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

CDynProg Class Reference

Detailed Description

Dynamic Programming Class.

Structure and Function collection. This Class implements a Dynamic Programming functions.

Definition at line 77 of file DynProg.h.

Inheritance diagram for CDynProg:
Inheritance graph
[legend]

List of all members.

Public Member Functions

 CDynProg (int32_t p_num_svms=8)
virtual ~CDynProg ()
void set_num_states (int32_t N)
int32_t get_num_states ()
int32_t get_num_svms ()
void init_content_svm_value_array (const int32_t p_num_svms)
void init_tiling_data (int32_t *probe_pos, float64_t *intensities, const int32_t num_probes)
void precompute_tiling_plifs (CPlif **PEN, const int32_t *tiling_plif_ids, const int32_t num_tiling_plifs)
void resize_lin_feat (int32_t num_new_feat)
void set_p_vector (SGVector< float64_t > p)
void set_q_vector (SGVector< float64_t > q)
void set_a (SGMatrix< float64_t > a)
void set_a_id (SGMatrix< int32_t > a)
void set_a_trans_matrix (SGMatrix< float64_t > a_trans)
void init_mod_words_array (SGMatrix< int32_t > p_mod_words_array)
bool check_svm_arrays ()
void set_observation_matrix (SGNDArray< float64_t > seq)
int32_t get_num_positions ()
void set_content_type_array (SGMatrix< float64_t > seg_path)
void set_pos (SGVector< int32_t > pos)
void set_orf_info (SGMatrix< int32_t > orf_info)
void set_gene_string (SGVector< char > genestr)
void set_dict_weights (SGMatrix< float64_t > dictionary_weights)
void best_path_set_segment_loss (SGMatrix< float64_t > segment_loss)
void best_path_set_segment_ids_mask (int32_t *segment_ids, float64_t *segment_mask, int32_t m)
void set_sparse_features (CSparseFeatures< float64_t > *seq_sparse1, CSparseFeatures< float64_t > *seq_sparse2)
void set_plif_matrices (CPlifMatrix *pm)
SGVector< float64_t > get_scores ()
SGMatrix< int32_t > get_states ()
SGMatrix< int32_t > get_positions ()
void compute_nbest_paths (int32_t max_num_signals, bool use_orf, int16_t nbest, bool with_loss, bool with_multiple_sequences)
void best_path_trans_deriv (int32_t *my_state_seq, int32_t *my_pos_seq, int32_t my_seq_len, const float64_t *seq_array, int32_t max_num_signals)
void set_my_state_seq (int32_t *my_state_seq)
void set_my_pos_seq (int32_t *my_pos_seq)
void get_path_scores (float64_t **my_scores, int32_t *seq_len)
void get_path_losses (float64_t **my_losses, int32_t *seq_len)
T_STATES get_N () const
 access function for number of states N
void set_q (T_STATES offset, float64_t value)
void set_p (T_STATES offset, float64_t value)
void set_a (T_STATES line_, T_STATES column, float64_t value)
float64_t get_q (T_STATES offset) const
float64_t get_q_deriv (T_STATES offset) const
float64_t get_p (T_STATES offset) const
float64_t get_p_deriv (T_STATES offset) const
void precompute_content_values ()
float64_t * get_lin_feat (int32_t &dim1, int32_t &dim2)
void set_lin_feat (float64_t *p_lin_feat, int32_t p_num_svms, int32_t p_seq_len)
void create_word_string ()
void precompute_stop_codons ()
float64_t get_a (T_STATES line_, T_STATES column) const
float64_t get_a_deriv (T_STATES line_, T_STATES column) const
void set_intron_list (CIntronList *intron_list, int32_t num_plifs)
CSegmentLoss * get_segment_loss_object ()
void long_transition_settings (bool use_long_transitions, int32_t threshold, int32_t max_len)

Protected Member Functions

void lookup_content_svm_values (const int32_t from_state, const int32_t to_state, const int32_t from_pos, const int32_t to_pos, float64_t *svm_values, int32_t frame)
void lookup_tiling_plif_values (const int32_t from_state, const int32_t to_state, const int32_t len, float64_t *svm_values)
int32_t find_frame (const int32_t from_state)
int32_t raw_intensities_interval_query (const int32_t from_pos, const int32_t to_pos, float64_t *intensities, int32_t type)
bool extend_orf (int32_t orf_from, int32_t orf_to, int32_t start, int32_t &last_pos, int32_t to)
virtual const char * get_name () const

Protected Attributes

int32_t m_num_degrees
int32_t m_num_svms
CArray< int32_t > m_word_degree
CArray< int32_t > m_cum_num_words
int32_t * m_cum_num_words_array
CArray< int32_t > m_num_words
int32_t * m_num_words_array
CArray2< int32_t > m_mod_words
int32_t * m_mod_words_array
CArray< bool > m_sign_words
bool * m_sign_words_array
CArray< int32_t > m_string_words
int32_t * m_string_words_array
CArray< int32_t > m_num_unique_words
bool m_svm_arrays_clean
int32_t m_max_a_id
CArray3< float64_t > m_observation_matrix
CArray< int32_t > m_pos
int32_t m_seq_len
CArray2< int32_t > m_orf_info
CArray2< float64_t > m_segment_sum_weights
CArray< CPlifBase * > m_plif_list
CArray2< CPlifBase * > m_PEN
CArray2< CPlifBase * > m_PEN_state_signals
CArray< char > m_genestr
uint16_t *** m_wordstr
CArray2< float64_t > m_dict_weights
CArray3< float64_t > m_segment_loss
CArray< int32_t > m_segment_ids
CArray< float64_t > m_segment_mask
CArray< int32_t > m_my_state_seq
CArray< int32_t > m_my_pos_seq
CArray< float64_t > m_my_scores
CArray< float64_t > m_my_losses
CSegmentLoss * m_seg_loss_obj
CArray< float64_t > m_scores
CArray2< int32_t > m_states
CArray2< int32_t > m_positions
CSparseFeatures< float64_t > * m_seq_sparse1
CSparseFeatures< float64_t > * m_seq_sparse2
CPlifMatrix * m_plif_matrices
CArray< bool > m_genestr_stop
CIntronList * m_intron_list
int32_t m_num_intron_plifs
CArray2< float64_t > m_lin_feat
float64_t * m_raw_intensities
int32_t * m_probe_pos
int32_t * m_num_probes_cum
int32_t * m_num_lin_feat_plifs_cum
int32_t m_num_raw_data
bool m_long_transitions
int32_t m_long_transition_threshold
model specific variables.

these are p,q,a,b,N,M etc

int32_t m_N
 number of states
CArray2< int32_t > m_transition_matrix_a_id
 transition matrix
CArray2< float64_t > m_transition_matrix_a
CArray2< float64_t > m_transition_matrix_a_deriv
CArray< float64_t > m_initial_state_distribution_p
 initial distribution of states
CArray< float64_t > m_initial_state_distribution_p_deriv
CArray< float64_t > m_end_state_distribution_q
 distribution of end-states
CArray< float64_t > m_end_state_distribution_q_deriv

Static Protected Attributes

static int32_t word_degree_default [4] = {3,4,5,6}
static int32_t cum_num_words_default [5] = {0,64,320,1344,5440}
static int32_t frame_plifs [3] = {4,5,6}
static int32_t num_words_default [4] = {64,256,1024,4096}
static int32_t mod_words_default [32]
static bool sign_words_default [16]
static int32_t string_words_default [16]

Constructor & Destructor Documentation

CDynProg ( int32_t  p_num_svms = 8  ) 

constructor

Parameters:
p_num_svms number of SVMs

Definition at line 48 of file DynProg.cpp.

~CDynProg (  )  [virtual]

Definition at line 147 of file DynProg.cpp.

Member Function Documentation

void best_path_set_segment_ids_mask ( int32_t *  segment_ids,
float64_t *  segment_mask,
int32_t  m 
)

set best path segmend ids mask

Parameters:
segment_ids segment ids
segment_mask segment mask
m dimension m

Definition at line 820 of file DynProg.cpp.

void best_path_set_segment_loss ( SGMatrix< float64_t >  segment_loss  ) 

set best path segment loss

Parameters:
segment_loss segment loss

Definition at line 803 of file DynProg.cpp.

void best_path_trans_deriv ( int32_t *  my_state_seq,
int32_t *  my_pos_seq,
int32_t  my_seq_len,
const float64_t *  seq_array,
int32_t  max_num_signals 
)

given a path though the state model and the corresponding positions compute the features. This can be seen as the derivative of the score (output of dynamic program) with respect to the parameters

Parameters:
my_state_seq state sequence of the path
my_pos_seq sequence of positions
my_seq_len length of state and position sequences
seq_array array of features
max_num_signals maximal number of signals

Definition at line 2053 of file DynProg.cpp.

bool check_svm_arrays (  ) 

check SVM arrays call this function to check consistency

Returns:
whether arrays are ok

Definition at line 606 of file DynProg.cpp.

void compute_nbest_paths ( int32_t  max_num_signals,
bool  use_orf,
int16_t  nbest,
bool  with_loss,
bool  with_multiple_sequences 
)

run the viterbi algorithm to compute the n best viterbi paths

Parameters:
max_num_signals maximal number of signals for a single state
use_orf whether orf shall be used
nbest number of best paths (n)
with_loss use loss
with_multiple_sequences !!!not functional set to false!!!

Definition at line 949 of file DynProg.cpp.

void create_word_string (  ) 

create word string from char* Jonas

Definition at line 366 of file DynProg.cpp.

bool extend_orf ( int32_t  orf_from,
int32_t  orf_to,
int32_t  start,
int32_t &  last_pos,
int32_t  to 
) [protected]

extend orf

Parameters:
orf_from orf from
orf_to orf to
start start
last_pos last position
to to

Definition at line 898 of file DynProg.cpp.

int32_t find_frame ( const int32_t  from_state  )  [protected]

find frame

Parameters:
from_state from state
float64_t get_a ( T_STATES  line_,
T_STATES  column 
) const

access function for matrix a

Parameters:
line_ row in matrix 0...N-1
column column in matrix 0...N-1
Returns:
value at position line colum

Definition at line 446 of file DynProg.h.

float64_t get_a_deriv ( T_STATES  line_,
T_STATES  column 
) const

access function for matrix a derivated

Parameters:
line_ row in matrix 0...N-1
column column in matrix 0...N-1
Returns:
value at position line colum

Definition at line 457 of file DynProg.h.

float64_t* get_lin_feat ( int32_t &  dim1,
int32_t &  dim2 
)

return array of precomputed linear features like content predictions and PLiFed tiling array data Jonas

Returns:
lin_feat_array

Definition at line 413 of file DynProg.h.

T_STATES get_N (  )  const

access function for number of states N

Definition at line 328 of file DynProg.h.

virtual const char* get_name (  )  const [protected, virtual]
Returns:
object name

Implements CSGObject.

Definition at line 566 of file DynProg.h.

int32_t get_num_positions (  ) 

get number of positions; the dynamic program is sparse encoded and this function gives the number of positions that can actually be part of a predicted path

Returns:
number of positions

Definition at line 684 of file DynProg.cpp.

int32_t get_num_states (  ) 

get num states

Definition at line 239 of file DynProg.cpp.

int32_t get_num_svms (  ) 

get num svms

Definition at line 195 of file DynProg.cpp.

float64_t get_p ( T_STATES  offset  )  const

access function for probability of initial states

Parameters:
offset index 0...N-1
Returns:
value at offset

Definition at line 387 of file DynProg.h.

float64_t get_p_deriv ( T_STATES  offset  )  const

access function for derivated probability of initial states

Parameters:
offset index 0...N-1
Returns:
value at offset

Definition at line 397 of file DynProg.h.

void get_path_losses ( float64_t **  my_losses,
int32_t *  seq_len 
)

get path losses

best_path_trans_deriv result retrieval functions

Parameters:
my_losses my losses
seq_len length of sequence

Definition at line 882 of file DynProg.cpp.

void get_path_scores ( float64_t **  my_scores,
int32_t *  seq_len 
)

get path scores

best_path_trans_deriv result retrieval functions

Parameters:
my_scores scores
seq_len length of sequence

Definition at line 868 of file DynProg.cpp.

SGMatrix< int32_t > get_positions (  ) 

best path get positions

Returns:
positions positions

Definition at line 858 of file DynProg.cpp.

float64_t get_q ( T_STATES  offset  )  const

access function for probability of end states

Parameters:
offset index 0...N-1
Returns:
value at offset

Definition at line 367 of file DynProg.h.

float64_t get_q_deriv ( T_STATES  offset  )  const

access function for derivated probability of end states

Parameters:
offset index 0...N-1
Returns:
value at offset

Definition at line 377 of file DynProg.h.

SGVector< float64_t > get_scores (  ) 

best path get scores

Returns:
scores scores

Definition at line 840 of file DynProg.cpp.

CSegmentLoss* get_segment_loss_object (  ) 

get the segment loss object

Definition at line 470 of file DynProg.h.

SGMatrix< int32_t > get_states (  ) 

best path get states

Returns:
states states

Definition at line 848 of file DynProg.cpp.

void init_content_svm_value_array ( const int32_t  p_num_svms  ) 

init CArray for precomputed content svm values with size seq_len x num_svms

Parameters:
p_num_svms,: number of svm weight vectors for content prediction

Definition at line 274 of file DynProg.cpp.

void init_mod_words_array ( SGMatrix< int32_t >  p_mod_words_array  ) 

init mod words array

Parameters:
p_mod_words_array new mod words array

Definition at line 584 of file DynProg.cpp.

void init_tiling_data ( int32_t *  probe_pos,
float64_t *  intensities,
const int32_t  num_probes 
)

init CArray for precomputed tiling intensitie-plif-values with size seq_len x num_svms

Parameters:
probe_pos local positions of probes
intensities intensities of probes
num_probes number of probes

Definition at line 244 of file DynProg.cpp.

void long_transition_settings ( bool  use_long_transitions,
int32_t  threshold,
int32_t  max_len 
)

settings for long transition handling

Parameters:
use_long_transitions use the long transition approximation
threshold use long transition for segments larger than
max_len allow transitions up to

Definition at line 481 of file DynProg.h.

void lookup_content_svm_values ( const int32_t  from_state,
const int32_t  to_state,
const int32_t  from_pos,
const int32_t  to_pos,
float64_t *  svm_values,
int32_t  frame 
) [protected]

lookup content SVM values

Parameters:
from_state from state
to_state to state
from_pos from position
to_pos to position
svm_values SVM values
frame frame

Definition at line 2481 of file DynProg.cpp.

void lookup_tiling_plif_values ( const int32_t  from_state,
const int32_t  to_state,
const int32_t  len,
float64_t *  svm_values 
) [protected]

lookup tiling Plif values

Parameters:
from_state from state
to_state to state
len length
svm_values SVM values
void precompute_content_values (  ) 

create array of precomputed content svm values

Definition at line 397 of file DynProg.cpp.

void precompute_stop_codons (  ) 

precompute stop codons

Definition at line 200 of file DynProg.cpp.

void precompute_tiling_plifs ( CPlif **  PEN,
const int32_t *  tiling_plif_ids,
const int32_t  num_tiling_plifs 
)

precompute tiling Plifs

Parameters:
PEN Plif PEN
tiling_plif_ids tiling plif id's
num_tiling_plifs number of tiling plifs

Definition at line 317 of file DynProg.cpp.

int32_t raw_intensities_interval_query ( const int32_t  from_pos,
const int32_t  to_pos,
float64_t *  intensities,
int32_t  type 
) [protected]

raw intensities interval query

Parameters:
from_pos from position
to_pos to position
intensities intensities
type type
Returns:
an integer

Definition at line 2455 of file DynProg.cpp.

void resize_lin_feat ( int32_t  num_new_feat  ) 

append rows to linear features array

Parameters:
num_new_feat number of new rows to add

Definition at line 284 of file DynProg.cpp.

void set_a ( SGMatrix< float64_t >  a  ) 

set matrix a

Parameters:
a new matrix a

Definition at line 462 of file DynProg.cpp.

void set_a ( T_STATES  line_,
T_STATES  column,
float64_t  value 
)

access function for matrix a

Parameters:
line_ row in matrix 0...N-1
column column in matrix 0...N-1
value value to be set

Definition at line 357 of file DynProg.h.

void set_a_id ( SGMatrix< int32_t >  a  ) 

set a id

Parameters:
a new a id

Definition at line 470 of file DynProg.cpp.

void set_a_trans_matrix ( SGMatrix< float64_t >  a_trans  ) 

set a transition matrix

Parameters:
a_trans transition matrix a

Definition at line 483 of file DynProg.cpp.

void set_content_type_array ( SGMatrix< float64_t >  seg_path  ) 

set an array of length #(candidate positions) which specifies the content type of each pos and a mask that determines to which extend the loss should be applied to this position; this is a way to encode label confidence via weights between zero and one

Parameters:
seg_path seg path

Definition at line 689 of file DynProg.cpp.

void set_dict_weights ( SGMatrix< float64_t >  dictionary_weights  ) 

set best path dict weights

Parameters:
dictionary_weights dictionary weights

Definition at line 784 of file DynProg.cpp.

void set_gene_string ( SGVector< char >  genestr  ) 

set best path genesstr

Parameters:
genestr gene string

Definition at line 760 of file DynProg.cpp.

void set_intron_list ( CIntronList *  intron_list,
int32_t  num_plifs 
)

set intron list

Parameters:
intron_list 
num_plifs number of intron plifs

Definition at line 2534 of file DynProg.cpp.

void set_lin_feat ( float64_t *  p_lin_feat,
int32_t  p_num_svms,
int32_t  p_seq_len 
)

set your own array of precomputed linear features like content predictions and PLiFed tiling array data Jonas

Parameters:
p_lin_feat array of features
p_num_svms number of tracks
p_seq_len number of candidate positions

Definition at line 426 of file DynProg.h.

void set_my_pos_seq ( int32_t *  my_pos_seq  ) 

set best path my position sequence

Parameters:
my_pos_seq my position sequence

Definition at line 776 of file DynProg.cpp.

void set_my_state_seq ( int32_t *  my_state_seq  ) 

set best path my state sequence

Parameters:
my_state_seq my state sequence

Definition at line 768 of file DynProg.cpp.

void set_num_states ( int32_t  N  ) 

set number of states use this to set N first

Parameters:
N new N

Definition at line 223 of file DynProg.cpp.

void set_observation_matrix ( SGNDArray< float64_t >  seq  ) 

set best path seq

Parameters:
seq signal features

Definition at line 662 of file DynProg.cpp.

void set_orf_info ( SGMatrix< int32_t >  orf_info  ) 

set best path orf info only for compute_nbest_paths

Parameters:
orf_info the orf info

Definition at line 728 of file DynProg.cpp.

void set_p ( T_STATES  offset,
float64_t  value 
)

access function for probability of first state

Parameters:
offset index 0...N-1
value value to be set

Definition at line 346 of file DynProg.h.

void set_p_vector ( SGVector< float64_t >  p  ) 

set vector p

Parameters:
p new vector p

Definition at line 447 of file DynProg.cpp.

void set_plif_matrices ( CPlifMatrix *  pm  ) 

set plif matrices

Parameters:
pm plif matrix object

Definition at line 751 of file DynProg.cpp.

void set_pos ( SGVector< int32_t >  pos  ) 

set best path pos

Parameters:
pos the position vector

Definition at line 722 of file DynProg.cpp.

void set_q ( T_STATES  offset,
float64_t  value 
)

access function for probability of end states

Parameters:
offset index 0...N-1
value value to be set

Definition at line 337 of file DynProg.h.

void set_q_vector ( SGVector< float64_t >  q  ) 

set vector q

Parameters:
q new vector q

Definition at line 455 of file DynProg.cpp.

void set_sparse_features ( CSparseFeatures< float64_t > *  seq_sparse1,
CSparseFeatures< float64_t > *  seq_sparse2 
)

set sparse feature matrices

Definition at line 737 of file DynProg.cpp.

Member Data Documentation

int32_t cum_num_words_default = {0,64,320,1344,5440} [static, protected]

default values storing the cumulative sum of the number of kmers that exist for the different degrees e.g. matlab spoken: cumsum(4.^[3 4 5 6])

Definition at line 778 of file DynProg.h.

int32_t frame_plifs = {4,5,6} [static, protected]

default values defining which of the plif are the frame specific plifs

Definition at line 782 of file DynProg.h.

CArray<int32_t> m_cum_num_words [protected]

cum num words

Definition at line 631 of file DynProg.h.

int32_t* m_cum_num_words_array [protected]

cum num words array

Definition at line 633 of file DynProg.h.

CArray2<float64_t> m_dict_weights [protected]

dict weights

Definition at line 695 of file DynProg.h.

CArray<float64_t> m_end_state_distribution_q [protected]

distribution of end-states

Definition at line 618 of file DynProg.h.

CArray<float64_t> m_end_state_distribution_q_deriv [protected]

Definition at line 619 of file DynProg.h.

CArray<char> m_genestr [protected]

a single string (to be segmented)

Definition at line 678 of file DynProg.h.

CArray<bool> m_genestr_stop [protected]

storeage of stop codons array of size length(sequence)

Definition at line 733 of file DynProg.h.

CArray<float64_t> m_initial_state_distribution_p [protected]

initial distribution of states

Definition at line 614 of file DynProg.h.

CArray<float64_t> m_initial_state_distribution_p_deriv [protected]

Definition at line 615 of file DynProg.h.

CIntronList* m_intron_list [protected]

administers a list of introns and quality scores and provides functions for fast access

Definition at line 737 of file DynProg.h.

CArray2<float64_t> m_lin_feat [protected]

array for storage of precomputed linear features linge content svm values or pliffed tiling data Jonas

Definition at line 746 of file DynProg.h.

int32_t m_long_transition_threshold [protected]

threshold for transitions that are computed the traditional way

Definition at line 763 of file DynProg.h.

bool m_long_transitions [protected]

use long transition approximation

Definition at line 760 of file DynProg.h.

int32_t m_max_a_id [protected]

max a id

Definition at line 658 of file DynProg.h.

CArray2<int32_t> m_mod_words [protected]

mod words

Definition at line 639 of file DynProg.h.

int32_t* m_mod_words_array [protected]

mod words array

Definition at line 641 of file DynProg.h.

CArray<float64_t> m_my_losses [protected]

my losses

Definition at line 709 of file DynProg.h.

CArray<int32_t> m_my_pos_seq [protected]

my position sequence

Definition at line 705 of file DynProg.h.

CArray<float64_t> m_my_scores [protected]

my scores

Definition at line 707 of file DynProg.h.

CArray<int32_t> m_my_state_seq [protected]

my state seq

Definition at line 703 of file DynProg.h.

int32_t m_N [protected]

number of states

Definition at line 606 of file DynProg.h.

int32_t m_num_degrees [protected]

number of degress

Definition at line 624 of file DynProg.h.

int32_t m_num_intron_plifs [protected]

number of intron features and plifs

Definition at line 740 of file DynProg.h.

int32_t* m_num_lin_feat_plifs_cum [protected]

num lin feat plifs cum

Definition at line 755 of file DynProg.h.

int32_t* m_num_probes_cum [protected]

number of probes

Definition at line 753 of file DynProg.h.

int32_t m_num_raw_data [protected]

number of additional data tracks like tiling, RNA-Seq, ...

Definition at line 757 of file DynProg.h.

int32_t m_num_svms [protected]

number of SVMs

Definition at line 626 of file DynProg.h.

CArray<int32_t> m_num_unique_words [protected]

SVM start position number of unique words

Definition at line 654 of file DynProg.h.

CArray<int32_t> m_num_words [protected]

num words

Definition at line 635 of file DynProg.h.

int32_t* m_num_words_array [protected]

num words array

Definition at line 637 of file DynProg.h.

CArray3<float64_t> m_observation_matrix [protected]

sequence

Definition at line 662 of file DynProg.h.

CArray2<int32_t> m_orf_info [protected]

orf info

Definition at line 668 of file DynProg.h.

CArray2<CPlifBase*> m_PEN [protected]

PEN

Definition at line 674 of file DynProg.h.

CArray2<CPlifBase*> m_PEN_state_signals [protected]

PEN state signals

Definition at line 676 of file DynProg.h.

CArray<CPlifBase*> m_plif_list [protected]

Plif list

Definition at line 672 of file DynProg.h.

CPlifMatrix* m_plif_matrices [protected]

plif matrices

Definition at line 728 of file DynProg.h.

CArray<int32_t> m_pos [protected]

candidate position

Definition at line 664 of file DynProg.h.

CArray2<int32_t> m_positions [protected]

positions

Definition at line 721 of file DynProg.h.

int32_t* m_probe_pos [protected]

probe position

Definition at line 751 of file DynProg.h.

float64_t* m_raw_intensities [protected]

raw intensities

Definition at line 749 of file DynProg.h.

CArray<float64_t> m_scores [protected]

scores

Definition at line 717 of file DynProg.h.

CSegmentLoss* m_seg_loss_obj [protected]

segment loss object containing the functions to compute the segment loss

Definition at line 713 of file DynProg.h.

CArray<int32_t> m_segment_ids [protected]

segment IDs

Definition at line 699 of file DynProg.h.

CArray3<float64_t> m_segment_loss [protected]

segment loss

Definition at line 697 of file DynProg.h.

CArray<float64_t> m_segment_mask [protected]

segment mask

Definition at line 701 of file DynProg.h.

CArray2<float64_t> m_segment_sum_weights [protected]

segment sum weights

Definition at line 670 of file DynProg.h.

int32_t m_seq_len [protected]

number of candidate positions

Definition at line 666 of file DynProg.h.

CSparseFeatures<float64_t>* m_seq_sparse1 [protected]

sparse feature matrix dim1

Definition at line 724 of file DynProg.h.

CSparseFeatures<float64_t>* m_seq_sparse2 [protected]

sparse feature matrix dim2

Definition at line 726 of file DynProg.h.

CArray<bool> m_sign_words [protected]

sign words

Definition at line 643 of file DynProg.h.

bool* m_sign_words_array [protected]

sign words array

Definition at line 645 of file DynProg.h.

CArray2<int32_t> m_states [protected]

states

Definition at line 719 of file DynProg.h.

CArray<int32_t> m_string_words [protected]

string words

Definition at line 647 of file DynProg.h.

int32_t* m_string_words_array [protected]

string words array

Definition at line 649 of file DynProg.h.

bool m_svm_arrays_clean [protected]

SVM arrays clean

Definition at line 656 of file DynProg.h.

CArray2<float64_t> m_transition_matrix_a [protected]

Definition at line 610 of file DynProg.h.

CArray2<float64_t> m_transition_matrix_a_deriv [protected]

Definition at line 611 of file DynProg.h.

CArray2<int32_t> m_transition_matrix_a_id [protected]

transition matrix

Definition at line 609 of file DynProg.h.

CArray<int32_t> m_word_degree [protected]

word degree

Definition at line 629 of file DynProg.h.

uint16_t*** m_wordstr [protected]

wordstr is a vector of L n-gram indices, with wordstr(i) representing a number betweeen 0 and 4095 corresponding to the 6-mer in genestr(i-5:i) pos is a vector of candidate transition positions (it is input to compute_nbest_paths) t_end is some index in pos

svs has been initialized by init_svm_values

At the end of this procedure, svs.svm_values[i+s*svs.seqlen] has the value of the s-th SVM on genestr(pos(t_end-i):pos(t_end)) for every i satisfying pos(t_end)-pos(t_end-i) <= svs.maxlookback

The SVM weights are precomputed in m_dict_weights

Definition at line 693 of file DynProg.h.

int32_t mod_words_default [static, protected]
Initial value:
 {1,1,1,1,1,1,1,1,
                                    1,1,1,1,1,1,1,1,
                                    0,0,0,0,0,0,0,0,
                                    0,0,0,0,0,0,0,0}

default values

Definition at line 789 of file DynProg.h.

int32_t num_words_default = {64,256,1024,4096} [static, protected]

default values like cum_num_words_default but not cumsumed: e.g. 4.^[3 4 5 6]

Definition at line 786 of file DynProg.h.

bool sign_words_default [static, protected]
Initial value:
 {true,true,true,true,true,true,true,true,
                                      false,false,false,false,false,false,false,false}

default values

Definition at line 792 of file DynProg.h.

int32_t string_words_default [static, protected]
Initial value:
 {0,0,0,0,0,0,0,0,
                                       1,1,1,1,1,1,1,1}

default values

Definition at line 795 of file DynProg.h.

int32_t word_degree_default = {3,4,5,6} [static, protected]

maximal length of a long transition Note: is ignored in the current implementation => arbitrarily long transitions can be decodeddefault values defining the k-mer degrees used for content type prediction

Definition at line 773 of file DynProg.h.

The documentation for this class was generated from the following files:
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines
SHOGUN Machine Learning Toolbox - Documentation