SHOGUN
v3.2.0
|
Dynamic Programming Class.
Structure and Function collection. This Class implements a Dynamic Programming functions.
CDynProg | ( | int32_t | p_num_svms = 8 | ) |
~CDynProg | ( | ) | [virtual] |
Definition at line 141 of file DynProg.cpp.
void best_path_set_segment_ids_mask | ( | int32_t * | segment_ids, |
float64_t * | segment_mask, | ||
int32_t | m | ||
) |
set best path segmend ids mask
segment_ids | segment ids |
segment_mask | segment mask |
m | dimension m |
Definition at line 814 of file DynProg.cpp.
void best_path_set_segment_loss | ( | SGMatrix< float64_t > | segment_loss | ) |
set best path segment loss
segment_loss | segment loss |
Definition at line 797 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
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 2051 of file DynProg.cpp.
void build_gradient_parameter_dictionary | ( | CMap< TParameter *, CSGObject * > * | dict | ) | [inherited] |
Builds a dictionary of all parameters in SGObject as well of those of SGObjects that are parameters of this object. Dictionary maps parameters to the objects that own them.
dict | dictionary of parameters to be built. |
Definition at line 1156 of file SGObject.cpp.
bool check_svm_arrays | ( | ) |
check SVM arrays call this function to check consistency
Definition at line 600 of file DynProg.cpp.
Creates a clone of the current object. This is done via recursively traversing all parameters, which corresponds to a deep copy. Calling equals on the cloned object always returns true although none of the memory of both objects overlaps.
Definition at line 1273 of file SGObject.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
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 943 of file DynProg.cpp.
void create_word_string | ( | ) |
create word string from char* Jonas
Definition at line 360 of file DynProg.cpp.
A deep copy. All the instance variables will also be copied.
Definition at line 126 of file SGObject.h.
Recursively compares the current SGObject to another one. Compares all registered numerical parameters, recursion upon complex (SGObject) parameters. Does not compare pointers!
May be overwritten but please do with care! Should not be necessary in most cases.
other | object to compare with |
accuracy | accuracy to use for comparison (optional) |
Definition at line 1177 of file SGObject.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
orf_from | orf from |
orf_to | orf to |
start | start |
last_pos | last position |
to | to |
Definition at line 892 of file DynProg.cpp.
int32_t find_frame | ( | const int32_t | from_state | ) | [protected] |
find frame
from_state | from state |
float64_t get_a_deriv | ( | T_STATES | line_, |
T_STATES | column | ||
) | const |
SGIO * get_global_io | ( | ) | [inherited] |
Parallel * get_global_parallel | ( | ) | [inherited] |
Version * get_global_version | ( | ) | [inherited] |
float64_t* get_lin_feat | ( | int32_t & | dim1, |
int32_t & | dim2 | ||
) |
SGStringList< char > get_modelsel_names | ( | ) | [inherited] |
Definition at line 1060 of file SGObject.cpp.
char * get_modsel_param_descr | ( | const char * | param_name | ) | [inherited] |
Returns description of a given parameter string, if it exists. SG_ERROR otherwise
param_name | name of the parameter |
Definition at line 1084 of file SGObject.cpp.
index_t get_modsel_param_index | ( | const char * | param_name | ) | [inherited] |
Returns index of model selection parameter with provided index
param_name | name of model selection parameter |
Definition at line 1097 of file SGObject.cpp.
virtual const char* get_name | ( | ) | const [protected, virtual] |
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
Definition at line 678 of file DynProg.cpp.
int32_t get_num_states | ( | ) |
get num states
Definition at line 233 of file DynProg.cpp.
int32_t get_num_svms | ( | ) |
get num svms
Definition at line 190 of file DynProg.cpp.
float64_t get_p_deriv | ( | T_STATES | offset | ) | const |
void get_path_losses | ( | float64_t ** | my_losses, |
int32_t * | seq_len | ||
) |
get path losses
best_path_trans_deriv result retrieval functions
my_losses | my losses |
seq_len | length of sequence |
Definition at line 876 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
my_scores | scores |
seq_len | length of sequence |
Definition at line 862 of file DynProg.cpp.
SGMatrix< int32_t > get_positions | ( | ) |
float64_t get_q_deriv | ( | T_STATES | offset | ) | const |
SGVector< float64_t > get_scores | ( | ) |
SGMatrix< int32_t > get_states | ( | ) |
void init_content_svm_value_array | ( | const int32_t | p_num_svms | ) |
init CDynamicArray for precomputed content svm values with size seq_len x num_svms
p_num_svms,: | number of svm weight vectors for content prediction |
Definition at line 268 of file DynProg.cpp.
void init_mod_words_array | ( | SGMatrix< int32_t > | p_mod_words_array | ) |
init mod words array
p_mod_words_array | new mod words array |
Definition at line 578 of file DynProg.cpp.
void init_tiling_data | ( | int32_t * | probe_pos, |
float64_t * | intensities, | ||
const int32_t | num_probes | ||
) |
init CDynamicArray for precomputed tiling intensitie-plif-values with size seq_len x num_svms
probe_pos | local positions of probes |
intensities | intensities of probes |
num_probes | number of probes |
Definition at line 238 of file DynProg.cpp.
bool is_generic | ( | EPrimitiveType * | generic | ) | const [virtual, inherited] |
If the SGSerializable is a class template then TRUE will be returned and GENERIC is set to the type of the generic.
generic | set to the type of the generic if returning TRUE |
Definition at line 228 of file SGObject.cpp.
DynArray< TParameter * > * load_all_file_parameters | ( | int32_t | file_version, |
int32_t | current_version, | ||
CSerializableFile * | file, | ||
const char * | prefix = "" |
||
) | [inherited] |
maps all parameters of this instance to the provided file version and loads all parameter data from the file into an array, which is sorted (basically calls load_file_parameter(...) for all parameters and puts all results into a sorted array)
file_version | parameter version of the file |
current_version | version from which mapping begins (you want to use Version::get_version_parameter() for this in most cases) |
file | file to load from |
prefix | prefix for members |
Definition at line 633 of file SGObject.cpp.
DynArray< TParameter * > * load_file_parameters | ( | const SGParamInfo * | param_info, |
int32_t | file_version, | ||
CSerializableFile * | file, | ||
const char * | prefix = "" |
||
) | [inherited] |
loads some specified parameters from a file with a specified version The provided parameter info has a version which is recursively mapped until the file parameter version is reached. Note that there may be possibly multiple parameters in the mapping, therefore, a set of TParameter instances is returned
param_info | information of parameter |
file_version | parameter version of the file, must be <= provided parameter version |
file | file to load from |
prefix | prefix for members |
Definition at line 474 of file SGObject.cpp.
bool load_serializable | ( | CSerializableFile * | file, |
const char * | prefix = "" , |
||
int32_t | param_version = Version::get_version_parameter() |
||
) | [virtual, inherited] |
Load this object from file. If it will fail (returning FALSE) then this object will contain inconsistent data and should not be used!
file | where to load from |
prefix | prefix for members |
param_version | (optional) a parameter version different to (this is mainly for testing, better do not use) |
Definition at line 305 of file SGObject.cpp.
void load_serializable_post | ( | ) | throw (ShogunException) [protected, virtual, inherited] |
Can (optionally) be overridden to post-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::LOAD_SERIALIZABLE_POST is called.
ShogunException | Will be thrown if an error occurres. |
Reimplemented in CKernel, CWeightedDegreePositionStringKernel, CList, CAlphabet, CLinearHMM, CGaussianKernel, CInverseMultiQuadricKernel, CCircularKernel, and CExponentialKernel.
Definition at line 989 of file SGObject.cpp.
void load_serializable_pre | ( | ) | throw (ShogunException) [protected, virtual, inherited] |
Can (optionally) be overridden to pre-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::LOAD_SERIALIZABLE_PRE is called.
ShogunException | Will be thrown if an error occurres. |
Reimplemented in CDynamicArray< T >, CDynamicArray< float64_t >, CDynamicArray< float32_t >, CDynamicArray< int32_t >, CDynamicArray< char >, CDynamicArray< bool >, and CDynamicObjectArray.
Definition at line 984 of file SGObject.cpp.
void long_transition_settings | ( | bool | use_long_transitions, |
int32_t | threshold, | ||
int32_t | max_len | ||
) |
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
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
from_state | from state |
to_state | to state |
len | length |
svm_values | SVM values |
void map_parameters | ( | DynArray< TParameter * > * | param_base, |
int32_t & | base_version, | ||
DynArray< const SGParamInfo * > * | target_param_infos | ||
) | [inherited] |
Takes a set of TParameter instances (base) with a certain version and a set of target parameter infos and recursively maps the base level wise to the current version using CSGObject::migrate(...). The base is replaced. After this call, the base version containing parameters should be of same version/type as the initial target parameter infos. Note for this to work, the migrate methods and all the internal parameter mappings have to match
param_base | set of TParameter instances that are mapped to the provided target parameter infos |
base_version | version of the parameter base |
target_param_infos | set of SGParamInfo instances that specify the target parameter base |
Definition at line 671 of file SGObject.cpp.
TParameter * migrate | ( | DynArray< TParameter * > * | param_base, |
const SGParamInfo * | target | ||
) | [protected, virtual, inherited] |
creates a new TParameter instance, which contains migrated data from the version that is provided. The provided parameter data base is used for migration, this base is a collection of all parameter data of the previous version. Migration is done FROM the data in param_base TO the provided param info Migration is always one version step. Method has to be implemented in subclasses, if no match is found, base method has to be called.
If there is an element in the param_base which equals the target, a copy of the element is returned. This represents the case when nothing has changed and therefore, the migrate method is not overloaded in a subclass
param_base | set of TParameter instances to use for migration |
target | parameter info for the resulting TParameter |
Definition at line 878 of file SGObject.cpp.
void one_to_one_migration_prepare | ( | DynArray< TParameter * > * | param_base, |
const SGParamInfo * | target, | ||
TParameter *& | replacement, | ||
TParameter *& | to_migrate, | ||
char * | old_name = NULL |
||
) | [protected, virtual, inherited] |
This method prepares everything for a one-to-one parameter migration. One to one here means that only ONE element of the parameter base is needed for the migration (the one with the same name as the target). Data is allocated for the target (in the type as provided in the target SGParamInfo), and a corresponding new TParameter instance is written to replacement. The to_migrate pointer points to the single needed TParameter instance needed for migration. If a name change happened, the old name may be specified by old_name. In addition, the m_delete_data flag of to_migrate is set to true. So if you want to migrate data, the only thing to do after this call is converting the data in the m_parameter fields. If unsure how to use - have a look into an example for this. (base_migration_type_conversion.cpp for example)
param_base | set of TParameter instances to use for migration |
target | parameter info for the resulting TParameter |
replacement | (used as output) here the TParameter instance which is returned by migration is created into |
to_migrate | the only source that is used for migration |
old_name | with this parameter, a name change may be specified |
Definition at line 818 of file SGObject.cpp.
void precompute_content_values | ( | ) |
create array of precomputed content svm values
Definition at line 391 of file DynProg.cpp.
void precompute_stop_codons | ( | ) |
precompute stop codons
Definition at line 195 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
PEN | Plif PEN |
tiling_plif_ids | tiling plif id's |
num_tiling_plifs | number of tiling plifs |
Definition at line 311 of file DynProg.cpp.
void print_modsel_params | ( | ) | [inherited] |
prints all parameter registered for model selection and their type
Definition at line 1036 of file SGObject.cpp.
void print_serializable | ( | const char * | prefix = "" | ) | [virtual, inherited] |
prints registered parameters out
prefix | prefix for members |
Definition at line 240 of file SGObject.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
from_pos | from position |
to_pos | to position |
intensities | intensities |
type | type |
Definition at line 2455 of file DynProg.cpp.
void resize_lin_feat | ( | int32_t | num_new_feat | ) |
append rows to linear features array
num_new_feat | number of new rows to add |
Definition at line 278 of file DynProg.cpp.
bool save_serializable | ( | CSerializableFile * | file, |
const char * | prefix = "" , |
||
int32_t | param_version = Version::get_version_parameter() |
||
) | [virtual, inherited] |
Save this object to file.
file | where to save the object; will be closed during returning if PREFIX is an empty string. |
prefix | prefix for members |
param_version | (optional) a parameter version different to (this is mainly for testing, better do not use) |
Definition at line 246 of file SGObject.cpp.
void save_serializable_post | ( | ) | throw (ShogunException) [protected, virtual, inherited] |
Can (optionally) be overridden to post-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::SAVE_SERIALIZABLE_POST is called.
ShogunException | Will be thrown if an error occurres. |
Reimplemented in CKernel.
Definition at line 999 of file SGObject.cpp.
void save_serializable_pre | ( | ) | throw (ShogunException) [protected, virtual, inherited] |
Can (optionally) be overridden to pre-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::SAVE_SERIALIZABLE_PRE is called.
ShogunException | Will be thrown if an error occurres. |
Reimplemented in CKernel, CDynamicArray< T >, CDynamicArray< float64_t >, CDynamicArray< float32_t >, CDynamicArray< int32_t >, CDynamicArray< char >, CDynamicArray< bool >, and CDynamicObjectArray.
Definition at line 994 of file SGObject.cpp.
void set_a_trans_matrix | ( | SGMatrix< float64_t > | a_trans | ) |
set a transition matrix
a_trans | transition matrix a |
Definition at line 477 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
seg_path | seg path |
Definition at line 683 of file DynProg.cpp.
void set_dict_weights | ( | SGMatrix< float64_t > | dictionary_weights | ) |
set best path dict weights
dictionary_weights | dictionary weights |
Definition at line 778 of file DynProg.cpp.
void set_gene_string | ( | SGVector< char > | genestr | ) |
void set_generic< complex128_t > | ( | ) | [inherited] |
set generic type to T
Definition at line 41 of file SGObject.cpp.
void set_global_io | ( | SGIO * | io | ) | [inherited] |
void set_global_parallel | ( | Parallel * | parallel | ) | [inherited] |
set the parallel object
parallel | parallel object to use |
Definition at line 180 of file SGObject.cpp.
void set_global_version | ( | Version * | version | ) | [inherited] |
set the version object
version | version object to use |
Definition at line 215 of file SGObject.cpp.
void set_intron_list | ( | CIntronList * | intron_list, |
int32_t | num_plifs | ||
) |
set intron list
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 | ||
) |
void set_my_pos_seq | ( | int32_t * | my_pos_seq | ) |
set best path my position sequence
my_pos_seq | my position sequence |
Definition at line 770 of file DynProg.cpp.
void set_my_state_seq | ( | int32_t * | my_state_seq | ) |
set best path my state sequence
my_state_seq | my state sequence |
Definition at line 762 of file DynProg.cpp.
void set_num_states | ( | int32_t | N | ) |
set number of states use this to set N first
N | new N |
Definition at line 218 of file DynProg.cpp.
void set_observation_matrix | ( | SGNDArray< float64_t > | seq | ) |
void set_orf_info | ( | SGMatrix< int32_t > | orf_info | ) |
set best path orf info only for compute_nbest_paths
orf_info | the orf info |
Definition at line 722 of file DynProg.cpp.
void set_p_vector | ( | SGVector< float64_t > | p | ) |
void set_plif_matrices | ( | CPlifMatrix * | pm | ) |
void set_q_vector | ( | SGVector< float64_t > | q | ) |
void set_sparse_features | ( | CSparseFeatures< float64_t > * | seq_sparse1, |
CSparseFeatures< float64_t > * | seq_sparse2 | ||
) |
set sparse feature matrices
Definition at line 731 of file DynProg.cpp.
virtual CSGObject* shallow_copy | ( | ) | const [virtual, inherited] |
A shallow copy. All the SGObject instance variables will be simply assigned and SG_REF-ed.
Reimplemented in CGaussianKernel.
Definition at line 117 of file SGObject.h.
void unset_generic | ( | ) | [inherited] |
unset generic type
this has to be called in classes specializing a template class
Definition at line 235 of file SGObject.cpp.
bool update_parameter_hash | ( | ) | [virtual, inherited] |
Updates the hash of current parameter combination.
Definition at line 187 of file SGObject.cpp.
int32_t cum_num_words_default = {0,64,320,1344,5440} [static, protected] |
int32_t frame_plifs = {4,5,6} [static, protected] |
io
Definition at line 473 of file SGObject.h.
CDynamicArray<int32_t> m_cum_num_words [protected] |
int32_t* m_cum_num_words_array [protected] |
CDynamicArray<float64_t> m_dict_weights [protected] |
CDynamicArray<float64_t> m_end_state_distribution_q [protected] |
CDynamicArray<float64_t> m_end_state_distribution_q_deriv [protected] |
CDynamicArray<char> m_genestr [protected] |
CDynamicArray<bool> m_genestr_stop [protected] |
Parameter* m_gradient_parameters [inherited] |
parameters wrt which we can compute gradients
Definition at line 488 of file SGObject.h.
uint32_t m_hash [inherited] |
Hash of parameter values
Definition at line 494 of file SGObject.h.
CDynamicArray<float64_t> m_initial_state_distribution_p [protected] |
CDynamicArray<float64_t> m_initial_state_distribution_p_deriv [protected] |
CIntronList* m_intron_list [protected] |
CDynamicArray<float64_t> m_lin_feat [protected] |
int32_t m_long_transition_threshold [protected] |
bool m_long_transitions [protected] |
int32_t m_max_a_id [protected] |
CDynamicArray<int32_t> m_mod_words [protected] |
int32_t* m_mod_words_array [protected] |
Parameter* m_model_selection_parameters [inherited] |
model selection parameters
Definition at line 485 of file SGObject.h.
CDynamicArray<float64_t> m_my_losses [protected] |
CDynamicArray<int32_t> m_my_pos_seq [protected] |
CDynamicArray<float64_t> m_my_scores [protected] |
CDynamicArray<int32_t> m_my_state_seq [protected] |
int32_t m_num_degrees [protected] |
int32_t m_num_intron_plifs [protected] |
int32_t* m_num_lin_feat_plifs_cum [protected] |
int32_t* m_num_probes_cum [protected] |
int32_t m_num_raw_data [protected] |
int32_t m_num_svms [protected] |
CDynamicArray<int32_t> m_num_unique_words [protected] |
CDynamicArray<int32_t> m_num_words [protected] |
int32_t* m_num_words_array [protected] |
CDynamicArray<float64_t> m_observation_matrix [protected] |
CDynamicArray<int32_t> m_orf_info [protected] |
ParameterMap* m_parameter_map [inherited] |
map for different parameter versions
Definition at line 491 of file SGObject.h.
Parameter* m_parameters [inherited] |
parameters
Definition at line 482 of file SGObject.h.
CDynamicObjectArray m_plif_list [protected] |
CPlifMatrix* m_plif_matrices [protected] |
CDynamicArray<int32_t> m_pos [protected] |
CDynamicArray<int32_t> m_positions [protected] |
int32_t* m_probe_pos [protected] |
float64_t* m_raw_intensities [protected] |
CDynamicArray<float64_t> m_scores [protected] |
CSegmentLoss* m_seg_loss_obj [protected] |
CDynamicArray<int32_t> m_segment_ids [protected] |
CDynamicArray<float64_t> m_segment_loss [protected] |
CDynamicArray<float64_t> m_segment_mask [protected] |
CDynamicArray<float64_t> m_segment_sum_weights [protected] |
int32_t m_seq_len [protected] |
CSparseFeatures<float64_t>* m_seq_sparse1 [protected] |
CSparseFeatures<float64_t>* m_seq_sparse2 [protected] |
CDynamicArray<bool> m_sign_words [protected] |
bool* m_sign_words_array [protected] |
CDynamicArray<int32_t> m_states [protected] |
CDynamicArray<int32_t> m_string_words [protected] |
int32_t* m_string_words_array [protected] |
bool m_svm_arrays_clean [protected] |
CDynamicArray<float64_t> m_transition_matrix_a [protected] |
CDynamicArray<float64_t> m_transition_matrix_a_deriv [protected] |
CDynamicArray<int32_t> m_transition_matrix_a_id [protected] |
CDynamicArray<int32_t> m_word_degree [protected] |
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
int32_t mod_words_default [static, protected] |
int32_t num_words_default = {64,256,1024,4096} [static, protected] |
parallel
Definition at line 476 of file SGObject.h.
bool sign_words_default [static, protected] |
int32_t string_words_default [static, protected] |
version
Definition at line 479 of file SGObject.h.
int32_t word_degree_default = {3,4,5,6} [static, protected] |