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Several studies [5], [15] [17], [19] have reported the performance of MHC-II binding peptide prediction methods using datasets of unique peptides.
The performance is analyzed and compared with several existing methods using datasets obtained from the Protein Information Resource center.
We evaluated the methods using datasets simulated to represent different scenarios corresponding to a given combination of parameters of number of true hits, the amount of noise, the skewness of the data, the strength of chemotherapeutic drug effect, and the RNAi effect.
We evaluated the methods using datasets simulated to present different scenarios corresponding to a given combination of the following parameters: sample size (5 or 10), proportion of differentially expressed genes (5% or 10%), ratio of up-regulated vs. down-regulated (1 1 or 3 1), lower bound of fold change (1.5 or 1.1), and lower bound of depth (5 or 1).
Predictive accuracy, the correlation between the predicted and the true breeding values r g, g ^, was estimated by the ratio of predictive ability s g, ^ p to the square root of heritability for each of the indirect methods using datasets with and without outliers.
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We tested the five DCEA methods using dataset GSE3068 obtained from GEO (Table 1).
Hence, these methods use datasets of proteins of known structures to calculate conditional probabilities that certain residues or atoms will appear in different contexts.
We compared the performance of the three methods using simulated datasets and a real biological dataset, in which an overexpression line CBF2_OX was compared with wild type control.
The effectiveness of the proposed method is validated using datasets from rolling element bearings and planetary gearboxes.
Secondly, because the true tree is not known for biological supertree datasets, it is difficult to evaluate supertree methods using biological datasets.
Hence, there have been numerous works investigating efficient methods using reduced datasets.
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Justyna Jupowicz-Kozak
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