Variations of the AUROC and AUPR specifications of with perturbations on .

<p>To make the variations clearer, only deviations of the AUROC and AUPR specifications from those of the unperturbed are shown here.</p

Variations of the AUROC and AUPR specifications of as a function of the parameter .

<p>To make the variations clearer, this figure only shows the deviations of the AUROC and the AUPR specifications with the sampled from those with .</p

Estimated Number of Genes with a Zero In-degree.

<p>Estimated Number of Genes with a Zero In-degree.</p

Prediction Performances for the DREAM3 Networks Using Method Integrations.^†

†<p>As noted in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031194#pone.0031194-Pinna1" target="_blank">[22]</a>, is obtained for after a comparison with the actual network. On the other hand, the optimal can hardly be obtained in actual estimations for each of , , . The purposes to include their inference results here are only to clarify estimation performance degradations when an empirical parameter is adopted.</p><p>*Due to the some reasons as those of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031194#pone-0031194-t001" target="_blank">Table 1</a>, these -values can not be distinguished from zero in actual computations, which makes it impossible to compare scores of the adopted GRN topology estimation methods.</p

Variations of the AUROC and AUPR specifications with the threshold value

<p><b>.</b> To make the variations clearer, the specifications shown are their deviations from those respectively with (for the -score based method) and with (for the algorithm suggested in this paper).</p

Prediction Performances for the DREAM3 Networks.^†

<p>RPV-Z: relative performance variation with respect to the -score based method; RPV-B: relative performance variation with respect to the best team; ARPV: averaged relative performance variation of the 5 networks.</p>†<p>, which stands for the method with the optimal normalization parameter , generally can not be applied in actual estimations. The purposes to include its inference results here are only to make it clear that significant estimation performance degradation does not occur when the parameter deviates from its optimal value.</p><p>*Due to some precision issues of the method suggested by the DREAM project organizers, these -values can not be distinguished from zero in actual computations, which makes it impossible to compare scores of the adopted GRN topology estimation methods.</p

Prediction Performances for the DREAM4 Networks.^†

<p>RPV-Z: relative performance variation with respect to the -score based method; RPV-B: relative performance variation with respect to the best team; ARPV: averaged relative performance variation of the 5 networks.</p>†<p>The purposes to include the inference results of are completely the same as those of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031194#pone-0031194-t001" target="_blank">Table 1</a>. That is, to clarify that deviation of the parameter from its optimal value usually does not lead to significant estimation performance degradations.</p

Precision-recall curves of some typical estimations.

<p>Precision-recall curves of some typical estimations.</p

Variations of the AUROC and AUPR specifications of as a function of the parameter .

<p>To make the variations clearer, this figure only shows the deviations of the AUROC and the AUPR specifications with the sampled from those with .</p

Prediction Performances for the DREAM3 Networks Integrating Knockdown and Knockout Data.

<p>KD: estimation performance using knockdown experimental data only; KO: estimation performance using knockout experimental data only; MIX: estimation performance using both knockdown and knockout experimental data.</p><p>*Due to the some reasons as those of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031194#pone-0031194-t001" target="_blank">Table 1</a>, these -values can not be distinguished from zero in actual computations, which makes it impossible to compare scores of the corresponding GRN topology estimation methods. Using the same treatments of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031194#pone.0031194-Prill1" target="_blank">[16]</a>, these scores are designated to be .</p