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 ) 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:
where maps a sequence
that consists of letters in
to a feature vector of size
. In this feature vector each entry denotes how often the k-mer appears in that
.
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.
Definition at line 50 of file WeightedCommWordStringKernel.h.
Public Member Functions | |
CWeightedCommWordStringKernel (int32_t size, bool use_sign) | |
CWeightedCommWordStringKernel (CStringFeatures< uint16_t > *l, CStringFeatures< uint16_t > *r, bool use_sign=false, int32_t size=10) | |
virtual | ~CWeightedCommWordStringKernel () |
virtual bool | init (CFeatures *l, CFeatures *r) |
virtual void | cleanup () |
virtual float64_t | compute_optimized (int32_t idx) |
virtual void | add_to_normal (int32_t idx, float64_t weight) |
void | merge_normal () |
bool | set_wd_weights () |
bool | set_weights (float64_t *w, int32_t d) |
virtual EKernelType | get_kernel_type () |
virtual const char * | get_name () const |
virtual EFeatureType | get_feature_type () |
virtual float64_t * | compute_scoring (int32_t max_degree, int32_t &num_feat, int32_t &num_sym, float64_t *target, int32_t num_suppvec, int32_t *IDX, float64_t *alphas, bool do_init=true) |
Protected Member Functions | |
virtual float64_t | compute_helper (int32_t idx_a, int32_t idx_b, bool do_sort) |
Protected Attributes | |
int32_t | degree |
float64_t * | weights |
CWeightedCommWordStringKernel | ( | int32_t | size, | |
bool | use_sign | |||
) |
constructor
size | cache size | |
use_sign | if sign shall be used |
Definition at line 18 of file WeightedCommWordStringKernel.cpp.
CWeightedCommWordStringKernel | ( | CStringFeatures< uint16_t > * | l, | |
CStringFeatures< uint16_t > * | r, | |||
bool | use_sign = false , |
|||
int32_t | size = 10 | |||
) |
constructor
l | features of left-hand side | |
r | features of right-hand side | |
use_sign | if sign shall be used | |
size | cache size |
Definition at line 26 of file WeightedCommWordStringKernel.cpp.
~CWeightedCommWordStringKernel | ( | ) | [virtual] |
Definition at line 37 of file WeightedCommWordStringKernel.cpp.
void add_to_normal | ( | int32_t | idx, | |
float64_t | weight | |||
) | [virtual] |
add to normal
idx | where to add | |
weight | what to add |
Reimplemented from CCommWordStringKernel.
Definition at line 185 of file WeightedCommWordStringKernel.cpp.
void cleanup | ( | ) | [virtual] |
clean up kernel
Reimplemented from CCommWordStringKernel.
Definition at line 53 of file WeightedCommWordStringKernel.cpp.
float64_t compute_helper | ( | int32_t | idx_a, | |
int32_t | idx_b, | |||
bool | do_sort | |||
) | [protected, virtual] |
helper for compute
idx_a | index a | |
idx_b | index b | |
do_sort | if sorting shall be performed |
Reimplemented from CCommWordStringKernel.
Definition at line 90 of file WeightedCommWordStringKernel.cpp.
float64_t compute_optimized | ( | int32_t | idx | ) | [virtual] |
compute optimized
idx | index to compute |
Reimplemented from CCommWordStringKernel.
Definition at line 247 of file WeightedCommWordStringKernel.cpp.
float64_t * compute_scoring | ( | int32_t | max_degree, | |
int32_t & | num_feat, | |||
int32_t & | num_sym, | |||
float64_t * | target, | |||
int32_t | num_suppvec, | |||
int32_t * | IDX, | |||
float64_t * | alphas, | |||
bool | do_init = true | |||
) | [virtual] |
compute scoring
max_degree | maximum degree | |
num_feat | number of features | |
num_sym | number of symbols | |
target | target | |
num_suppvec | number of support vectors | |
IDX | IDX | |
alphas | alphas | |
do_init | if initialization shall be performed |
Reimplemented from CCommWordStringKernel.
Definition at line 282 of file WeightedCommWordStringKernel.cpp.
virtual EFeatureType get_feature_type | ( | ) | [virtual] |
return feature type the kernel can deal with
Reimplemented from CCommWordStringKernel.
Definition at line 131 of file WeightedCommWordStringKernel.h.
virtual EKernelType get_kernel_type | ( | ) | [virtual] |
return what type of kernel we are
Reimplemented from CCommWordStringKernel.
Definition at line 119 of file WeightedCommWordStringKernel.h.
virtual const char* get_name | ( | ) | const [virtual] |
return the kernel's name
Reimplemented from CCommWordStringKernel.
Definition at line 125 of file WeightedCommWordStringKernel.h.
initialize kernel
l | features of left-hand side | |
r | features of right-hand side |
Reimplemented from CCommWordStringKernel.
Definition at line 42 of file WeightedCommWordStringKernel.cpp.
void merge_normal | ( | ) |
merge normal
Definition at line 215 of file WeightedCommWordStringKernel.cpp.
bool set_wd_weights | ( | ) |
set weighted degree weights
Definition at line 61 of file WeightedCommWordStringKernel.cpp.
bool set_weights | ( | float64_t * | w, | |
int32_t | d | |||
) |
set custom weights (swig compatible)
w | weights | |
d | degree (must match number of weights) |
Definition at line 79 of file WeightedCommWordStringKernel.cpp.
int32_t degree [protected] |
degree
Definition at line 161 of file WeightedCommWordStringKernel.h.
weights for each of the subkernels of degree 1...d
Definition at line 164 of file WeightedCommWordStringKernel.h.