scholarly journals Deep belief network–Based Matrix Factorization Model for MicroRNA-Disease Associations Prediction

2020 ◽  
Vol 16 ◽  
pp. 117693432091970 ◽  
Author(s):  
Yulian Ding ◽  
Fei Wang ◽  
Xiujuan Lei ◽  
Bo Liao ◽  
Fang-Xiang Wu
Keyword(s):  
Matrix Factorization ◽  
Critical Role ◽  
Experimental Studies ◽  
Score Function ◽  
Disease Association ◽  
Deep Belief Network ◽  
Time Saving ◽  
Belief Network ◽  
Related Data ◽  
Disease Associations

MicroRNAs (miRNAs) are small single-stranded noncoding RNAs that have shown to play a critical role in regulating gene expression. In past decades, cumulative experimental studies have verified that miRNAs are implicated in many complex human diseases and might be potential biomarkers for various types of diseases. With the increase of miRNA-related data and the development of analysis methodologies, some computational methods have been developed for predicting miRNA-disease associations, which are more economical and time-saving than traditional biological experimental approaches. In this study, a novel computational model, deep belief network (DBN)-based matrix factorization (DBN-MF), is proposed for miRNA-disease association prediction. First, the raw interaction features of miRNAs and diseases were obtained from the miRNA-disease adjacent matrix. Second, 2 DBNs were used for unsupervised learning of the features of miRNAs and diseases, respectively, based on the raw interaction features. Finally, a classifier consisting of 2 DBNs and a cosine score function was trained with the initial weights of DBN from the last step. During the training, the miRNA-disease adjacent matrix was factorized into 2 feature matrices for the representation of miRNAs and diseases, and the final prediction label was obtained according to the feature matrices. The experimental results show that the proposed model outperforms the state-of-the-art approaches in miRNA-disease association prediction based on the 10-fold cross-validation. Besides, the effectiveness of our model was further demonstrated by case studies.

MDAPlatform: a Component-based Platform for Constructing and Assessing miRNA-disease association Prediction Methods

2021 ◽  
Vol 16 ◽  
Author(s):  
Yayan Zhang ◽  
Guihua Duan ◽  
Cheng Yan ◽  
Haolun Yi ◽  
Fang-Xiang Wu ◽  
...  
Keyword(s):  
Computational Models ◽  
Critical Role ◽  
Prediction Method ◽  
Disease Association ◽  
Prediction Methods ◽  
Comparison Results ◽  
Disease Associations ◽  
Pros And Cons ◽  
Clinical Drugs ◽  
Validation Experiments

Background: Increasing evidence has indicated that miRNA-disease association prediction plays a critical role in the study of clinical drugs. Researchers have proposed many computational models for miRNA-disease prediction. However, there is no unified platform to compare and analyze the pros and cons or share the code and data of these models. Objective: In this study, we develop an easy-to-use platform (MDAPlatform) to construct and assess miRNA-disease association prediction method. Methods: MDAPlatform integrates the relevant data of miRNA, disease and miRNA-disease associations that are used in previous miRNA-disease association prediction studies. Based on the componentized model, it develops differet components of previous computational methods. Results: Users can conduct cross validation experiments and compare their methods with other methods, and the visualized comparison results are also provided. Conclusion: Based on the componentized model, MDAPlatform provides easy-to-operate interfaces to construct the miRNA-disease association method, which is beneficial to develop new miRNA-disease association prediction methods in the future.

scholarly journals DNILMF-LDA: Prediction of lncRNA-Disease Associations by Dual-Network Integrated Logistic Matrix Factorization and Bayesian Optimization

Genes ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 608 ◽  
Author(s):  
Yan Li ◽  
Junyi Li ◽  
Naizheng Bian
Keyword(s):  
Matrix Factorization ◽  
Disease Diagnosis ◽  
Disease Association ◽  
Bayesian Optimization ◽  
Model Parameters ◽  
Target Interaction ◽  
Disease Associations ◽  
Auc Value ◽  
Similarity Networks ◽  
Fold Cross Validation

Identifying associations between lncRNAs and diseases can help understand disease-related lncRNAs and facilitate disease diagnosis and treatment. The dual-network integrated logistic matrix factorization (DNILMF) model has been used for drug–target interaction prediction, and good results have been achieved. We firstly applied DNILMF to lncRNA–disease association prediction (DNILMF-LDA). We combined different similarity kernel matrices of lncRNAs and diseases by using nonlinear fusion to extract the most important information in fused matrices. Then, lncRNA–disease association networks and similarity networks were built simultaneously. Finally, the Gaussian process mutual information (GP-MI) algorithm of Bayesian optimization was adopted to optimize the model parameters. The 10-fold cross-validation result showed that the area under receiving operating characteristic (ROC) curve (AUC) value of DNILMF-LDA was 0.9202, and the area under precision-recall (PR) curve (AUPR) was 0.5610. Compared with LRLSLDA, SIMCLDA, BiwalkLDA, and TPGLDA, the AUC value of our method increased by 38.81%, 13.07%, 8.35%, and 6.75%, respectively. The AUPR value of our method increased by 52.66%, 40.05%, 37.01%, and 44.25%. These results indicate that DNILMF-LDA is an effective method for predicting the associations between lncRNAs and diseases.

Computational drug repositioning based on multi-similarities bilinear matrix factorization

2020 ◽  
Author(s):  
Mengyun Yang ◽  
Gaoyan Wu ◽  
Qichang Zhao ◽  
Yaohang Li ◽  
Jianxin Wang
Keyword(s):  
Matrix Factorization ◽  
Drug Repositioning ◽  
Disease Association ◽  
Biological Entity ◽  
Biomedical Data ◽  
Supplementary Data ◽  
Practical Applications ◽  
Disease Associations ◽  
Association Matrix ◽  
Similarity Matrices

Abstract With the development of high-throughput technology and the accumulation of biomedical data, the prior information of biological entity can be calculated from different aspects. Specifically, drug–drug similarities can be measured from target profiles, drug–drug interaction and side effects. Similarly, different methods and data sources to calculate disease ontology can result in multiple measures of pairwise disease similarities. Therefore, in computational drug repositioning, developing a dynamic method to optimize the fusion process of multiple similarities is a crucial and challenging task. In this study, we propose a multi-similarities bilinear matrix factorization (MSBMF) method to predict promising drug-associated indications for existing and novel drugs. Instead of fusing multiple similarities into a single similarity matrix, we concatenate these similarity matrices of drug and disease, respectively. Applying matrix factorization methods, we decompose the drug–disease association matrix into a drug-feature matrix and a disease-feature matrix. At the same time, using these feature matrices as basis, we extract effective latent features representing the drug and disease similarity matrices to infer missing drug–disease associations. Moreover, these two factored matrices are constrained by non-negative factorization to ensure that the completed drug–disease association matrix is biologically interpretable. In addition, we numerically solve the MSBMF model by an efficient alternating direction method of multipliers algorithm. The computational experiment results show that MSBMF obtains higher prediction accuracy than the state-of-the-art drug repositioning methods in cross-validation experiments. Case studies also demonstrate the effectiveness of our proposed method in practical applications. Availability: The data and code of MSBMF are freely available at https://github.com/BioinformaticsCSU/MSBMF. Corresponding author: Jianxin Wang, School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, P. R. China. E-mail: [email protected] Supplementary Data: Supplementary data are available online at https://academic.oup.com/bib.

scholarly journals miRNA-Disease Association Prediction with Collaborative Matrix Factorization

Complexity ◽  
2017 ◽  
Vol 2017 ◽  
pp. 1-9 ◽  
Author(s):  
Zhen Shen ◽  
You-Hua Zhang ◽  
Kyungsook Han ◽  
Asoke K. Nandi ◽  
Barry Honig ◽  
...  
Keyword(s):  
Matrix Factorization ◽  
Noncoding Rna ◽  
Esophageal Neoplasms ◽  
Kidney Neoplasms ◽  
Disease Association ◽  
Computational Method ◽  
Experimental Identification ◽  
Novel Mirna ◽  
Disease Associations ◽  
High Prediction

As one of the factors in the noncoding RNA family, microRNAs (miRNAs) are involved in the development and progression of various complex diseases. Experimental identification of miRNA-disease association is expensive and time-consuming. Therefore, it is necessary to design efficient algorithms to identify novel miRNA-disease association. In this paper, we developed the computational method of Collaborative Matrix Factorization for miRNA-Disease Association prediction (CMFMDA) to identify potential miRNA-disease associations by integrating miRNA functional similarity, disease semantic similarity, and experimentally verified miRNA-disease associations. Experiments verified that CMFMDA achieves intended purpose and application values with its short consuming-time and high prediction accuracy. In addition, we used CMFMDA on Esophageal Neoplasms and Kidney Neoplasms to reveal their potential related miRNAs. As a result, 84% and 82% of top 50 predicted miRNA-disease pairs for these two diseases were confirmed by experiment. Not only this, but also CMFMDA could be applied to new diseases and new miRNAs without any known associations, which overcome the defects of many previous computational methods.

Deep-belief network for predicting potential miRNA-disease associations

2020 ◽  
Author(s):  
Xing Chen ◽  
Tian-Hao Li ◽  
Yan Zhao ◽  
Chun-Chun Wang ◽  
Chi-Chi Zhu
Keyword(s):  
Computational Models ◽  
Cross Validation ◽  
Biological Data ◽  
Deep Belief Network ◽  
Computational Method ◽  
Restricted Boltzmann Machines ◽  
Belief Network ◽  
Disease Associations ◽  
Leave One Out ◽  
The Impact

Abstract MicroRNA (miRNA) plays an important role in the occurrence, development, diagnosis and treatment of diseases. More and more researchers begin to pay attention to the relationship between miRNA and disease. Compared with traditional biological experiments, computational method of integrating heterogeneous biological data to predict potential associations can effectively save time and cost. Considering the limitations of the previous computational models, we developed the model of deep-belief network for miRNA-disease association prediction (DBNMDA). We constructed feature vectors to pre-train restricted Boltzmann machines for all miRNA-disease pairs and applied positive samples and the same number of selected negative samples to fine-tune DBN to obtain the final predicted scores. Compared with the previous supervised models that only use pairs with known label for training, DBNMDA innovatively utilizes the information of all miRNA-disease pairs during the pre-training process. This step could reduce the impact of too few known associations on prediction accuracy to some extent. DBNMDA achieves the AUC of 0.9104 based on global leave-one-out cross validation (LOOCV), the AUC of 0.8232 based on local LOOCV and the average AUC of 0.9048 ± 0.0026 based on 5-fold cross validation. These AUCs are better than other previous models. In addition, three different types of case studies for three diseases were implemented to demonstrate the accuracy of DBNMDA. As a result, 84% (breast neoplasms), 100% (lung neoplasms) and 88% (esophageal neoplasms) of the top 50 predicted miRNAs were verified by recent literature. Therefore, we could conclude that DBNMDA is an effective method to predict potential miRNA-disease associations.

scholarly journals MiRNA-disease association prediction via hypergraph learning based on high-dimensionality features

2021 ◽  
Vol 21 (S1) ◽  
Author(s):  
Yu-Tian Wang ◽  
Qing-Wen Wu ◽  
Zhen Gao ◽  
Jian-Cheng Ni ◽  
Chun-Hou Zheng
Keyword(s):  
Computational Models ◽  
Cross Validation ◽  
Nearest Neighbor ◽  
Experimental Studies ◽  
Prediction Method ◽  
Disease Association ◽  
High Dimensionality ◽  
K Nearest Neighbor ◽  
Hypergraph Learning ◽  
Disease Associations

Abstract Background MicroRNAs (miRNAs) have been confirmed to have close relationship with various human complex diseases. The identification of disease-related miRNAs provides great insights into the underlying pathogenesis of diseases. However, it is still a big challenge to identify which miRNAs are related to diseases. As experimental methods are in general expensive and time‐consuming, it is important to develop efficient computational models to discover potential miRNA-disease associations. Methods This study presents a novel prediction method called HFHLMDA, which is based on high-dimensionality features and hypergraph learning, to reveal the association between diseases and miRNAs. Firstly, the miRNA functional similarity and the disease semantic similarity are integrated to form an informative high-dimensionality feature vector. Then, a hypergraph is constructed by the K-Nearest-Neighbor (KNN) method, in which each miRNA-disease pair and its k most relevant neighbors are linked as one hyperedge to represent the complex relationships among miRNA-disease pairs. Finally, the hypergraph learning model is designed to learn the projection matrix which is used to calculate uncertain miRNA-disease association score. Result Compared with four state-of-the-art computational models, HFHLMDA achieved best results of 92.09% and 91.87% in leave-one-out cross validation and fivefold cross validation, respectively. Moreover, in case studies on Esophageal neoplasms, Hepatocellular Carcinoma, Breast Neoplasms, 90%, 98%, and 96% of the top 50 predictions have been manually confirmed by previous experimental studies. Conclusion MiRNAs have complex connections with many human diseases. In this study, we proposed a novel computational model to predict the underlying miRNA-disease associations. All results show that the proposed method is effective for miRNA–disease association predication.

Hierarchical Extension Based on the Boolean Matrix for LncRNA-Disease Association Prediction

2020 ◽  
Vol 20 (6) ◽  
pp. 452-460
Author(s):  
Lin Tang ◽  
Yu Liang ◽  
Xin Jin ◽  
Lin Liu ◽  
Wei Zhou
Keyword(s):  
Computational Models ◽  
Characteristic Curve ◽  
Experimental Studies ◽  
Potential Method ◽  
Disease Association ◽  
Biological Data ◽  
Boolean Matrix ◽  
Disease Associations ◽  
Association Data ◽  
Association Matrix

Background: Accumulating experimental studies demonstrated that long non-coding RNAs (LncRNAs) play crucial roles in the occurrence and development progress of various complex human diseases. Nonetheless, only a small portion of LncRNA–disease associations have been experimentally verified at present. Automatically predicting LncRNA–disease associations based on computational models can save the huge cost of wet-lab experiments. Methods and Result: To develop effective computational models to integrate various heterogeneous biological data for the identification of potential disease-LncRNA, we propose a hierarchical extension based on the Boolean matrix for LncRNA-disease association prediction model (HEBLDA). HEBLDA discovers the intrinsic hierarchical correlation based on the property of the Boolean matrix from various relational sources. Then, HEBLDA integrates these hierarchical associated matrices by fusion weights. Finally, HEBLDA uses the hierarchical associated matrix to reconstruct the LncRNA– disease association matrix by hierarchical extending. HEBLDA is able to work for potential diseases or LncRNA without known association data. In 5-fold cross-validation experiments, HEBLDA obtained an area under the receiver operating characteristic curve (AUC) of 0.8913, improving previous classical methods. Besides, case studies show that HEBLDA can accurately predict candidate disease for several LncRNAs. Conclusion: Based on its ability to discover the more-richer correlated structure of various data sources, we can anticipate that HEBLDA is a potential method that can obtain more comprehensive association prediction in a broad field.

NMCMDA: neural multicategory MiRNA–disease association prediction

2021 ◽  
Author(s):  
Jingru Wang ◽  
Jin Li ◽  
Kun Yue ◽  
Li Wang ◽  
Yuyun Ma ◽  
...  
Keyword(s):  
Cost Effective ◽  
Underlying Mechanism ◽  
Disease Association ◽  
Disease Category ◽  
Convolutional Network ◽  
Time Saving ◽  
Disease Associations ◽  
Multiple Category ◽  
Latent Representations ◽  
Main Components

Abstract Motivation There is growing evidence showing that the dysregulations of miRNAs cause diseases through various kinds of the underlying mechanism. Thus, predicting the multiple-category associations between microRNAs (miRNAs) and diseases plays an important role in investigating the roles of miRNAs in diseases. Moreover, in contrast with traditional biological experiments which are time-consuming and expensive, computational approaches for the prediction of multicategory miRNA–disease associations are time-saving and cost-effective that are highly desired for us. Results We present a novel data-driven end-to-end learning-based method of neural multiple-category miRNA–disease association prediction (NMCMDA) for predicting multiple-category miRNA–disease associations. The NMCMDA has two main components: (i) encoder operates directly on the miRNA–disease heterogeneous network and leverages Graph Neural Network to learn miRNA and disease latent representations, respectively. (ii) Decoder yields miRNA–disease association scores with the learned latent representations as input. Various kinds of encoders and decoders are proposed for NMCMDA. Finally, the NMCMDA with the encoder of Relational Graph Convolutional Network and the neural multirelational decoder (NMR-RGCN) achieves the best prediction performance. We compared the NMCMDA with other baselines on three experimental datasets. The experimental results show that the NMR-RGCN is significantly superior to the state-of-the-art method TDRC in terms of Top-1 precision, Top-1 Recall, and Top-1 F1. Additionally, case studies are provided for two high-risk human diseases (namely, breast cancer and lung cancer) and we also provide the prediction and validation of top-10 miRNA–disease-category associations based on all known data of HMDD v3.2, which further validate the effectiveness and feasibility of the proposed method.

scholarly journals Predicting Alzheimer Disease From Mild Cognitive Impairment With a Deep Belief Network Based on 18F-FDG-PET Images

2019 ◽  
Vol 18 ◽  
pp. 153601211987728 ◽  
Author(s):  
Ting Shen ◽  
Jiehui Jiang ◽  
Jiaying Lu ◽  
Min Wang ◽  
Chuantao Zuo ◽  
...  
Keyword(s):  
Cognitive Impairment ◽  
Mild Cognitive Impairment ◽  
Alzheimer Disease ◽  
Critical Role ◽  
Feature Learning ◽  
Deep Belief Network ◽  
Metabolic Imaging ◽  
Support Vector ◽  
Belief Network ◽  
18F Fluorodeoxyglucose

Objective: Accurate diagnosis of early Alzheimer disease (AD) plays a critical role in preventing the progression of memory impairment. We aimed to develop a new deep belief network (DBN) framework using 18F-fluorodeoxyglucose (FDG) positron emission tomography (PET) metabolic imaging to identify patients at the mild cognitive impairment (MCI) stage with presymptomatic AD and to discriminate them from other patients with MCI. Methods: 18F-fluorodeoxyglucose-PET images of 109 patients recruited in the ongoing longitudinal Alzheimer’s Disease Neuroimaging Initiative study were included in this analysis. Patients were grouped into 2 classes: (1) stable mild cognitive impairment (n = 62) or (2) progressive mild cognitive impairment (n = 47). Our framework is composed of 4 steps: (1) image preprocessing: normalization and smoothing; (2) identification of regions of interest (ROIs); (3) feature learning using deep neural networks; and (4) classification by support vector machine with 3 kernels. All classification experiments were performed with a 5-fold cross-validation. Accuracy, sensitivity, and specificity were used to validate the results. Result: A total of 1103 ROIs were obtained. One hundred features were learned from ROIs using the DBN. The classification accuracy using linear, polynomial, and RBF kernels was 83.9%, 79.2%, and 86.6%, respectively. This method may be a powerful tool for personalized precision medicine in the population with prediction of early AD progression.

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