Public Member Functions | Static Public Member Functions | Protected Member Functions | Protected Attributes

CWeightedDegreePositionStringKernel Class Reference


Detailed Description

The Weighted Degree Position String kernel (Weighted Degree kernel with shifts).

The WD-shift kernel of order d compares two sequences ${\bf x}$ and ${\bf x'}$ of length L by summing all contributions of k-mer matches of lengths $k\in\{1,\dots,d\}$, weighted by coefficients $\beta_k$ allowing for a positional tolerance of up to shift s.

It is formally defined as

\begin{eqnarray*} &&\!\!\!\!\!\!\!k({\bf x}_i,{\bf x}_j)=\sum_{k=1}^d\beta_k\sum_{l=1}^{\!\!\!\!L-k+1\!\!\!\!}\gamma_l\sum_{\begin{array}{c}s=0\\ \!\!\!\!s+l\leq L\!\!\!\!\end{array}}^{S(l)} \delta_s\;\mu_{k,l,s,{{\bf x}_i},{{\bf x}_j}},\\ &&\!\!\!\!\!\!\!\!\!\! {\footnotesize \mu_{k,l,s,{{\bf x}_i},{{\bf x}_j}}\!\!\! =\!\! I({\bf u}_{k,l+s}({\bf x}_i)\! =\!{\bf u}_{k,l}({\bf x}_j))\! +\!I({\bf u}_{k,l}({\bf x}_i)\! =\!{\bf u}_{k,l+s}({\bf x}_j))},\nonumber \end{eqnarray*}

where $\beta_j$ are the weighting coefficients of the j-mers, $\gamma_l$ is a weighting over the position in the sequence, $\delta_s=1/(2(s+1))$ is the weight assigned to shifts (in either direction) of extent s, and S(l) determines the shift range at position l.

Definition at line 48 of file WeightedDegreePositionStringKernel.h.

Inheritance diagram for CWeightedDegreePositionStringKernel:
Inheritance graph
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List of all members.

Public Member Functions

 CWeightedDegreePositionStringKernel (int32_t size, int32_t degree, int32_t max_mismatch=0, int32_t mkl_stepsize=1)
 CWeightedDegreePositionStringKernel (int32_t size, float64_t *weights, int32_t degree, int32_t max_mismatch, int32_t *shift, int32_t shift_len, int32_t mkl_stepsize=1)
 CWeightedDegreePositionStringKernel (CStringFeatures< char > *l, CStringFeatures< char > *r, int32_t degree)
virtual ~CWeightedDegreePositionStringKernel ()
virtual bool init (CFeatures *l, CFeatures *r)
virtual void cleanup ()
virtual EKernelType get_kernel_type ()
virtual const char * get_name () const
virtual bool init_optimization (int32_t p_count, int32_t *IDX, float64_t *alphas)
virtual bool init_optimization (int32_t count, int32_t *IDX, float64_t *alphas, int32_t tree_num, int32_t upto_tree=-1)
virtual bool delete_optimization ()
virtual float64_t compute_optimized (int32_t idx)
virtual void compute_batch (int32_t num_vec, int32_t *vec_idx, float64_t *target, int32_t num_suppvec, int32_t *IDX, float64_t *alphas, float64_t factor=1.0)
virtual void clear_normal ()
virtual void add_to_normal (int32_t idx, float64_t weight)
virtual int32_t get_num_subkernels ()
void compute_by_subkernel (int32_t idx, float64_t *subkernel_contrib)
const float64_tget_subkernel_weights (int32_t &num_weights)
void set_subkernel_weights (float64_t *weights2, int32_t num_weights2)
float64_tcompute_abs_weights (int32_t &len)
bool is_tree_initialized ()
int32_t get_max_mismatch ()
int32_t get_degree ()
float64_tget_degree_weights (int32_t &d, int32_t &len)
float64_tget_weights (int32_t &num_weights)
float64_tget_position_weights (int32_t &len)
bool set_shifts (int32_t *shifts, int32_t len)
virtual bool set_weights (float64_t *weights, int32_t d, int32_t len=0)
virtual bool set_wd_weights ()
virtual bool set_position_weights (float64_t *pws, int32_t len)
bool set_position_weights_lhs (float64_t *pws, int32_t len, int32_t num)
bool set_position_weights_rhs (float64_t *pws, int32_t len, int32_t num)
bool init_block_weights ()
bool init_block_weights_from_wd ()
bool init_block_weights_from_wd_external ()
bool init_block_weights_const ()
bool init_block_weights_linear ()
bool init_block_weights_sqpoly ()
bool init_block_weights_cubicpoly ()
bool init_block_weights_exp ()
bool init_block_weights_log ()
bool init_block_weights_external ()
bool delete_position_weights ()
bool delete_position_weights_lhs ()
bool delete_position_weights_rhs ()
virtual float64_t compute_by_tree (int32_t idx)
virtual void compute_by_tree (int32_t idx, float64_t *LevelContrib)
float64_tcompute_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 *weights)
char * compute_consensus (int32_t &num_feat, int32_t num_suppvec, int32_t *IDX, float64_t *alphas)
float64_textract_w (int32_t max_degree, int32_t &num_feat, int32_t &num_sym, float64_t *w_result, int32_t num_suppvec, int32_t *IDX, float64_t *alphas)
float64_tcompute_POIM (int32_t max_degree, int32_t &num_feat, int32_t &num_sym, float64_t *poim_result, int32_t num_suppvec, int32_t *IDX, float64_t *alphas, float64_t *distrib)
void prepare_POIM2 (float64_t *distrib, int32_t num_sym, int32_t num_feat)
void compute_POIM2 (int32_t max_degree, CSVM *svm)
void get_POIM2 (float64_t **poim, int32_t *result_len)
void cleanup_POIM2 ()
 cleanup POIM2

Static Public Member Functions

static void * compute_batch_helper (void *p)

Protected Member Functions

void create_empty_tries ()
virtual void add_example_to_tree (int32_t idx, float64_t weight)
void add_example_to_single_tree (int32_t idx, float64_t weight, int32_t tree_num)
virtual float64_t compute (int32_t idx_a, int32_t idx_b)
float64_t compute_with_mismatch (char *avec, int32_t alen, char *bvec, int32_t blen)
float64_t compute_without_mismatch (char *avec, int32_t alen, char *bvec, int32_t blen)
float64_t compute_without_mismatch_matrix (char *avec, int32_t alen, char *bvec, int32_t blen)
float64_t compute_without_mismatch_position_weights (char *avec, float64_t *posweights_lhs, int32_t alen, char *bvec, float64_t *posweights_rhs, int32_t blen)
virtual void remove_lhs ()

Protected Attributes

float64_tweights
float64_tposition_weights
float64_tposition_weights_lhs
float64_tposition_weights_rhs
bool * position_mask
float64_tweights_buffer
int32_t mkl_stepsize
int32_t degree
int32_t length
int32_t max_mismatch
int32_t seq_length
int32_t * shift
int32_t shift_len
int32_t max_shift
bool block_computation
int32_t num_block_weights_external
float64_tblock_weights_external
float64_tblock_weights
EWDKernType type
int32_t which_degree
CTrie< DNATrie > tries
CTrie< POIMTrie > poim_tries
bool tree_initialized
bool use_poim_tries
float64_tm_poim_distrib
float64_tm_poim
int32_t m_poim_num_sym
int32_t m_poim_num_feat
int32_t m_poim_result_len
CAlphabetalphabet

Constructor & Destructor Documentation

CWeightedDegreePositionStringKernel ( int32_t  size,
int32_t  degree,
int32_t  max_mismatch = 0,
int32_t  mkl_stepsize = 1 
)

constructor

Parameters:
sizecache size
degreedegree
max_mismatchmaximum mismatch
mkl_stepsizeMKL stepsize

Definition at line 52 of file WeightedDegreePositionStringKernel.cpp.

CWeightedDegreePositionStringKernel ( int32_t  size,
float64_t weights,
int32_t  degree,
int32_t  max_mismatch,
int32_t *  shift,
int32_t  shift_len,
int32_t  mkl_stepsize = 1 
)

constructor

Parameters:
sizecache size
weightsweights
degreedegree
max_mismatchmaximum mismatch
shiftposition shifts
shift_lennumber of shifts
mkl_stepsizeMKL stepsize

Definition at line 71 of file WeightedDegreePositionStringKernel.cpp.

CWeightedDegreePositionStringKernel ( CStringFeatures< char > *  l,
CStringFeatures< char > *  r,
int32_t  degree 
)

constructor

Parameters:
lfeatures of left-hand side
rfeatures of right-hand side
degreedegree

Definition at line 95 of file WeightedDegreePositionStringKernel.cpp.

Definition at line 116 of file WeightedDegreePositionStringKernel.cpp.


Member Function Documentation

void add_example_to_single_tree ( int32_t  idx,
float64_t  weight,
int32_t  tree_num 
) [protected]

add example to single tree

Parameters:
idxindex
weightweight
tree_numwhich tree

Definition at line 700 of file WeightedDegreePositionStringKernel.cpp.

void add_example_to_tree ( int32_t  idx,
float64_t  weight 
) [protected, virtual]

add example to tree

Parameters:
idxindex
weightweight

Definition at line 646 of file WeightedDegreePositionStringKernel.cpp.

virtual void add_to_normal ( int32_t  idx,
float64_t  weight 
) [virtual]

add to normal

Parameters:
idxwhere to add
weightwhat to add

Reimplemented from CKernel.

Definition at line 208 of file WeightedDegreePositionStringKernel.h.

void cleanup (  ) [virtual]

clean up kernel

Reimplemented from CKernel.

Definition at line 222 of file WeightedDegreePositionStringKernel.cpp.

void cleanup_POIM2 (  )

cleanup POIM2

Definition at line 1946 of file WeightedDegreePositionStringKernel.cpp.

virtual void clear_normal (  ) [virtual]

clear normal subkernel functionality

Reimplemented from CKernel.

Definition at line 182 of file WeightedDegreePositionStringKernel.h.

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

Parameters:
idx_aindex a
idx_bindex b
Returns:
computed kernel function at indices a,b

Implements CKernel.

Definition at line 603 of file WeightedDegreePositionStringKernel.cpp.

float64_t * compute_abs_weights ( int32_t &  len )

compute abs weights

Parameters:
lenlen
Returns:
computed abs weights

Definition at line 838 of file WeightedDegreePositionStringKernel.cpp.

void compute_batch ( int32_t  num_vec,
int32_t *  vec_idx,
float64_t target,
int32_t  num_suppvec,
int32_t *  IDX,
float64_t alphas,
float64_t  factor = 1.0 
) [virtual]

compute batch

Parameters:
num_vecnumber of vectors
vec_idxvector index
targettarget
num_suppvecnumber of support vectors
IDXIDX
alphasalphas
factorfactor

Reimplemented from CKernel.

Definition at line 1305 of file WeightedDegreePositionStringKernel.cpp.

void * compute_batch_helper ( void *  p ) [static]

helper for compute batch

Parameters:
pthread parameter

Definition at line 1247 of file WeightedDegreePositionStringKernel.cpp.

void compute_by_subkernel ( int32_t  idx,
float64_t subkernel_contrib 
) [virtual]

compute by subkernel

Parameters:
idxindex
subkernel_contribsubkernel contribution

Reimplemented from CKernel.

Definition at line 232 of file WeightedDegreePositionStringKernel.h.

float64_t compute_by_tree ( int32_t  idx ) [virtual]

compute by tree

Parameters:
idxindex
Returns:
computed value

Definition at line 756 of file WeightedDegreePositionStringKernel.cpp.

void compute_by_tree ( int32_t  idx,
float64_t LevelContrib 
) [virtual]

compute by tree

Parameters:
idxindex
LevelContriblevel contribution

Definition at line 795 of file WeightedDegreePositionStringKernel.cpp.

char * compute_consensus ( int32_t &  num_feat,
int32_t  num_suppvec,
int32_t *  IDX,
float64_t alphas 
)

compute consensus string

Parameters:
num_featnumber of features
num_suppvecnumber of support vectors
IDXIDX
alphasalphas
Returns:
consensus string

Definition at line 1574 of file WeightedDegreePositionStringKernel.cpp.

virtual float64_t compute_optimized ( int32_t  idx ) [virtual]

compute optimized

Parameters:
idxindex to compute
Returns:
optimized value at given index

Reimplemented from CKernel.

Definition at line 150 of file WeightedDegreePositionStringKernel.h.

float64_t * compute_POIM ( int32_t  max_degree,
int32_t &  num_feat,
int32_t &  num_sym,
float64_t poim_result,
int32_t  num_suppvec,
int32_t *  IDX,
float64_t alphas,
float64_t distrib 
)

compute POIM

Parameters:
max_degreemaximum degree
num_featnumber of features
num_symnumber of symbols
poim_resultpoim
num_suppvecnumber of support vectors
IDXIDX
alphasalphas
distribdistribution
Returns:
computed POIMs

Definition at line 1754 of file WeightedDegreePositionStringKernel.cpp.

void compute_POIM2 ( int32_t  max_degree,
CSVM svm 
)

compute POIM2

Parameters:
max_degreemaximum degree
svmSVM

Definition at line 1902 of file WeightedDegreePositionStringKernel.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 weights 
)

compute positional scoring function, which assigns a weight per position, per symbol in the sequence

Parameters:
max_degreemaximum degree
num_featnumber of features
num_symnumber of symbols
targettarget
num_suppvecnumber of support vectors
IDXIDX
weightsweights
Returns:
computed scores

Definition at line 1418 of file WeightedDegreePositionStringKernel.cpp.

float64_t compute_with_mismatch ( char *  avec,
int32_t  alen,
char *  bvec,
int32_t  blen 
) [protected]

compute with mismatch

Parameters:
avecvector a
alenlength of vector a
bvecvector b
blenlength of vector b
Returns:
computed value

Definition at line 313 of file WeightedDegreePositionStringKernel.cpp.

float64_t compute_without_mismatch ( char *  avec,
int32_t  alen,
char *  bvec,
int32_t  blen 
) [protected]

compute without mismatch

Parameters:
avecvector a
alenlength of vector a
bvecvector b
blenlength of vector b
Returns:
computed value

Definition at line 393 of file WeightedDegreePositionStringKernel.cpp.

float64_t compute_without_mismatch_matrix ( char *  avec,
int32_t  alen,
char *  bvec,
int32_t  blen 
) [protected]

compute without mismatch matrix

Parameters:
avecvector a
alenlength of vector a
bvecvector b
blenlength of vector b
Returns:
computed value

Definition at line 458 of file WeightedDegreePositionStringKernel.cpp.

float64_t compute_without_mismatch_position_weights ( char *  avec,
float64_t posweights_lhs,
int32_t  alen,
char *  bvec,
float64_t posweights_rhs,
int32_t  blen 
) [protected]

compute without mismatch position weights

Parameters:
avecvector a
posweights_lhsposition weights left-hand side
alenlength of vector a
bvecvector b
posweights_rhsposition weights right-hand side
blenlength of vector b
Returns:
computed value

Definition at line 522 of file WeightedDegreePositionStringKernel.cpp.

void create_empty_tries (  ) [protected]

create emtpy tries

Definition at line 154 of file WeightedDegreePositionStringKernel.cpp.

bool delete_optimization (  ) [virtual]

delete optimization

Returns:
if deleting was successful

Reimplemented from CKernel.

Definition at line 288 of file WeightedDegreePositionStringKernel.cpp.

bool delete_position_weights (  )

delete position weights

Returns:
if deleting was successful

Definition at line 480 of file WeightedDegreePositionStringKernel.h.

bool delete_position_weights_lhs (  )

delete position weights left-hand side

Returns:
if deleting was successful

Definition at line 491 of file WeightedDegreePositionStringKernel.h.

bool delete_position_weights_rhs (  )

delete position weights right-hand side

Returns:
if deleting was successful

Definition at line 502 of file WeightedDegreePositionStringKernel.h.

float64_t * extract_w ( int32_t  max_degree,
int32_t &  num_feat,
int32_t &  num_sym,
float64_t w_result,
int32_t  num_suppvec,
int32_t *  IDX,
float64_t alphas 
)

extract w

Parameters:
max_degreemaximum degree
num_featnumber of features
num_symnumber of symbols
w_resultw
num_suppvecnumber of support vectors
IDXIDX
alphasalphas
Returns:
w

Definition at line 1691 of file WeightedDegreePositionStringKernel.cpp.

int32_t get_degree (  )

get degree

Returns:
the degree

Definition at line 325 of file WeightedDegreePositionStringKernel.h.

float64_t* get_degree_weights ( int32_t &  d,
int32_t &  len 
)

get degree weights

Parameters:
ddegree weights will be stored here
lennumber of degree weights will be stored here

Definition at line 332 of file WeightedDegreePositionStringKernel.h.

virtual EKernelType get_kernel_type (  ) [virtual]

return what type of kernel we are

Returns:
kernel type WEIGHTEDDEGREEPOS

Implements CKernel.

Definition at line 103 of file WeightedDegreePositionStringKernel.h.

int32_t get_max_mismatch (  )

get maximum mismatch

Returns:
maximum mismatch

Definition at line 319 of file WeightedDegreePositionStringKernel.h.

virtual const char* get_name (  ) const [virtual]

return the kernel's name

Returns:
name WeightedDegreePos

Implements CSGObject.

Definition at line 109 of file WeightedDegreePositionStringKernel.h.

virtual int32_t get_num_subkernels (  ) [virtual]

get number of subkernels

Returns:
number of subkernels

Reimplemented from CKernel.

Definition at line 218 of file WeightedDegreePositionStringKernel.h.

void get_POIM2 ( float64_t **  poim,
int32_t *  result_len 
)

get POIM2

Parameters:
poimPOIMs (returned)
result_len(returned)

Definition at line 1937 of file WeightedDegreePositionStringKernel.cpp.

float64_t* get_position_weights ( int32_t &  len )

get position weights

Parameters:
lennumber of position weights will be stored here
Returns:
position weights

Definition at line 363 of file WeightedDegreePositionStringKernel.h.

const float64_t* get_subkernel_weights ( int32_t &  num_weights ) [virtual]

get subkernel weights

Parameters:
num_weightsnumber of weights will be stored here
Returns:
subkernel weights

Reimplemented from CKernel.

Definition at line 249 of file WeightedDegreePositionStringKernel.h.

float64_t* get_weights ( int32_t &  num_weights )

get weights

Parameters:
num_weightsnumber of weights will be stored here
Returns:
weights

Definition at line 344 of file WeightedDegreePositionStringKernel.h.

bool init ( CFeatures l,
CFeatures r 
) [virtual]

initialize kernel

Parameters:
lfeatures of left-hand side
rfeatures of right-hand side
Returns:
if initializing was successful

Reimplemented from CStringKernel< char >.

Definition at line 173 of file WeightedDegreePositionStringKernel.cpp.

bool init_block_weights (  )

initialize block weights

Returns:
if initialization was successful

Definition at line 1218 of file WeightedDegreePositionStringKernel.cpp.

bool init_block_weights_const (  )

initialize block weights constant

Returns:
if initialization was successful

Definition at line 1103 of file WeightedDegreePositionStringKernel.cpp.

bool init_block_weights_cubicpoly (  )

initialize block weights cubic polynomial

Returns:
if initialization was successful

Definition at line 1148 of file WeightedDegreePositionStringKernel.cpp.

bool init_block_weights_exp (  )

initialize block weights exponential

Returns:
if initialization was successful

Definition at line 1165 of file WeightedDegreePositionStringKernel.cpp.

bool init_block_weights_external (  )

initialize block weights external

Returns:
if initialization was successful

Definition at line 1199 of file WeightedDegreePositionStringKernel.cpp.

bool init_block_weights_from_wd (  )

initialize block weights from weighted degree

Returns:
if initialization was successful

Definition at line 1055 of file WeightedDegreePositionStringKernel.cpp.

bool init_block_weights_from_wd_external (  )

initialize block weights from external weighted degree

Returns:
if initialization was successful

Definition at line 1075 of file WeightedDegreePositionStringKernel.cpp.

bool init_block_weights_linear (  )

initialize block weights linear

Returns:
if initialization was successful

Definition at line 1117 of file WeightedDegreePositionStringKernel.cpp.

bool init_block_weights_log (  )

initialize block weights logarithmic

Returns:
if initialization was successful

Definition at line 1182 of file WeightedDegreePositionStringKernel.cpp.

bool init_block_weights_sqpoly (  )

initialize block weights squared polynomial

Returns:
if initialization was successful

Definition at line 1131 of file WeightedDegreePositionStringKernel.cpp.

virtual bool init_optimization ( int32_t  p_count,
int32_t *  IDX,
float64_t alphas 
) [virtual]

initialize optimization

Parameters:
p_countcount
IDXindex
alphasalphas
Returns:
if initializing was successful

Reimplemented from CKernel.

Definition at line 118 of file WeightedDegreePositionStringKernel.h.

bool init_optimization ( int32_t  count,
int32_t *  IDX,
float64_t alphas,
int32_t  tree_num,
int32_t  upto_tree = -1 
) [virtual]

initialize optimization do initialization for tree_num up to upto_tree, use tree_num=-1 to construct all trees

Parameters:
countcount
IDXIDX
alphasalphas
tree_numwhich tree
upto_treeup to this tree
Returns:
if initializing was successful

Definition at line 242 of file WeightedDegreePositionStringKernel.cpp.

bool is_tree_initialized (  )

check if tree is initialized

Returns:
if tree is initialized

Definition at line 313 of file WeightedDegreePositionStringKernel.h.

void prepare_POIM2 ( float64_t distrib,
int32_t  num_sym,
int32_t  num_feat 
)

prepare POIM2

Parameters:
num_featnumber of features
num_symnumber of symbols
distribdistribution

Definition at line 1890 of file WeightedDegreePositionStringKernel.cpp.

void remove_lhs (  ) [protected, virtual]

remove lhs from kernel

Reimplemented from CKernel.

Definition at line 143 of file WeightedDegreePositionStringKernel.cpp.

bool set_position_weights ( float64_t pws,
int32_t  len 
) [virtual]

set position weights

Parameters:
pwsnew position weights
lennumber of position weights
Returns:
if setting was successful

Definition at line 930 of file WeightedDegreePositionStringKernel.cpp.

bool set_position_weights_lhs ( float64_t pws,
int32_t  len,
int32_t  num 
)

set position weights for left-hand side

Parameters:
pwsnew position weights
lenlen
numnum
Returns:
if setting was successful

Definition at line 955 of file WeightedDegreePositionStringKernel.cpp.

bool set_position_weights_rhs ( float64_t pws,
int32_t  len,
int32_t  num 
)

set position weights for right-hand side

Parameters:
pwsnew position weights
lenlen
numnum
Returns:
if setting was successful

Definition at line 1001 of file WeightedDegreePositionStringKernel.cpp.

bool set_shifts ( int32_t *  shifts,
int32_t  len 
)

set shifts

Parameters:
shiftsnew shifts
lennumber of shifts

Definition at line 844 of file WeightedDegreePositionStringKernel.cpp.

void set_subkernel_weights ( float64_t weights2,
int32_t  num_weights2 
) [virtual]

set subkernel weights

Parameters:
weights2weights
num_weights2number of weights

Reimplemented from CKernel.

Definition at line 271 of file WeightedDegreePositionStringKernel.h.

bool set_wd_weights (  ) [virtual]

set wd weights

Returns:
if setting was successful

Definition at line 869 of file WeightedDegreePositionStringKernel.cpp.

bool set_weights ( float64_t weights,
int32_t  d,
int32_t  len = 0 
) [virtual]

set weights

Parameters:
weightsnew weights
ddegree
lennumber of weights

Definition at line 907 of file WeightedDegreePositionStringKernel.cpp.


Member Data Documentation

CAlphabet* alphabet [protected]

alphabet of features

Definition at line 765 of file WeightedDegreePositionStringKernel.h.

bool block_computation [protected]

if block computation is used

Definition at line 728 of file WeightedDegreePositionStringKernel.h.

float64_t* block_weights [protected]

(internal) block weights

Definition at line 736 of file WeightedDegreePositionStringKernel.h.

external block weights

Definition at line 733 of file WeightedDegreePositionStringKernel.h.

int32_t degree [protected]

degree

Definition at line 711 of file WeightedDegreePositionStringKernel.h.

int32_t length [protected]

length

Definition at line 713 of file WeightedDegreePositionStringKernel.h.

float64_t* m_poim [protected]

temporary memory for the interface to the poim functions

Definition at line 755 of file WeightedDegreePositionStringKernel.h.

float64_t* m_poim_distrib [protected]

temporary memory for the interface to the poim functions

Definition at line 753 of file WeightedDegreePositionStringKernel.h.

int32_t m_poim_num_feat [protected]

length of string (==num_feat)

Definition at line 760 of file WeightedDegreePositionStringKernel.h.

int32_t m_poim_num_sym [protected]

number of symbols

Definition at line 758 of file WeightedDegreePositionStringKernel.h.

int32_t m_poim_result_len [protected]

total size of poim array

Definition at line 762 of file WeightedDegreePositionStringKernel.h.

int32_t max_mismatch [protected]

maximum mismatch

Definition at line 716 of file WeightedDegreePositionStringKernel.h.

int32_t max_shift [protected]

maximum shift

Definition at line 725 of file WeightedDegreePositionStringKernel.h.

int32_t mkl_stepsize [protected]

MKL stepsize

Definition at line 708 of file WeightedDegreePositionStringKernel.h.

int32_t num_block_weights_external [protected]

number of external block weights

Definition at line 731 of file WeightedDegreePositionStringKernel.h.

CTrie<POIMTrie> poim_tries [protected]

POIM tries

Definition at line 745 of file WeightedDegreePositionStringKernel.h.

bool* position_mask [protected]

position mask

Definition at line 703 of file WeightedDegreePositionStringKernel.h.

position weights

Definition at line 697 of file WeightedDegreePositionStringKernel.h.

position weights left-hand side

Definition at line 699 of file WeightedDegreePositionStringKernel.h.

position weights right-hand side

Definition at line 701 of file WeightedDegreePositionStringKernel.h.

int32_t seq_length [protected]

length of sequence

Definition at line 718 of file WeightedDegreePositionStringKernel.h.

int32_t* shift [protected]

shifts

Definition at line 721 of file WeightedDegreePositionStringKernel.h.

int32_t shift_len [protected]

length of shifts

Definition at line 723 of file WeightedDegreePositionStringKernel.h.

bool tree_initialized [protected]

if tree is initialized

Definition at line 748 of file WeightedDegreePositionStringKernel.h.

CTrie<DNATrie> tries [protected]

tries

Definition at line 743 of file WeightedDegreePositionStringKernel.h.

EWDKernType type [protected]

WeightedDegree kernel type

Definition at line 738 of file WeightedDegreePositionStringKernel.h.

bool use_poim_tries [protected]

makes add_example_to_tree (ONLY!) use POIMTrie

Definition at line 750 of file WeightedDegreePositionStringKernel.h.

float64_t* weights [protected]

weights

Definition at line 695 of file WeightedDegreePositionStringKernel.h.

float64_t* weights_buffer [protected]

weights buffer

Definition at line 706 of file WeightedDegreePositionStringKernel.h.

int32_t which_degree [protected]

which degree

Definition at line 740 of file WeightedDegreePositionStringKernel.h.


The documentation for this class was generated from the following files:
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SHOGUN Machine Learning Toolbox - Documentation