% The WeightedCommWordString kernel may be used to compute the weighted
% spectrum kernel (i.e. a spectrum kernel for 1 to K-mers, where each k-mer
% length is weighted by some coefficient \f$\beta_k\f$) from strings that have
% been mapped into unsigned 16bit integers.
% 
% These 16bit integers correspond to k-mers. To applicable in this kernel they
% need to be sorted (e.g. via the SortWordString pre-processor).
% 
% It basically uses the algorithm in the unix "comm" command (hence the name)
% to compute:
% 
% k({\bf x},({\bf x'})= \sum_{k=1}^K\beta_k\Phi_k({\bf x})\cdot \Phi_k({\bf x'})
% 
% where \f$\Phi_k\f$ maps a sequence \f${\bf x}\f$ that consists of letters in
% \f$\Sigma\f$ to a feature vector of size \f$|\Sigma|^k\f$. In this feature
% vector each entry denotes how often the k-mer appears in that \f${\bf x}\f$.
% 
% Note that this representation is especially tuned to small alphabets
% (like the 2-bit alphabet DNA), for which it enables spectrum kernels
% of order 8.
% 
% For this kernel the linadd speedups are quite efficiently implemented using
% direct maps.
% 

% Weighted Comm Word String
print WeightedCommWordString
add_preproc SORTWORDSTRING
set_kernel WEIGHTEDCOMMSTRING WORD 10 0 FULL

set_features TRAIN ../data/fm_train_dna.dat DNA
convert TRAIN STRING CHAR STRING WORD 3 2 0 n
attach_preproc TRAIN
km_train.txt = get_kernel_matrix TRAIN

set_features TEST ../data/fm_test_dna.dat DNA
convert TEST STRING CHAR STRING WORD 3 2 0 n
attach_preproc TEST
km_test.txt = get_kernel_matrix TEST
