Dataset Information

An EM-Based Method for Q-Matrix Validation.

ABSTRACT: With the purpose to assist the subject matter experts in specifying their Q-matrices, the authors used expectation-maximization (EM)-based algorithm to investigate three alternative Q-matrix validation methods, namely, the maximum likelihood estimation (MLE), the marginal maximum likelihood estimation (MMLE), and the intersection and difference (ID) method. Their efficiency was compared, respectively, with that of the sequential EM-based δ method and its extension (ς²), the γ method, and the nonparametric method in terms of correct recovery rate, true negative rate, and true positive rate under the deterministic-inputs, noisy "and" gate (DINA) model and the reduced reparameterized unified model (rRUM). Simulation results showed that for the rRUM, the MLE performed better for low-quality tests, whereas the MMLE worked better for high-quality tests. For the DINA model, the ID method tended to produce better quality Q-matrix estimates than other methods for large sample sizes (i.e., 500 or 1,000). In addition, the Q-matrix was more precisely estimated under the discrete uniform distribution than under the multivariate normal threshold model for all the above methods. On average, the ς² and ID method with higher true negative rates are better for correcting misspecified Q-entries, whereas the MLE with higher true positive rates is better for retaining the correct Q-entries. Experiment results on real data set confirmed the effectiveness of the MLE.

SUBMITTER: Wang W

PROVIDER: S-EPMC6373855 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature

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An EM-Based Method for Q-Matrix Validation.

Wang Wenyi W Song Lihong L Ding Shuliang S Meng Yaru Y Cao Canxi C Jie Yongjing Y

Applied psychological measurement 20180220 6

With the purpose to assist the subject matter experts in specifying their Q-matrices, the authors used expectation-maximization (EM)-based algorithm to investigate three alternative Q-matrix validation methods, namely, the maximum likelihood estimation (MLE), the marginal maximum likelihood estimation (MMLE), and the intersection and difference (ID) method. Their efficiency was compared, respectively, with that of the sequential EM-based δ method and its extension (ς<sup>2</sup>), the γ method, ...[more]

PMID: 30787487

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Project description:SummaryTopology determination is one of the most important intermediate steps toward building the atomic structure of proteins from their medium-resolution cryo-electron microscopy (cryo-EM) map. The main goal in the topology determination is to identify correct matches (i.e. assignment and direction) between secondary structure elements (SSEs) (α-helices and β-sheets) detected in a protein sequence and cryo-EM density map. Despite many recent advances in molecular biology technologies, the problem remains a challenging issue. To overcome the problem, this article proposes a linear programming-based topology determination (LPTD) method to solve the secondary structure topology problem in three-dimensional geometrical space. Through modeling of the protein's sequence with the aid of extracting highly reliable features and a distance-based scoring function, the secondary structure matching problem is transformed into a complete weighted bipartite graph matching problem. Subsequently, an algorithm based on linear programming is developed as a decision-making strategy to extract the true topology (native topology) between all possible topologies. The proposed automatic framework is verified using 12 experimental and 15 simulated α-β proteins. Results demonstrate that LPTD is highly efficient and extremely fast in such a way that for 77% of cases in the dataset, the native topology has been detected in the first rank topology in <2 s. Besides, this method is able to successfully handle large complex proteins with as many as 65 SSEs. Such a large number of SSEs have never been solved with current tools/methods.Availability and implementationThe LPTD package (source code and data) is publicly available at https://github.com/B-Behkamal/LPTD. Moreover, two test samples as well as the instruction of utilizing the graphical user interface have been provided in the shared readme file.Supplementary informationSupplementary data are available at Bioinformatics online.

Dataset Information

An EM-Based Method for Q-Matrix Validation.

Publications

An EM-Based Method for Q-Matrix Validation.

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