Dataset Information

FMLNCSIM: fuzzy measure-based lncRNA functional similarity calculation model.

ABSTRACT: Accumulating experimental studies have indicated the influence of lncRNAs on various critical biological processes as well as disease development and progression. Calculating lncRNA functional similarity is of high value in inferring lncRNA functions and identifying potential lncRNA-disease associations. However, little effort has been attempt to measure the functional similarity among lncRNAs on a large scale. In this study, we developed a Fuzzy Measure-based LNCRNA functional SIMilarity calculation model (FMLNCSIM) based on the assumption that functionally similar lncRNAs tend to be associated with similar diseases. The performance improvement of FMLNCSIM mainly comes from the combination of information content and the concept of fuzzy measure, which was applied to the directed acyclic graphs of disease MeSH descriptors. To evaluate the effectiveness of FMLNCSIM, we further combined it with the previously proposed model of Laplacian Regularized Least Squares for lncRNA-Disease Association (LRLSLDA). As a result, the integrated model, LRLSLDA-FMLNCSIM, achieve good performance in the frameworks of global LOOCV (AUCs of 0.8266 and 0.9338 based on LncRNADisease and MNDR database) and 5-fold cross validation (average AUCs of 0.7979 and 0.9237 based on LncRNADisease and MNDR database), which significantly improve the performance of previous classical models. It is anticipated that FMLNCSIM could be used for searching functionally similar lncRNAs and inferring lncRNA functions in the future researches.

SUBMITTER: Chen X

PROVIDER: S-EPMC5216773 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature

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FMLNCSIM: fuzzy measure-based lncRNA functional similarity calculation model.

Chen Xing X Huang Yu-An YA Wang Xue-Song XS You Zhu-Hong ZH Chan Keith C C KC

Oncotarget 20160701 29

Accumulating experimental studies have indicated the influence of lncRNAs on various critical biological processes as well as disease development and progression. Calculating lncRNA functional similarity is of high value in inferring lncRNA functions and identifying potential lncRNA-disease associations. However, little effort has been attempt to measure the functional similarity among lncRNAs on a large scale. In this study, we developed a Fuzzy Measure-based LNCRNA functional SIMilarity calcul ...[more]

PMID: 27322210

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Project description:This paper proposes a tuning method based on the Pythagorean fuzzy similarity measure and multi-criteria decision-making to determine the most suitable controller parameters for Fractional-order Proportional Integral Derivative (FOPID) and Integer-order Proportional Integral-Proportional Derivative (PI-PD) controllers. Due to the power of the Pythagorean fuzzy approach to evaluate a phenomenon with two memberships known as membership and non-membership, a multi-objective cost function based on the Pythagorean similarity measure is defined. The transient and steady-state properties of the system output were used for the multi-objective cost function. Thus, the determination of the controller parameters was considered a multi-criteria decision-making problem. Ant colony optimization for continuous domains (ACOR) and artificial bee colony (ABC) optimization are utilized to minimize multi-objective cost functions. The proposed method in the study was applied to three different systems: a second-order non-minimum phase stable system, a first-order unstable system with time delay, and a fractional-order unstable system with time delay, to validate its effectiveness. The cost function utilized in the proposed method is compared with the performance measures widely used in the literature based on the integral of the error, such as IAE (Integral Absolute Error), ITAE (Integral Time Absolute Error), ISE (Integral Square Error), and ITSE (Integral Time Square Error). The proposed method provides a more effective control performance by improving the system response characteristics compared to other cost functions. With the proposed method, the undershoot rate could be significantly reduced in the non-minimum phase system. In the other two systems, significant improvements were achieved compared to other methods by reducing the overshoot rate and oscillation. The proposed method does not require knowing the mathematical model of the system and offers a solution that does not require complex calculations. The proposed method can be used alone. Or it can be used as a second and fine-tuning method after a tuning process.

Dataset Information

FMLNCSIM: fuzzy measure-based lncRNA functional similarity calculation model.

Publications

FMLNCSIM: fuzzy measure-based lncRNA functional similarity calculation model.

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