The Regulaty Modules kernel, based on the WD kernel, as published in Schultheiss et al., Bioinformatics (2009) on regulatory sequences.
Definition at line 25 of file RegulatoryModulesStringKernel.h.
Public Member Functions | |
CRegulatoryModulesStringKernel (void) | |
CRegulatoryModulesStringKernel (int32_t size, float64_t width, int32_t degree, int32_t shift, int32_t window) | |
CRegulatoryModulesStringKernel (CStringFeatures< char > *lstr, CStringFeatures< char > *rstr, CSimpleFeatures< uint16_t > *lpos, CSimpleFeatures< uint16_t > *rpos, float64_t width, int32_t degree, int32_t shift, int32_t window, int32_t size=10) | |
virtual | ~CRegulatoryModulesStringKernel () |
virtual bool | init (CFeatures *l, CFeatures *r) |
virtual EKernelType | get_kernel_type () |
virtual const char * | get_name () const |
void | set_motif_positions (CSimpleFeatures< uint16_t > *positions_lhs, CSimpleFeatures< uint16_t > *positions_rhs) |
virtual void | register_params () |
Protected Member Functions | |
virtual float64_t | compute (int32_t idx_a, int32_t idx_b) |
float64_t | compute_wds (char *avec, char *bvec, int32_t len) |
void | set_wd_weights () |
Protected Attributes | |
float64_t | width |
int32_t | degree |
int32_t | shift |
int32_t | window |
CSimpleFeatures< uint16_t > * | motif_positions_lhs |
CSimpleFeatures< uint16_t > * | motif_positions_rhs |
int32_t | alen |
int32_t | blen |
float64_t * | position_weights |
float64_t * | weights |
CRegulatoryModulesStringKernel | ( | void | ) |
default constructor
Definition at line 19 of file RegulatoryModulesStringKernel.cpp.
CRegulatoryModulesStringKernel | ( | int32_t | size, | |
float64_t | width, | |||
int32_t | degree, | |||
int32_t | shift, | |||
int32_t | window | |||
) |
constructor
size | cache size | |
width | width of gaussian kernel | |
degree | degree of wds kernel | |
shift | shift of wds kernel | |
window | size of window around motifs to compute wds kernels on |
Definition at line 27 of file RegulatoryModulesStringKernel.cpp.
CRegulatoryModulesStringKernel | ( | CStringFeatures< char > * | lstr, | |
CStringFeatures< char > * | rstr, | |||
CSimpleFeatures< uint16_t > * | lpos, | |||
CSimpleFeatures< uint16_t > * | rpos, | |||
float64_t | width, | |||
int32_t | degree, | |||
int32_t | shift, | |||
int32_t | window, | |||
int32_t | size = 10 | |||
) |
constructor
lstr | string features of left-hand side | |
rstr | string features of right-hand side | |
lpos | motif positions on lhs | |
rpos | motif positions on rhs | |
width | width of gaussian kernel | |
degree | degree of wds kernel | |
shift | shift of wds kernel | |
window | size of window around motifs to compute wds kernels on | |
size | cache size |
Definition at line 35 of file RegulatoryModulesStringKernel.cpp.
~CRegulatoryModulesStringKernel | ( | ) | [virtual] |
default destructor
Definition at line 46 of file RegulatoryModulesStringKernel.cpp.
float64_t compute | ( | int32_t | idx_a, | |
int32_t | idx_b | |||
) | [protected, virtual] |
compute kernel function for features a and b idx_{a,b} denote the index of the feature vectors in the corresponding feature object
idx_a | index a | |
idx_b | index b |
Implements CKernel.
Definition at line 85 of file RegulatoryModulesStringKernel.cpp.
float64_t compute_wds | ( | char * | avec, | |
char * | bvec, | |||
int32_t | len | |||
) | [protected] |
compute WDS kernel for features a and b
avec | vector a | |
bvec | vector b | |
len | length of string |
Definition at line 133 of file RegulatoryModulesStringKernel.cpp.
virtual EKernelType get_kernel_type | ( | ) | [virtual] |
return what type of kernel we are
Implements CStringKernel< char >.
Definition at line 72 of file RegulatoryModulesStringKernel.h.
virtual const char* get_name | ( | void | ) | const [virtual] |
return the kernel's name
Reimplemented from CStringKernel< char >.
Definition at line 78 of file RegulatoryModulesStringKernel.h.
initialize kernel
l | features of left-hand side | |
r | features of right-hand side |
Reimplemented from CStringKernel< char >.
Definition at line 52 of file RegulatoryModulesStringKernel.cpp.
void register_params | ( | ) | [virtual] |
Separate the function of parameter registration This can be the first stage of a *general* framework for cross-validation or other parameter-based operations
Reimplemented from CKernel.
Definition at line 217 of file RegulatoryModulesStringKernel.cpp.
void set_motif_positions | ( | CSimpleFeatures< uint16_t > * | positions_lhs, | |
CSimpleFeatures< uint16_t > * | positions_rhs | |||
) |
set motif positions
positions_lhs | motif positions on lhs | |
positions_rhs | motif positions on rhs |
Definition at line 69 of file RegulatoryModulesStringKernel.cpp.
void set_wd_weights | ( | ) | [protected] |
set standard weighted degree kernel weighting
Definition at line 198 of file RegulatoryModulesStringKernel.cpp.
int32_t alen [protected] |
the length of matrix of motif positions -- for serialization purposes
Definition at line 134 of file RegulatoryModulesStringKernel.h.
int32_t blen [protected] |
the length of matrix of motif positions -- for serialization purposes
Definition at line 136 of file RegulatoryModulesStringKernel.h.
int32_t degree [protected] |
degree of Weighted Degree kernel part
Definition at line 120 of file RegulatoryModulesStringKernel.h.
CSimpleFeatures<uint16_t>* motif_positions_lhs [protected] |
Matrix of motif positions from sequences left-hand side
Definition at line 128 of file RegulatoryModulesStringKernel.h.
CSimpleFeatures<uint16_t>* motif_positions_rhs [protected] |
Matrix of motif positions from sequences right-hand side
Definition at line 131 of file RegulatoryModulesStringKernel.h.
float64_t* position_weights [protected] |
scaling weights in window
Definition at line 139 of file RegulatoryModulesStringKernel.h.
int32_t shift [protected] |
shift of Weighted Degree with Shifts kernel part
Definition at line 122 of file RegulatoryModulesStringKernel.h.
weights of WD kernel
Definition at line 142 of file RegulatoryModulesStringKernel.h.
width of Gaussian kernel part
Definition at line 117 of file RegulatoryModulesStringKernel.h.
int32_t window [protected] |
size of window around motifs
Definition at line 125 of file RegulatoryModulesStringKernel.h.