randomization test
Recently Published Documents


TOTAL DOCUMENTS

193
(FIVE YEARS 41)

H-INDEX

27
(FIVE YEARS 4)

Symmetry ◽  
2022 ◽  
Vol 14 (1) ◽  
pp. 97
Author(s):  
Monica Billio ◽  
Lorenzo Frattarolo ◽  
Dominique Guégan

We use a recently proposed fast test of copula radial symmetry based on multiplier bootstrap and obtain an equivalent randomization test. The literature shows the statistical superiority of the randomization approach in the bivariate case. We extend the comparison of statistical performance focusing on the high-dimensional regime in a simulation study. We document radial asymmetry in the joint distribution of the percentage changes of sectorial industrial production indices of the European Union.


2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
Neda Shakour ◽  
Farzin Hadizadeh ◽  
Prashant Kesharwani ◽  
Amirhossein Sahebkar

Sortase A (SrtA) is an enzyme that catalyzes the attachment of proteins to the cell wall of Gram-positive bacterial membrane, preventing the spread of pathogenic bacterial strains. Here, one class of oxadiazole compounds was distinguished as an efficient inhibitor of SrtA via the “S. aureus Sortase A” substrate-based virtual screening. The current study on 3D-QSAR was done by utilizing preparation of the structure in the Schrödinger software suite and an assessment of 120 derivatives with the crystal structure of 1,2,4-oxadiazole which was extracted from the PDB data bank. The docking operation of the best compound in terms of pMIC ( pMIC = 2.77 ) was done to determine the drug likeliness and binding form of 1,2,4-oxadiazole derivatives as antibiotics in the active site. Using the kNN-MFA way, seven models of 3D-QSAR were created and amongst them, and one model was selected as the best. The chosen model based on q 2 (pred_ r 2 ) and R 2 values related to the sixth factor of PLS illustrates better and more acceptable external and internal predictions. Values of crossvalidation (pred_ r 2 ), validation ( q 2 ), and F were observed 0.5479, 0.6319, and 179.0, respectively, for a test group including 24 molecules and the training group including 96 molecules. The external reliability outcomes showed that the acceptable and the selective 3D-QSAR model had a high predictive potential ( R 2 = 0.9235 ) which was confirmed by the Y -randomization test. Besides, the model applicability domain was described successfully to validate the estimation of the model.


2021 ◽  
Vol 1 (1) ◽  
pp. 48-67
Author(s):  
Xavier Chee Wezen ◽  
Clement Sim Jun Wen ◽  
Lilian Siaw Yung Ping ◽  
Yeong Kah Ho ◽  
Kong Hao Qing ◽  
...  

Clathrin-mediated endocytosis (CME) is a normal biological process where cellular contents are transported into the cells. However, this process is often hijacked by different viruses to enter host cells and cause infections. Recently, two proteins that regulate CME – AAK1 and GAK – have been proposed as potential therapeutic targets for designing broad-spectrum antiviral drugs. In this work, we curated two compound datasets containing 83 AAK1 inhibitors and 196 GAK inhibitors each. Subsequently, machine learning methods, namely Random Forest, Elastic Net and Sequential Minimal Optimization, were used to construct Quantitative Structure Activity Relationship (QSAR) models to predict small molecule inhibitors of AAK1 and GAK. To ensure predictivity, these models were evaluated by using Leave-One-Out (LOO) cross validation and with an external test set. In all cases, our QSAR models achieved a q2LOO in range of 0.64 to 0.84 (Root Mean Squared Error; RMSE = 0.41 to 0.52) and a q2ext in range of 0.57 to 0.92 (RMSE = 0.36 to 0.61). Besides, our QSAR models were evaluated by using additional QSAR performance metrics and y-randomization test. Finally, by using a concensus scoring approach, nine chemical compounds from the Drugbank compound library were predicted as AAK1/GAK dual-target inhibitors. The electrostatic potential maps for the nine compounds were generated and compared against two known dual-target inhibitors, sunitinib and baricitinib. Our work provides the rationale to validate these nine compounds experimentally against the protein targets AAK1 and GAK.


2021 ◽  
Author(s):  
Konstantinos Zagganas ◽  
Georgios K Georgakilas ◽  
Thanasis Vergoulis ◽  
Theodore Dalamagas

Motivation: miRNA functional enrichment is a type of analysis that is used to predict which biological functions may be affected by a group of miRNAs or validate whether a list of dysreg- ulated miRNAs are linked to a diseased state. The standard method for functional enrichment analysis uses the hypergeometric distribution to produce p-values, depicting the strength of the association between a group of miRNAs and a biological function. However, in 2015, it was shown that this approach suffers from a bias related to miRNA targets produced by target prediction algorithms and a new randomization test was proposed. Results: In this paper, we demonstrate the existence of another underlying bias which affects gene annotation data sets; additionally, we show that the statistical measure used for the estab- lished randomization test is not sensitive enough to account for it. For this reason, we propose the use of an alternative statistical measure, the "two-sided overlap", and we show that it is able to alleviate the aforementioned issue. Finally, we develop BUFET2, a miRNA enrichment analysis tool that leverages this measure (along with the old one); it is based on BUFET, a fast and scalable implementation of the established randomization test. Availability and Implementation: BUFET2 is written in C++ and is packaged with a Python wrapper script that facilitates experiment execution. Moreover, BUFET2 also comes pre-packaged in a Linux Docker image published on Docker Hub, thus eliminating the need for code compilation. Finally, BUFET2 is also publicly available to execute through a REST API. All datasets used in the experiments throught this paper are openly accessible on Zenodo (https://doi.org/10.5281/zenodo.5175819).


2021 ◽  
Vol 4 (2) ◽  
pp. 238-248
Author(s):  
Tri Sugihartono ◽  
◽  
Rendy Rian Chrisna Putra ◽  

Procedures from the company to provide competency certification for and as official evidence that the news from the journalist is credible. In the practice of implementing the Competency Test, cheating is still found during the exam, various ways / forms of cheating that occur include cooperation between journalists (test participants). These problems are overcome by integrating the competency test system, using mobile technology and web applications that have been integrated so that they are more accessible. The Fisher Yates shuffle algorithm functions as a randomization of exam questions. Each test taker always has different exam questions, both from the numbering of questions and the order of answer choices. With the implementation of the Fisher Yates Suffle Algorithm, it can reduce acts of fraud or dishonesty by journalists. In addition, with the application of the Fisher Yates shuffle algorithm, it can make it easier for agencies to provide competent employee competencies. The results of the randomization test on the first 3 questions that appeared to the respondents resulted in the conclusion that the Fisher-Yates shuffle algorithm had a 100% success rate in randomizing the order of questions that were displayed to respondents


Author(s):  
Wesley Tansey ◽  
Victor Veitch ◽  
Haoran Zhang ◽  
Raul Rabadan ◽  
David M. Blei

Sign in / Sign up

Export Citation Format

Share Document