We tested for overfitting by comparing the training and validation loss for divergence. Our results show that the language structure for descriptive terms can be programmatically learned.

Download Full-text

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

10.21203/rs.3.rs-302084/v1 ◽

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.

Download Full-text

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

10.21203/rs.3.rs-281525/v1 ◽

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

Download Full-text

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

F1000Research ◽

10.12688/f1000research.72980.1 ◽

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.

Download Full-text