The CommUlongString kernel may be used to compute the spectrum kernel from strings that have been mapped into unsigned 64bit integers.
These 64bit integers correspond to k-mers. To be applicable in this kernel they need to be sorted (e.g. via the SortUlongString pre-processor).
It basically uses the algorithm in the unix "comm" command (hence the name) to compute the kernel function.
In this feature vector each entry denotes how often the k-mer appears in that . Note that this representation enables spectrum kernels of
order 8 for 8bit alphabets (like binaries) and order 32 for 2-bit alphabets like DNA. For this kernel the linadd speedups are implemented
(though there is room for improvement here when a whole set of sequences is ADDed) using sorted lists.
