scholarly journals SNF-NN: Computational Method To Predict Drug-Disease Interactions Using Similarity Network Fusion and Neural Networks

2020 ◽  
Author(s):  
Tamer Jarada ◽  
Jon Rokne ◽  
Reda Alhajj
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Cross Validation ◽  
Drug Repositioning ◽  
Computational Method ◽  
Machine Learning Techniques ◽  
Similarity Network ◽  
Novel Drug ◽  
Similarity Information ◽  
Fold Cross Validation

Abstract Drug repositioning is an emerging approach in pharmaceutical research for identifying novel therapeutic potentials for approved drugs and discover therapies for untreated diseases. Due to its time and cost efficiency, drug repositioning plays an instrumental role in optimizing the drug development process compared to the traditional de novo drug discovery process. Advances in the genomics, together with the enormous growth of large-scale publicly available data and the availability of high-performance computing capabilities, have further motivated the development of computational drug repositioning approaches. More recently, the rise of machine learning techniques, together with the availability of powerful computers, has made the area of computational drug repositioning an area of intense activities. In this study, a novel framework SNF-NN based on deep learning is presented, where novel drugdisease interactions are predicted using drug-related similarity information, disease-related similarity information, and known drug-disease interactions. Heterogeneous similarity information related to drugs and disease is fed to the proposed framework in order to predict novel drug-disease interactions. SNF-NN uses similarity selection, similarity network fusion, and a highly tuned novel neural network model to predict new drug-disease interactions. The robustness of SNF-NN is evaluated by comparing its performance with nine baseline machine learning methods. The proposed framework outperforms all baseline methods (AUC − ROC = 0.867, and AUC − P R=0.876) using stratified 10-fold cross-validation. To further demonstrate the reliability and robustness of SNF-NN, two datasets are used to fairly validate the proposed framework’s performance against seven recent state-of-the-art methods for drug-disease interaction prediction. SNF-NN achieves remarkable performance in stratified 10-fold cross-validation with AUC − ROC ranging from 0.879 to 0.931 and AUC − P R from 0.856 to 0.903. Moreover, the efficiency of SNF-NN by is verified by validating predicted unknown drug-disease interactions against clinical trials and published studies. In conclusion, computational drug repositioning research can significantly benefit from integrating similarity measures in heterogeneous networks and deep learning models for predicting novel drug-disease interactions

scholarly journals SNF-NN: computational method to predict drug-disease interactions using similarity network fusion and neural networks

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Tamer N. Jarada ◽  
Jon G. Rokne ◽  
Reda Alhajj
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Cross Validation ◽  
Drug Repositioning ◽  
Computational Method ◽  
Machine Learning Techniques ◽  
Similarity Network ◽  
Novel Drug ◽  
Similarity Information ◽  
Fold Cross Validation

Abstract Background Drug repositioning is an emerging approach in pharmaceutical research for identifying novel therapeutic potentials for approved drugs and discover therapies for untreated diseases. Due to its time and cost efficiency, drug repositioning plays an instrumental role in optimizing the drug development process compared to the traditional de novo drug discovery process. Advances in the genomics, together with the enormous growth of large-scale publicly available data and the availability of high-performance computing capabilities, have further motivated the development of computational drug repositioning approaches. More recently, the rise of machine learning techniques, together with the availability of powerful computers, has made the area of computational drug repositioning an area of intense activities. Results In this study, a novel framework SNF-NN based on deep learning is presented, where novel drug-disease interactions are predicted using drug-related similarity information, disease-related similarity information, and known drug-disease interactions. Heterogeneous similarity information related to drugs and disease is fed to the proposed framework in order to predict novel drug-disease interactions. SNF-NN uses similarity selection, similarity network fusion, and a highly tuned novel neural network model to predict new drug-disease interactions. The robustness of SNF-NN is evaluated by comparing its performance with nine baseline machine learning methods. The proposed framework outperforms all baseline methods ($$AUC-ROC$$ A U C - R O C = 0.867, and $$AUC-PR$$ A U C - P R =0.876) using stratified 10-fold cross-validation. To further demonstrate the reliability and robustness of SNF-NN, two datasets are used to fairly validate the proposed framework’s performance against seven recent state-of-the-art methods for drug-disease interaction prediction. SNF-NN achieves remarkable performance in stratified 10-fold cross-validation with $$AUC-ROC$$ A U C - R O C ranging from 0.879 to 0.931 and $$AUC-PR$$ A U C - P R from 0.856 to 0.903. Moreover, the efficiency of SNF-NN is verified by validating predicted unknown drug-disease interactions against clinical trials and published studies. Conclusion In conclusion, computational drug repositioning research can significantly benefit from integrating similarity measures in heterogeneous networks and deep learning models for predicting novel drug-disease interactions. The data and implementation of SNF-NN are available at http://pages.cpsc.ucalgary.ca/ tnjarada/snf-nn.php.

scholarly journals Machine Learning Methods in Drug Discovery

Molecules ◽  
2020 ◽  
Vol 25 (22) ◽  
pp. 5277
Author(s):  
Lauv Patel ◽  
Tripti Shukla ◽  
Xiuzhen Huang ◽  
David W. Ussery ◽  
Shanzhi Wang
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Drug Discovery ◽  
High Throughput Screening ◽  
Drug Targets ◽  
Learning Algorithms ◽  
Machine Learning Techniques ◽  
Online Information ◽  
Drug Candidates ◽  
Novel Drug

The advancements of information technology and related processing techniques have created a fertile base for progress in many scientific fields and industries. In the fields of drug discovery and development, machine learning techniques have been used for the development of novel drug candidates. The methods for designing drug targets and novel drug discovery now routinely combine machine learning and deep learning algorithms to enhance the efficiency, efficacy, and quality of developed outputs. The generation and incorporation of big data, through technologies such as high-throughput screening and high through-put computational analysis of databases used for both lead and target discovery, has increased the reliability of the machine learning and deep learning incorporated techniques. The use of these virtual screening and encompassing online information has also been highlighted in developing lead synthesis pathways. In this review, machine learning and deep learning algorithms utilized in drug discovery and associated techniques will be discussed. The applications that produce promising results and methods will be reviewed.

scholarly journals 6mAPred-MSFF: A Deep Learning Model for Predicting DNA N6-Methyladenine Sites across Species Based on a Multi-Scale Feature Fusion Mechanism

2021 ◽  
Vol 11 (16) ◽  
pp. 7731
Author(s):  
Rao Zeng ◽  
Minghong Liao
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Prediction Accuracy ◽  
Cross Validation ◽  
Feature Fusion ◽  
Experimental Comparison ◽  
Scale Feature ◽  
Learning Framework ◽  
Multi Scale ◽  
Fold Cross Validation

DNA methylation is one of the most extensive epigenetic modifications. DNA N6-methyladenine (6mA) plays a key role in many biology regulation processes. An accurate and reliable genome-wide identification of 6mA sites is crucial for systematically understanding its biological functions. Some machine learning tools can identify 6mA sites, but their limited prediction accuracy and lack of robustness limit their usability in epigenetic studies, which implies the great need of developing new computational methods for this problem. In this paper, we developed a novel computational predictor, namely the 6mAPred-MSFF, which is a deep learning framework based on a multi-scale feature fusion mechanism to identify 6mA sites across different species. In the predictor, we integrate the inverted residual block and multi-scale attention mechanism to build lightweight and deep neural networks. As compared to existing predictors using traditional machine learning, our deep learning framework needs no prior knowledge of 6mA or manually crafted sequence features and sufficiently capture better characteristics of 6mA sites. By benchmarking comparison, our deep learning method outperforms the state-of-the-art methods on the 5-fold cross-validation test on the seven datasets of six species, demonstrating that the proposed 6mAPred-MSFF is more effective and generic. Specifically, our proposed 6mAPred-MSFF gives the sensitivity and specificity of the 5-fold cross-validation on the 6mA-rice-Lv dataset as 97.88% and 94.64%, respectively. Our model trained with the rice data predicts well the 6mA sites of other five species: Arabidopsis thaliana, Fragaria vesca, Rosa chinensis, Homo sapiens, and Drosophila melanogaster with a prediction accuracy 98.51%, 93.02%, and 91.53%, respectively. Moreover, via experimental comparison, we explored performance impact by training and testing our proposed model under different encoding schemes and feature descriptors.

scholarly journals Secure Cyber Defense: An Analysis of Network Intrusion-Based Dataset CCD-IDSv1 with Machine Learning and Deep Learning Models

Electronics ◽  
2021 ◽  
Vol 10 (15) ◽  
pp. 1747
Author(s):  
Niraj Thapa ◽  
Zhipeng Liu ◽  
Addison Shaver ◽  
Albert Esterline ◽  
Balakrishna Gokaraju ◽  
...  
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Intrusion Detection ◽  
Anomaly Detection ◽  
Cross Validation ◽  
Real Life ◽  
Cyber Defense ◽  
Ensemble Models ◽  
Network Intrusion ◽  
Fold Cross Validation

Anomaly detection and multi-attack classification are major concerns for cyber defense. Several publicly available datasets have been used extensively for the evaluation of Intrusion Detection Systems (IDSs). However, most of the publicly available datasets may not contain attack scenarios based on evolving threats. The development of a robust network intrusion dataset is vital for network threat analysis and mitigation. Proactive IDSs are required to tackle ever-growing threats in cyberspace. Machine learning (ML) and deep learning (DL) models have been deployed recently to detect the various types of cyber-attacks. However, current IDSs struggle to attain both a high detection rate and a low false alarm rate. To address these issues, we first develop a Center for Cyber Defense (CCD)-IDSv1 labeled flow-based dataset in an OpenStack environment. Five different attacks with normal usage imitating real-life usage are implemented. The number of network features is increased to overcome the shortcomings of the previous network flow-based datasets such as CIDDS and CIC-IDS2017. Secondly, this paper presents a comparative analysis on the effectiveness of different ML and DL models on our CCD-IDSv1 dataset. In this study, we consider both cyber anomaly detection and multi-attack classification. To improve the performance, we developed two DL-based ensemble models: Ensemble-CNN-10 and Ensemble-CNN-LSTM. Ensemble-CNN-10 combines 10 CNN models developed from 10-fold cross-validation, whereas Ensemble-CNN-LSTM combines base CNN and LSTM models. This paper also presents feature importance for both anomaly detection and multi-attack classification. Overall, the proposed ensemble models performed well in both the 10-fold cross-validation and independent testing on our dataset. Together, these results suggest the robustness and effectiveness of the proposed IDSs based on ML and DL models on the CCD-IDSv1 intrusion detection dataset.

scholarly journals Computation of High-Performance Concrete Compressive Strength Using Standalone and Ensembled Machine Learning Techniques

Materials ◽  
2021 ◽  
Vol 14 (22) ◽  
pp. 7034
Author(s):  
Yue Xu ◽  
Waqas Ahmad ◽  
Ayaz Ahmad ◽  
Krzysztof Adam Ostrowski ◽  
Marta Dudek ◽  
...  
Keyword(s):  
Machine Learning ◽  
Random Forest ◽  
Support Vector Regression ◽  
High Performance ◽  
Cross Validation ◽  
High Performance Concrete ◽  
Machine Learning Techniques ◽  
Support Vector ◽  
Learning Techniques ◽  
Fold Cross Validation

The current trend in modern research revolves around novel techniques that can predict the characteristics of materials without consuming time, effort, and experimental costs. The adaptation of machine learning techniques to compute the various properties of materials is gaining more attention. This study aims to use both standalone and ensemble machine learning techniques to forecast the 28-day compressive strength of high-performance concrete. One standalone technique (support vector regression (SVR)) and two ensemble techniques (AdaBoost and random forest) were applied for this purpose. To validate the performance of each technique, coefficient of determination (R2), statistical, and k-fold cross-validation checks were used. Additionally, the contribution of input parameters towards the prediction of results was determined by applying sensitivity analysis. It was proven that all the techniques employed showed improved performance in predicting the outcomes. The random forest model was the most accurate, with an R2 value of 0.93, compared to the support vector regression and AdaBoost models, with R2 values of 0.83 and 0.90, respectively. In addition, statistical and k-fold cross-validation checks validated the random forest model as the best performer based on lower error values. However, the prediction performance of the support vector regression and AdaBoost models was also within an acceptable range. This shows that novel machine learning techniques can be used to predict the mechanical properties of high-performance concrete.

Prediction of K562 Cells Functional Inhibitors Based on Machine Learning Approaches

2020 ◽  
Vol 25 (40) ◽  
pp. 4296-4302 ◽  
Author(s):  
Yuan Zhang ◽  
Zhenyan Han ◽  
Qian Gao ◽  
Xiaoyi Bai ◽  
Chi Zhang ◽  
...  
Keyword(s):  
Machine Learning ◽  
Inclusion Bodies ◽  
Cross Validation ◽  
Independent Set ◽  
K562 Cells ◽  
Machine Learning Algorithms ◽  
Learning Approaches ◽  
Validation Test ◽  
Excess Number ◽  
Fold Cross Validation

Background: β thalassemia is a common monogenic genetic disease that is very harmful to human health. The disease arises is due to the deletion of or defects in β-globin, which reduces synthesis of the β-globin chain, resulting in a relatively excess number of α-chains. The formation of inclusion bodies deposited on the cell membrane causes a decrease in the ability of red blood cells to deform and a group of hereditary haemolytic diseases caused by massive destruction in the spleen. Methods: In this work, machine learning algorithms were employed to build a prediction model for inhibitors against K562 based on 117 inhibitors and 190 non-inhibitors. Results: The overall accuracy (ACC) of a 10-fold cross-validation test and an independent set test using Adaboost were 83.1% and 78.0%, respectively, surpassing Bayes Net, Random Forest, Random Tree, C4.5, SVM, KNN and Bagging. Conclusion: This study indicated that Adaboost could be applied to build a learning model in the prediction of inhibitors against K526 cells.

scholarly journals Detection and Severity Evaluation of Combined Rail Defects Using Deep Learning

Vibration ◽  
2021 ◽  
Vol 4 (2) ◽  
pp. 341-356
Author(s):  
Jessada Sresakoolchai ◽  
Sakdirat Kaewunruen
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Deep Learning ◽  
Mean Absolute Error ◽  
Absolute Error ◽  
Machine Learning Techniques ◽  
Rolling Stock ◽  
Raw Data ◽  
Learning Techniques ◽  
Combined Defects

Various techniques have been developed to detect railway defects. One of the popular techniques is machine learning. This unprecedented study applies deep learning, which is a branch of machine learning techniques, to detect and evaluate the severity of rail combined defects. The combined defects in the study are settlement and dipped joint. Features used to detect and evaluate the severity of combined defects are axle box accelerations simulated using a verified rolling stock dynamic behavior simulation called D-Track. A total of 1650 simulations are run to generate numerical data. Deep learning techniques used in the study are deep neural network (DNN), convolutional neural network (CNN), and recurrent neural network (RNN). Simulated data are used in two ways: simplified data and raw data. Simplified data are used to develop the DNN model, while raw data are used to develop the CNN and RNN model. For simplified data, features are extracted from raw data, which are the weight of rolling stock, the speed of rolling stock, and three peak and bottom accelerations from two wheels of rolling stock. In total, there are 14 features used as simplified data for developing the DNN model. For raw data, time-domain accelerations are used directly to develop the CNN and RNN models without processing and data extraction. Hyperparameter tuning is performed to ensure that the performance of each model is optimized. Grid search is used for performing hyperparameter tuning. To detect the combined defects, the study proposes two approaches. The first approach uses one model to detect settlement and dipped joint, and the second approach uses two models to detect settlement and dipped joint separately. The results show that the CNN models of both approaches provide the same accuracy of 99%, so one model is good enough to detect settlement and dipped joint. To evaluate the severity of the combined defects, the study applies classification and regression concepts. Classification is used to evaluate the severity by categorizing defects into light, medium, and severe classes, and regression is used to estimate the size of defects. From the study, the CNN model is suitable for evaluating dipped joint severity with an accuracy of 84% and mean absolute error (MAE) of 1.25 mm, and the RNN model is suitable for evaluating settlement severity with an accuracy of 99% and mean absolute error (MAE) of 1.58 mm.

scholarly journals Artificial intelligence-based computational framework for drug-target prioritization and inference of novel repositionable drugs for Alzheimer’s disease

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Shingo Tsuji ◽  
Takeshi Hase ◽  
Ayako Yachie-Kinoshita ◽  
Taiko Nishino ◽  
Samik Ghosh ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Deep Learning ◽  
Drug Target ◽  
Target Genes ◽  
Drug Repositioning ◽  
Therapeutic Targets ◽  
Machine Learning Techniques ◽  
Computational Framework ◽  
Novel Therapeutic

Abstract Background Identifying novel therapeutic targets is crucial for the successful development of drugs. However, the cost to experimentally identify therapeutic targets is huge and only approximately 400 genes are targets for FDA-approved drugs. As a result, it is inevitable to develop powerful computational tools that can identify potential novel therapeutic targets. Fortunately, the human protein-protein interaction network (PIN) could be a useful resource to achieve this objective. Methods In this study, we developed a deep learning-based computational framework that extracts low-dimensional representations of high-dimensional PIN data. Our computational framework uses latent features and state-of-the-art machine learning techniques to infer potential drug target genes. Results We applied our computational framework to prioritize novel putative target genes for Alzheimer’s disease and successfully identified key genes that may serve as novel therapeutic targets (e.g., DLG4, EGFR, RAC1, SYK, PTK2B, SOCS1). Furthermore, based on these putative targets, we could infer repositionable candidate-compounds for the disease (e.g., tamoxifen, bosutinib, and dasatinib). Conclusions Our deep learning-based computational framework could be a powerful tool to efficiently prioritize new therapeutic targets and enhance the drug repositioning strategy.

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