SHOGUN
v2.0.0
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Dynamic Programming Class.
Structure and Function collection. This Class implements a Dynamic Programming functions.
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) |
virtual CSGObject * | shallow_copy () const |
virtual CSGObject * | deep_copy () const |
virtual bool | is_generic (EPrimitiveType *generic) const |
template<class T > | |
void | set_generic () |
void | unset_generic () |
virtual void | print_serializable (const char *prefix="") |
virtual bool | save_serializable (CSerializableFile *file, const char *prefix="", int32_t param_version=VERSION_PARAMETER) |
virtual bool | load_serializable (CSerializableFile *file, const char *prefix="", int32_t param_version=VERSION_PARAMETER) |
DynArray< TParameter * > * | load_file_parameters (const SGParamInfo *param_info, int32_t file_version, CSerializableFile *file, const char *prefix="") |
DynArray< TParameter * > * | load_all_file_parameters (int32_t file_version, int32_t current_version, CSerializableFile *file, const char *prefix="") |
void | map_parameters (DynArray< TParameter * > *param_base, int32_t &base_version, DynArray< const SGParamInfo * > *target_param_infos) |
void | set_global_io (SGIO *io) |
SGIO * | get_global_io () |
void | set_global_parallel (Parallel *parallel) |
Parallel * | get_global_parallel () |
void | set_global_version (Version *version) |
Version * | get_global_version () |
SGStringList< char > | get_modelsel_names () |
void | print_modsel_params () |
char * | get_modsel_param_descr (const char *param_name) |
index_t | get_modsel_param_index (const char *param_name) |
void | build_parameter_dictionary (CMap< TParameter *, CSGObject * > &dict) |
Public Attributes | |
SGIO * | io |
Parallel * | parallel |
Version * | version |
Parameter * | m_parameters |
Parameter * | m_model_selection_parameters |
ParameterMap * | m_parameter_map |
uint32_t | m_hash |
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 |
virtual TParameter * | migrate (DynArray< TParameter * > *param_base, const SGParamInfo *target) |
virtual void | one_to_one_migration_prepare (DynArray< TParameter * > *param_base, const SGParamInfo *target, TParameter *&replacement, TParameter *&to_migrate, char *old_name=NULL) |
virtual void | load_serializable_pre () throw (ShogunException) |
virtual void | load_serializable_post () throw (ShogunException) |
virtual void | save_serializable_pre () throw (ShogunException) |
virtual void | save_serializable_post () throw (ShogunException) |
virtual bool | update_parameter_hash () |
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] |
CDynProg | ( | int32_t | p_num_svms = 8 | ) |
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Definition at line 144 of file DynProg.cpp.
void best_path_set_segment_ids_mask | ( | int32_t * | segment_ids, |
float64_t * | segment_mask, | ||
int32_t | m | ||
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set best path segmend ids mask
segment_ids | segment ids |
segment_mask | segment mask |
m | dimension m |
Definition at line 817 of file DynProg.cpp.
set best path segment loss
segment_loss | segment loss |
Definition at line 800 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 | ||
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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 2054 of file DynProg.cpp.
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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 1204 of file SGObject.cpp.
bool check_svm_arrays | ( | ) |
check SVM arrays call this function to check consistency
Definition at line 603 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 | ||
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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 946 of file DynProg.cpp.
void create_word_string | ( | ) |
create word string from char* Jonas
Definition at line 363 of file DynProg.cpp.
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A deep copy. All the instance variables will also be copied.
Definition at line 131 of file SGObject.h.
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extend orf
orf_from | orf from |
orf_to | orf to |
start | start |
last_pos | last position |
to | to |
Definition at line 895 of file DynProg.cpp.
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find frame
from_state | from state |
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float64_t* get_lin_feat | ( | int32_t & | dim1, |
int32_t & | dim2 | ||
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Definition at line 1108 of file SGObject.cpp.
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Returns description of a given parameter string, if it exists. SG_ERROR otherwise
param_name | name of the parameter |
Definition at line 1132 of file SGObject.cpp.
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Returns index of model selection parameter with provided index
param_name | name of model selection parameter |
Definition at line 1145 of file SGObject.cpp.
T_STATES get_N | ( | ) | const |
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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 681 of file DynProg.cpp.
int32_t get_num_states | ( | ) |
get num states
Definition at line 236 of file DynProg.cpp.
int32_t get_num_svms | ( | ) |
get num svms
Definition at line 192 of file DynProg.cpp.
void get_path_losses | ( | float64_t ** | my_losses, |
int32_t * | seq_len | ||
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get path losses
best_path_trans_deriv result retrieval functions
my_losses | my losses |
seq_len | length of sequence |
Definition at line 879 of file DynProg.cpp.
void get_path_scores | ( | float64_t ** | my_scores, |
int32_t * | seq_len | ||
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get path scores
best_path_trans_deriv result retrieval functions
my_scores | scores |
seq_len | length of sequence |
Definition at line 865 of file DynProg.cpp.
SGMatrix< int32_t > get_positions | ( | ) |
CSegmentLoss* get_segment_loss_object | ( | ) |
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 271 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 581 of file DynProg.cpp.
void init_tiling_data | ( | int32_t * | probe_pos, |
float64_t * | intensities, | ||
const int32_t | num_probes | ||
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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 241 of file DynProg.cpp.
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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 278 of file SGObject.cpp.
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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_PARAMETER for this in most cases) |
file | file to load from |
prefix | prefix for members |
Definition at line 679 of file SGObject.cpp.
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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 523 of file SGObject.cpp.
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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) |
Reimplemented in CModelSelectionParameters.
Definition at line 354 of file SGObject.cpp.
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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, CANOVAKernel, CInverseMultiQuadricKernel, CCircularKernel, and CExponentialKernel.
Definition at line 1033 of file SGObject.cpp.
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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. |
Definition at line 1028 of file SGObject.cpp.
void long_transition_settings | ( | bool | use_long_transitions, |
int32_t | threshold, | ||
int32_t | max_len | ||
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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 2484 of file DynProg.cpp.
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lookup tiling Plif values
from_state | from state |
to_state | to state |
len | length |
svm_values | SVM values |
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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 717 of file SGObject.cpp.
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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 923 of file SGObject.cpp.
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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 864 of file SGObject.cpp.
void precompute_content_values | ( | ) |
create array of precomputed content svm values
Definition at line 394 of file DynProg.cpp.
void precompute_stop_codons | ( | ) |
precompute stop codons
Definition at line 197 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 314 of file DynProg.cpp.
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prints all parameter registered for model selection and their type
Definition at line 1084 of file SGObject.cpp.
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prints registered parameters out
prefix | prefix for members |
Definition at line 290 of file SGObject.cpp.
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raw intensities interval query
from_pos | from position |
to_pos | to position |
intensities | intensities |
type | type |
Definition at line 2458 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 281 of file DynProg.cpp.
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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) |
Reimplemented in CModelSelectionParameters.
Definition at line 296 of file SGObject.cpp.
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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 1043 of file SGObject.cpp.
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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.
Definition at line 1038 of file SGObject.cpp.
void set_a_id | ( | SGMatrix< int32_t > | a | ) |
set a transition matrix
a_trans | transition matrix a |
Definition at line 480 of file DynProg.cpp.
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 686 of file DynProg.cpp.
set best path dict weights
dictionary_weights | dictionary weights |
Definition at line 781 of file DynProg.cpp.
void set_gene_string | ( | SGVector< char > | genestr | ) |
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set generic type to T
Definition at line 41 of file SGObject.cpp.
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set the parallel object
parallel | parallel object to use |
Definition at line 230 of file SGObject.cpp.
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set the version object
version | version object to use |
Definition at line 265 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 2537 of file DynProg.cpp.
void set_lin_feat | ( | float64_t * | p_lin_feat, |
int32_t | p_num_svms, | ||
int32_t | p_seq_len | ||
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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 773 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 765 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 220 of file DynProg.cpp.
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 725 of file DynProg.cpp.
void set_plif_matrices | ( | CPlifMatrix * | pm | ) |
void set_pos | ( | SGVector< int32_t > | pos | ) |
void set_sparse_features | ( | CSparseFeatures< float64_t > * | seq_sparse1, |
CSparseFeatures< float64_t > * | seq_sparse2 | ||
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set sparse feature matrices
Definition at line 734 of file DynProg.cpp.
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A shallow copy. All the SGObject instance variables will be simply assigned and SG_REF-ed.
Reimplemented in CGaussianKernel.
Definition at line 122 of file SGObject.h.
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unset generic type
this has to be called in classes specializing a template class
Definition at line 285 of file SGObject.cpp.
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Updates the hash of current parameter combination.
Definition at line 237 of file SGObject.cpp.
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io
Definition at line 462 of file SGObject.h.
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Hash of parameter values
Definition at line 480 of file SGObject.h.
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model selection parameters
Definition at line 474 of file SGObject.h.
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map for different parameter versions
Definition at line 477 of file SGObject.h.
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parameters
Definition at line 471 of file SGObject.h.
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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
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parallel
Definition at line 465 of file SGObject.h.
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version
Definition at line 468 of file SGObject.h.
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