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How to apply the novel dynamic ARDL simulations (dynardl) and Kernel-based regularized least squares (krls).

ABSTRACT: The application of dynamic Autoregressive Distributed Lag (dynardl) simulations and Kernel-based Regularized Least Squares (krls) to time series data is gradually gaining recognition in energy, environmental and health economics. The Kernel-based Regularized Least Squares technique is a simplified machine learning-based algorithm with strength in its interpretation and accounting for heterogeneity, additivity and nonlinear effects. The novel dynamic ARDL Simulations algorithm is useful for testing cointegration, long and short-run equilibrium relationships in both levels and differences. Advantageously, the novel dynamic ARDL Simulations has visualization interface to examine the possible counterfactual change in the desired variable based on the notion of ceteris paribus. Thus, the novel dynamic ARDL Simulations and Kernel-based Regularized Least Squares techniques are useful and improved time series techniques for policy formulation.•We customize ARDL and dynamic simulated ARDL by adding plot estimates with confidence intervals.•A step-by-step procedure of applying ARDL, dynamic ARDL Simulations and Kernel-based Regularized Least Squares is provided.•All techniques are applied to examine the economic effect of denuclearization in Switzerland by 2034.

SUBMITTER: Sarkodie SA

PROVIDER: S-EPMC7718150 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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How to apply the novel dynamic ARDL simulations (dynardl) and Kernel-based regularized least squares (krls).

Sarkodie Samuel Asumadu SA Owusu Phebe Asantewaa PA

MethodsX 20201127

The application of dynamic Autoregressive Distributed Lag (dynardl) simulations and Kernel-based Regularized Least Squares (krls) to time series data is gradually gaining recognition in energy, environmental and health economics. The Kernel-based Regularized Least Squares technique is a simplified machine learning-based algorithm with strength in its interpretation and accounting for heterogeneity, additivity and nonlinear effects. The novel dynamic ARDL Simulations algorithm is useful for testi ...[more]

PMID: 33304836

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Project description:BackgroundRecently, as the research of microRNA (miRNA) continues, there are plenty of experimental evidences indicating that miRNA could be associated with various human complex diseases development and progression. Hence, it is necessary and urgent to pay more attentions to the relevant study of predicting diseases associated miRNAs, which may be helpful for effective prevention, diagnosis and treatment of human diseases. Especially, constructing computational methods to predict potential miRNA-disease associations is worthy of more studies because of the feasibility and effectivity.MethodsIn this work, we developed a novel computational model of multiple kernels learning-based Kronecker regularized least squares for MiRNA-disease association prediction (MKRMDA), which could reveal potential miRNA-disease associations by automatically optimizing the combination of multiple kernels for disease and miRNA.ResultsMKRMDA obtained AUCs of 0.9040 and 0.8446 in global and local leave-one-out cross validation, respectively. Meanwhile, MKRMDA achieved average AUCs of 0.8894 ± 0.0015 in fivefold cross validation. Furthermore, we conducted three different kinds of case studies on some important human cancers for further performance evaluation. In the case studies of colonic cancer, esophageal cancer and lymphoma based on known miRNA-disease associations in HMDDv2.0 database, 76, 94 and 88% of the corresponding top 50 predicted miRNAs were confirmed by experimental reports, respectively. In another two kinds of case studies for new diseases without any known associated miRNAs and diseases only with known associations in HMDDv1.0 database, the verified ratios of two different cancers were 88 and 94%, respectively.ConclusionsAll the results mentioned above adequately showed the reliable prediction ability of MKRMDA. We anticipated that MKRMDA could serve to facilitate further developments in the field and the follow-up investigations by biomedical researchers.

Project description:BackgroundMicrobes are closely related to human health and diseases. Identification of disease-related microbes is of great significance for revealing the pathological mechanism of human diseases and understanding the interaction mechanisms between microbes and humans, which is also useful for the prevention, diagnosis and treatment of human diseases. Considering the known disease-related microbes are still insufficient, it is necessary to develop effective computational methods and reduce the time and cost of biological experiments.MethodsIn this work, we developed a novel computational method called MDAKRLS to discover potential microbe-disease associations (MDAs) based on the Kronecker regularized least squares. Specifically, we introduced the Hamming interaction profile similarity to measure the similarities of microbes and diseases besides Gaussian interaction profile kernel similarity. In addition, we introduced the Kronecker product to construct two kinds of Kronecker similarities between microbe-disease pairs. Then, we designed the Kronecker regularized least squares with different Kronecker similarities to obtain prediction scores, respectively, and calculated the final prediction scores by integrating the contributions of different similarities.ResultsThe AUCs value of global leave-one-out cross-validation and 5-fold cross-validation achieved by MDAKRLS were 0.9327 and 0.9023 ± 0.0015, which were significantly higher than five state-of-the-art methods used for comparison. Comparison results demonstrate that MDAKRLS has faster computing speed under two kinds of frameworks. In addition, case studies of inflammatory bowel disease (IBD) and asthma further showed 19 (IBD), 19 (asthma) of the top 20 prediction disease-related microbes could be verified by previously published biological or medical literature.ConclusionsAll the evaluation results adequately demonstrated that MDAKRLS has an effective and reliable prediction performance. It may be a useful tool to seek disease-related new microbes and help biomedical researchers to carry out follow-up studies.

Project description:BACKGROUND:Many evidences have demonstrated that circRNAs (circular RNA) play important roles in controlling gene expression of human, mouse and nematode. More importantly, circRNAs are also involved in many diseases through fine tuning of post-transcriptional gene expression by sequestering the miRNAs which associate with diseases. Therefore, identifying the circRNA-disease associations is very appealing to comprehensively understand the mechanism, treatment and diagnose of diseases, yet challenging. As the complex mechanism between circRNAs and diseases, wet-lab experiments are expensive and time-consuming to discover novel circRNA-disease associations. Therefore, it is of dire need to employ the computational methods to discover novel circRNA-disease associations. RESULT:In this study, we develop a method (DWNN-RLS) to predict circRNA-disease associations based on Regularized Least Squares of Kronecker product kernel. The similarity of circRNAs is computed from the Gaussian Interaction Profile(GIP) based on known circRNA-disease associations. In addition, the similarity of diseases is integrated by the mean of GIP similarity and sematic similarity which is computed by the direct acyclic graph (DAG) representation of diseases. The kernels of circRNA-disease pairs are constructed from the Kronecker product of the kernels of circRNAs and diseases. DWNN (decreasing weight k-nearest neighbor) method is adopted to calculate the initial relational score for new circRNAs and diseases. The Kronecker product kernel based regularised least squares approach is used to predict new circRNA-disease associations. We adopt 5-fold cross validation (5CV), 10-fold cross validation (10CV) and leave one out cross validation (LOOCV) to assess the prediction performance of our method, and compare it with other six competing methods (RLS-avg, RLS-Kron, NetLapRLS, KATZ, NBI, WP). CONLUSION:The experiment results show that DWNN-RLS reaches the AUC values of 0.8854, 0.9205 and 0.9701 in 5CV, 10CV and LOOCV, respectively, which illustrates that DWNN-RLS is superior to the competing methods RLS-avg, RLS-Kron, NetLapRLS, KATZ, NBI, WP. In addition, case studies also show that DWNN-RLS is an effective method to predict new circRNA-disease associations.

Dataset Information

How to apply the novel dynamic ARDL simulations (dynardl) and Kernel-based regularized least squares (krls).

Publications

How to apply the novel dynamic ARDL simulations (dynardl) and Kernel-based regularized least squares (krls).

Similar Datasets

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