Skip to main content

Table 7 Prediction sensitivities and specificities for the two datasets, GSE7895 ( D 1 ), GSE19667 ( D 2 )

From: Quantification of biological network perturbations for mechanistic insight and diagnostics using two-layer causal models

Type Method CV (D1/D2) D1D2 D2D1 Mean G-perf
Se Sp Se Sp Se Sp Test sets
All Genes tForwardLd 0.95/0.86 0.93/0.92 1.00 0.87 0.69 1.00 0.88
NSC 0.92/0.94 0.96/0.93 1.00 0.00 0.98 0.00 0.00
RF 0.75/0.96 1.00/0.97 1.00 0.31 0.98 0.95 0.76
SVM 0.84/0.94 0.98/0.96 1.00 0.00 1.00 0.00 0.00
Gene in transcript layer tForwardLd 0.95/0.89 0.92/0.93 0.97 0.91 0.61 0.85 0.83
LDA 0.92/0.94 0.80/0.97 0.62 0.27 0.86 0.40 0.50
NSC 0.96/0.92 0.93/0.95 1.00 0.00 1.00 0.00 0.00
RF 0.87/0.96 1.00/0.97 0.98 0.58 0.94 1.00 0.86
SVM 0.88/0.95 0.98/0.95 1.00 0.00 0.78 0.15 0.17
UBE downstream genes CORG + LDA 0.97/0.94 0.90/0.94 0.83 0.36 0.61 0.55 0.56
CORG + NSC 0.98/0.95 0.93/0.96 0.97 0.00 0.67 0.30 0.22
Best LDA (8-Methyl-IQX) 0.96/0.95 0.88/0.96 0.9 0.80 0.80 1.00 0.89
Best NSC (8-Methyl-IQX) 0.96/0.86 0.92/0.98 0.98 0.76 0.86 1.00 0.90
Backbone values tForwardLd 0.97/0.90 0.95/0.97 0.8 0.82 0.84 0.90 0.86
LDA 0.96/0.92 0.94/0.98 0.89 0.80 0.84 0.90 0.86
NSC 0.93/0.93 0.81/0.92 0.95 0.87 0.94 0.90 0.91
RF 0.93/0.91 0.80/0.91 0.97 0.73 0.88 0.85 0.85
SVM 0.93/0.93 0.88/0.91 0.98 0.62 0.88 0.90 0.83
  1. The predictions of the samples from the dataset D j based on the model trained on the dataset D i are reported in the columns D i D j . While not systematically having the best cross-validation performance, the predictors based on the backbone values show are more robust behavior when predicting one dataset based on the model trained on the other one. The mean of the G-performances ( = Sp · Se ) over the two independent test sets are shown in the rightmost column and is highlighted if >0.7. The best UBE-based models is chosen based on the mean cross-validation G-performance for the two datasets. The algorithms based on the backbone values leads systematically to good performances. The cross-validation standard errors are reported in Additional file 1: Table S1.