RNA secondary structure encoding and Graph Kernel Features: Top (A) The graph encoding preserves the nucleotide information (vertex labels) and the base pairs (edge labels), here depicted with different colors. (B) Additional vertices are inserted to induce features related to stacking base-pairs quadruplets (thin light gray vertices at the center of each stacking pair). Right: example of features induced by the graph kernel NSPDK for a pair of vertices u, v at distance 3 with radius 0,1,2. Neighborhood graphs are enclosed in dashed ovals