Dataset Information

LMTRDA: Using logistic model tree to predict MiRNA-disease associations by fusing multi-source information of sequences and similarities.

ABSTRACT: Emerging evidence has shown microRNAs (miRNAs) play an important role in human disease research. Identifying potential association among them is significant for the development of pathology, diagnose and therapy. However, only a tiny portion of all miRNA-disease pairs in the current datasets are experimentally validated. This prompts the development of high-precision computational methods to predict real interaction pairs. In this paper, we propose a new model of Logistic Model Tree for predicting miRNA-Disease Association (LMTRDA) by fusing multi-source information including miRNA sequences, miRNA functional similarity, disease semantic similarity, and known miRNA-disease associations. In particular, we introduce miRNA sequence information and extract its features using natural language processing technique for the first time in the miRNA-disease prediction model. In the cross-validation experiment, LMTRDA obtained 90.51% prediction accuracy with 92.55% sensitivity at the AUC of 90.54% on the HMDD V3.0 dataset. To further evaluate the performance of LMTRDA, we compared it with different classifier and feature descriptor models. In addition, we also validate the predictive ability of LMTRDA in human diseases including Breast Neoplasms, Breast Neoplasms and Lymphoma. As a result, 28, 27 and 26 out of the top 30 miRNAs associated with these diseases were verified by experiments in different kinds of case studies. These experimental results demonstrate that LMTRDA is a reliable model for predicting the association among miRNAs and diseases.

SUBMITTER: Wang L

PROVIDER: S-EPMC6464243 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

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Publications

LMTRDA: Using logistic model tree to predict MiRNA-disease associations by fusing multi-source information of sequences and similarities.

Wang Lei L You Zhu-Hong ZH Chen Xing X Li Yang-Ming YM Dong Ya-Nan YN Li Li-Ping LP Zheng Kai K

PLoS computational biology 20190327 3

Emerging evidence has shown microRNAs (miRNAs) play an important role in human disease research. Identifying potential association among them is significant for the development of pathology, diagnose and therapy. However, only a tiny portion of all miRNA-disease pairs in the current datasets are experimentally validated. This prompts the development of high-precision computational methods to predict real interaction pairs. In this paper, we propose a new model of Logistic Model Tree for predicti ...[more]

PMID: 30917115

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Project description:With the rapid development of biological research, microRNAs (miRNA) have become an attractive topic because lots of experimental studies have revealed the significant associations between miRNAs and diseases. However, considering that experiments are expensive and time-consuming, computational methods for predicting associations between miRNAs and diseases have become increasingly crucial. In this study, we proposed a neighborhood regularized logistic matrix factorization method for miRNA-disease association prediction (NRLMFMDA) by integrating miRNA functional similarity, disease semantic similarity, Gaussian interaction profile kernel similarity, and experimentally validation of disease-miRNA association. We used Gaussian interaction profile kernel similarity to cover the shortage of the traditional similarity to make it more reasonable and complete. Furthermore, NRLMFMDA also considered the important influences of the neighborhood information and took full advantage of them to improve the accuracy of the miRNA-disease association prediction. We also improved the accuracy by giving higher weights to the known association data in the process of calculating the potential association probabilities. In the global and the local leave-one-out cross validation, NRLMFMDA got the AUCs of 0.9068 and 0.8239, respectively. Moreover, the average AUC of NRLMFMDA in 5-fold cross validation was 0.8976 ± 0.0034. All the three kinds of cross validations have shown significant advantages to a number of previous models. In the case studies of breast neoplasms, esophageal neoplasms and lymphoma according to known miRNA-disease associations in the recent version of HMDD database, there were 78, 80, and 74% of top 50 predicted related miRNAs verified to have associations with these three diseases, respectively. In the further case studies for new disease without any known related miRNAs and the previous version of HMDD database, there were also high proportions of the predicted miRNAs verified by experimental reports. All the validation experiment results have demonstrated the effectiveness and practicability of NRLFMDA to predict the potential miRNA-disease associations.

Project description:One of the core issues of ecology is to understand the effects of landscape patterns on ecological processes. For this, we need to accurately capture changes in the fine landscape structures to avoid losing information about spatial heterogeneity. The landscape pattern indicators (LPIs) can characterize the spatial structures and give some information about landscape patterns. However, researches on LPIs had mainly focused on the horizontal structure of landscape patterns, while few studies addressed vertical relationships between the levels of hierarchical landscape structures. Thus, the ignorance of the vertical hierarchical relationships may cause serious biases and reduce LPIs' representational ability and accuracy. The hierarchy theory about the landscape pattern structures could notably reduce the loss of hierarchical information, and the information entropy could quantitatively describe the vertical status of landscape units. Therefore, we established a new multidimensional fusion method of LPIs based on hierarchy theory and information entropy. Here, we created a general fusion formula for commonly used simple LPIs based on two-grade land use data (whose land use classification system contains two grades/levels) and derived 3 fusion landscape pattern indicators (FLIs) with a case study. The results show that the information about fine spatial structure is captured by the fusion method. The regions with the most differences between the FLIs and the traditional LPIs are those with the largest vertical structure such as the ecological ecotones, where vertical structure was ignored before. The FLIs have a finer spatial representational ability and accuracy, not only retaining the main trend information of first-grade land use data, but also containing the internal detail information of second-grade land use data. Capturing finer spatial information of landscape patterns should encourage the application of fusion method, which should be suitable for more LPIs or more dimensional data. And the increased accuracy of FLIs will improve ecological models that rely on finer spatial information.

Dataset Information

LMTRDA: Using logistic model tree to predict MiRNA-disease associations by fusing multi-source information of sequences and similarities.

Publications

LMTRDA: Using logistic model tree to predict MiRNA-disease associations by fusing multi-source information of sequences and similarities.

Similar Datasets

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