Figure 5

The optimal radial basis width σ depends upon the number of close homologs to the query. In the figure, each point corresponds to one query sequence from the training set. For each query, the y-axis coordinate is the number of target sequences that PSI-BLAST assigns an E-value less than 0.01, and the x-axis coordinate is the difference in ROC₁ between RankProp with parameters σ = 10 and σ = 1000. The same analysis is shown in bar chart form (right). Each bar indicates the mean difference in ROC for all queries with number of homologs falling into a bin of size 200. Similar results (not shown) arise for other values of σ that we tried. Here, the error measure is the ROC₁ score.