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The constructed SVM models of three different regulatory features are measured, and models with the best predictive accuracy are selected for the mammalian proximal promoter prediction.
In real world performance testing, recurrent network architectures were shown to provide the best predictive accuracy due to the time-dependence of the EMAD signal.
The experimental results indicate that the best predictive accuracy and capability of generalization was achieved for SMA containing Mixed RCA RMSEE = 25.20119) while the worst predictive accuracy and capability of generalization was achieved for HMA containing Coarse RCA RMSEE = 35.56637).
In this case, the best predictive accuracy for the four models was obtained by using a decision tree (M5P).
In this case, the best predictive accuracy for the three models was obtained by using a decision tree (M5P) and evaluating using 4-fold cross validation.
The best predictive accuracy of 86.1% indicates that machine learning methods are able to detect a signal in the data and predict binding affinity to some extent.
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In Table 2, the best predictive accuracies of each method are listed.
Considering the analysis from a predictive point of view, note that in Table 2 the best prediction accuracy belongs to M3 (R2 = 0.56) and M5 (R2 = 0.68).
Methods 5 and 7 were therefore the most robust: to outliers and also gave the best estimates for predictive accuracy.
Considering only estimated correlations between zero and one, Methods 4 and 6 gave the best estimates of predictive accuracy among the five methods that use cross-validation, followed by Methods 3, 2 and 1, in that order.
As some data cleaning techniques may increase precision and lower recall, we can determine which technique will have the overall best effect on predictive accuracy by using the F-measure of these two values.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com