Plot of similarity threshold and equivalent concept pair number. The verizontal-axis value (0.75) at the beginning of the plateau in this figure was adopted as the similarity threshold. The intuition is: there is an initial drop followed by a plateau, which is in turn followed by a second drop. It is reasonable to conclude that threshold can possibly be assigned the value corresponding to the beginning of the plateau. Please refer to "Experiment Design and Results" section for more detailed explanation.
Huang et al. BMC Genomics 2008 9(Suppl 2):S16 doi:10.1186/1471-2164-9-S2-S16