Figure 4

Comparison of transfer functions for converting PSI-BLAST E-values to edge weights. The figure plots edge weight as a function of E-value for various transfer functions. The original RankProp algorithm assigns edge weights using the function exp(-D _ij /σ), where σ had to be chosen a priori. Curves for σ = 10, 100, 1000 are shown. Also shown is the curve produced by the probabilistic approach, in which the edge weight is the empirical probability of two proteins belonging to the same superfamily.