Calibrator Class Reference

Inheritance diagram for Calibrator:

Public Member Functions
virtual int	init (map< string, string > &mapper)
virtual int	Learn (const MedSamples &samples)
virtual int	Learn (const vector< MedSample > &samples)
virtual int	Learn (const vector< MedSample > &samples, const int samples_time_unit)
virtual int	Apply (MedSamples &samples)
virtual int	Apply (vector< MedSample > &samples)
void	Apply (const vector< float > &preds, vector< float > &probs) const
float	Apply (float pred) const
void	get_input_fields (vector< Effected_Field > &fields) const
	List of fields that are used by this post_processor.
void	get_output_fields (vector< Effected_Field > &fields) const
	List of fields that are being effected by this post_processor.
void	Learn (const MedFeatures &matrix)
void	Apply (MedFeatures &matrix)
calibration_entry	calibrate_pred (float pred)
float	calibrate_pred (float pred, int type) const
void	write_calibration_table (const string &calibration_table_file)
void	read_calibration_table (const string &fname)
void	dprint (const string &pref) const
void	learn_isotonic_regression (const vector< float > &x, const vector< float > &y, const vector< float > &weights, vector< float > &min_range, vector< float > &max_range, vector< float > &map_prob, int n_top_controls, int n_bottom_cases, bool verbose)
ADD_SERIALIZATION_FUNCS(calibration_type, estimator_type, binning_method, bins_num, time_unit, pos_sample_min_time_before_case, pos_sample_max_time_before_case, km_time_resolution, min_cases_for_calibration_smoothing_pct, do_calibration_smoothing, censor_controls, min_preds_in_bin, min_score_res, min_prob_res, fix_pred_order, poly_rank, control_weight_down_sample, cals, min_range, max_range, map_prob, platt_params, use_isotonic, n_top_controls, n_bottom_cases) protected void	smooth_calibration_entries (const vector< calibration_entry > &cals, vector< calibration_entry > &smooth_cals, double controls_factor)
Public Member Functions inherited from PostProcessor
virtual void	init_post_processor (MedModel &mdl)
void *	new_polymorphic (string dname)
	for polymorphic classes that want to be able to serialize/deserialize a pointer * to the derived class given its type one needs to implement this function to return a new to the derived class given its type (as in my_type)
virtual float	get_use_p ()
virtual int	get_use_split ()
Public Member Functions inherited from SerializableObject
virtual int	version () const
	Relevant for serializations.
virtual string	my_class_name () const
	For better handling of serializations it is highly recommended that each SerializableObject inheriting class will implement the next method.
virtual void	serialized_fields_name (vector< string > &field_names) const
	The names of the serialized fields.
virtual void	pre_serialization ()
virtual void	post_deserialization ()
virtual size_t	get_size ()
	Gets bytes sizes for serializations.
virtual size_t	serialize (unsigned char *blob)
	Serialiazing object to blob memory. return number ob bytes wrote to memory.
virtual size_t	deserialize (unsigned char *blob)
	Deserialiazing blob to object. returns number of bytes read.
size_t	serialize_vec (vector< unsigned char > &blob)
size_t	deserialize_vec (vector< unsigned char > &blob)
virtual size_t	serialize (vector< unsigned char > &blob)
virtual size_t	deserialize (vector< unsigned char > &blob)
virtual int	read_from_file (const string &fname)
	read and deserialize model
virtual int	write_to_file (const string &fname)
	serialize model and write to file
virtual int	read_from_file_unsafe (const string &fname)
	read and deserialize model without checking version number - unsafe read
int	init_from_string (string init_string)
	Init from string.
int	init_params_from_file (string init_file)
int	init_param_from_file (string file_str, string &param)
int	update_from_string (const string &init_string)
virtual int	update (map< string, string > &map)
	Virtual to update object from parsed fields.
virtual string	object_json () const

Data Fields
CalibrationTypes	calibration_type = probability_time_window
int	time_unit = MedTime::Days
string	estimator_type = "kaplan_meier"
string	binning_method = "equal_num_of_samples_per_bin"
int	bins_num = 1000
int	pos_sample_min_time_before_case = 0
int	pos_sample_max_time_before_case = 360
int	km_time_resolution = 1
int	min_cases_for_calibration_smoothing_pct = 10
int	do_calibration_smoothing = 1
int	censor_controls = 0
	censor controls without long-enough followup even in mean-outcome mode
string	weights_attr_name = "weight"
int	min_control_bins = -1
bool	use_isotonic = false
	If true will use isotonic on time_window.
int	min_preds_in_bin = 100
	minimal number of obseravtion to create bin
float	min_score_res = 0
	score resulotion value to round to and merge similar
float	min_prob_res = 0
	final probality resulotion value to round to and merge similar
bool	fix_pred_order = false
	If true will not allow higher scores to have lower probabilites.
int	poly_rank = 1
	Only in platt_scale - the polynon rank for optimizing sigmoid of prob.
double	control_weight_down_sample = 1
	factor weight for controls when downsampling controls by this factor
bool	verbose = true
	If true will print verbose information for calibration.
int	n_top_controls = 0
	number of controls to add with maximal-score for regularization of isotonic regression
int	n_bottom_cases = 0
	number of cases to add with minimal-score for regularization of isotonic regression
vector< calibration_entry >	cals
	for "time_window"
vector< float >	min_range
vector< float >	max_range
vector< float >	map_prob
	for "binning/isotonic-regression"
vector< double >	platt_params
	for "platt_scale"
Data Fields inherited from PostProcessor
PostProcessorTypes	processor_type = PostProcessorTypes::FTR_POSTPROCESS_LAST
int	use_split = -1
float	use_p = 0.0

Additional Inherited Members
Static Public Member Functions inherited from PostProcessor
static PostProcessor *	make_processor (const string &processor_name, const string &params="")
static PostProcessor *	make_processor (PostProcessorTypes type, const string &params="")
static PostProcessor *	create_processor (string &params)

Member Function Documentation

Apply()

void Calibrator::Apply ( MedFeatures &  matrix )

virtual

Reimplemented from PostProcessor.

dprint()

void Calibrator::dprint ( const string &  pref ) const

virtual

Reimplemented from PostProcessor.

get_input_fields()

void Calibrator::get_input_fields ( vector< Effected_Field > &  fields ) const

virtual

List of fields that are used by this post_processor.

Reimplemented from PostProcessor.

get_output_fields()

void Calibrator::get_output_fields ( vector< Effected_Field > &  fields ) const

virtual

List of fields that are being effected by this post_processor.

Options: "prediction:X", "attr:$NAME", "str_attr:$NAME", "feature:$NAME", "json"

Reimplemented from PostProcessor.

init()

int Calibrator::init ( map< string, string > &  mapper )

virtual

        if (field == "calibration_type") calibration_type = clibration_name_to_type(entry.second);
        else if (field == "estimator_type") estimator_type = entry.second;
        else if (field == "binning_method") binning_method = entry.second;
        else if (field == "bins_num") bins_num = stoi(entry.second);
        else if (field == "pos_sample_min_time_before_case") pos_sample_min_time_before_case = stoi(entry.second);
        else if (field == "pos_sample_max_time_before_case") pos_sample_max_time_before_case = stoi(entry.second);
        else if (field == "km_time_resolution") km_time_resolution = stoi(entry.second);
        else if (field == "do_calibration_smoothing") do_calibration_smoothing = stoi(entry.second);
        else if (field == "min_cases_for_calibration_smoothing_pct") min_cases_for_calibration_smoothing_pct = stoi(entry.second);
        else if (field == "min_preds_in_bin") min_preds_in_bin = stoi(entry.second);
        else if (field == "min_score_res") min_score_res = stof(entry.second);
        else if (field == "min_prob_res") min_prob_res = stof(entry.second);
        else if (field == "fix_pred_order") fix_pred_order = stoi(entry.second) > 0;
        else if (field == "poly_rank") poly_rank = stoi(entry.second);
        else if (field == "control_weight_down_sample") control_weight_down_sample = stof(entry.second);
        else if (field == "censor_controls") censor_controls = stoi(entry.second);
        else if (field == "n_top_controls") n_top_controls = stoi(entry.second);
        else if (field == "n_bottom_cases") n_bottom_cases = stoi(entry.second);
        else if (field == "verbose") verbose = stoi(entry.second) > 0;
        else if (field == "use_split") use_split = stoi(entry.second);
        else if (field == "use_p") use_p = stof(entry.second);
        else if (field == "weights_attr_name") weights_attr_name = entry.second;
        else if (field == "min_control_bins") min_control_bins = stoi(entry.second);
        else if (field == "use_isotonic") use_isotonic = stoi(entry.second) > 0;
        else if (field == "pp_type") {} //ignore
        else MTHROW_AND_ERR("unknown init option [%s] for Calibrator\n", field.c_str());

[Calibrator::init]

[Calibrator::init]

Reimplemented from SerializableObject.

Learn()

void Calibrator::Learn ( const MedFeatures &  matrix )

inlinevirtual

Reimplemented from PostProcessor.

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The documentation for this class was generated from the following files:

• Internal/MedProcessTools/MedProcessTools/Calibration.h
• Internal/MedProcessTools/MedProcessTools/Calibration.cpp