Table 2.

A Typology of Kernels for Small Molecules

Strategy	Input Data	Examples
Use classical fingerprints of molecular descriptors	1D to 4D structure	Tanimoto or inner products between fingerprints [40, 73, 74]
Use an infinite number of descriptors and a computational trick	2D structure	Walk kernels [23, 75-77] Shortest-path fragment kernel [78] Subtree kernel [79, 80] Cyclic fragment kernel [81]
	3D Structure	Pharmacophore kernel [24]
Use a measure of similarity	2D structure	Optimal alignment kernel [82]