OpenMS
LocalLinearMap Class Reference

Trained Local Linear Map (LLM) model for peak intensity prediction. More...

#include <OpenMS/ANALYSIS/PIP/LocalLinearMap.h>

Collaboration diagram for LocalLinearMap:
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Classes

struct  LLMParam
 Define parameters needed by the Local Linear Map (LLM) model. More...
 

Public Member Functions

 LocalLinearMap ()
 default constructor More...
 
virtual ~LocalLinearMap ()
 destructor More...
 
const LLMParamgetLLMParam () const
 return parameters of the LocalLinearMap model More...
 
const Matrix< double > & getCodebooks () const
 return position of the codebook vectors (18-dim) More...
 
const Matrix< double > & getMatrixA () const
 return linear mappings of the codebooks More...
 
const std::vector< double > & getVectorWout () const
 return linear bias More...
 
const Matrix< UInt > & getCord () const
 return coordinates of codebook vectors on the 2-d grid More...
 
void normalizeVector (std::vector< double > &aaIndexVariables)
 calculate and return normalized amino acid index variables from string representation of peptide More...
 
std::vector< double > neigh (const Matrix< UInt > &cord, Size win, double radius)
 calculate neighborhood function based on distance of prototypes to winner prototype on two-dimensional grid structure and neighborhood width. More...
 

Private Member Functions

Matrix< UIntgenCord_ (Size xdim, Size ydim)
 needed to store prototype coordinates More...
 
double dist_ (const Matrix< UInt > &u, const Matrix< UInt > &v, Size a, Size b)
 calculate distance between two prototypes More...
 
 LocalLinearMap (LocalLinearMap &rhs)
 Copy constructor not implemented => private. More...
 
LocalLinearMapoperator= (const LocalLinearMap &llm)
 Assignment operator not implemented => private. More...
 

Private Attributes

LLMParam param_
 parameters of the model More...
 
Matrix< double > code_
 codebook vectors More...
 
Matrix< double > A_
 linear mappings More...
 
std::vector< double > wout_
 linear bias More...
 
Matrix< UIntcord_
 coordinates of codebooks on grid More...
 

Detailed Description

Trained Local Linear Map (LLM) model for peak intensity prediction.

This class offers a model for predictions of peptide peak heights (referred to as intensities) by a Local Linear Map (LLM) model and is the basis of PeakIntensityPredictor.

A general introduction to the Peak Intensity Predictor (PIP) can be found in the PIP Tutorial.

The model trained needs two files for storing the position of the codebook vectors and the linear mappings (codebooks.data, linearMapping.data) This is the default model used by PeakIntensityPredictor.


Class Documentation

◆ OpenMS::LocalLinearMap::LLMParam

struct OpenMS::LocalLinearMap::LLMParam

Define parameters needed by the Local Linear Map (LLM) model.

Parameters xdim and ydim define the size of the two dimensional grid structure. Parameter radius gives the width of the Gaussian neighborhood function.

Collaboration diagram for LocalLinearMap::LLMParam:
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Class Members
double radius

width of Gaussian neighborhood function

UInt xdim

size of first coordinate

UInt ydim

size of second coordinate

Constructor & Destructor Documentation

◆ LocalLinearMap() [1/2]

default constructor

◆ ~LocalLinearMap()

virtual ~LocalLinearMap ( )
virtual

destructor

◆ LocalLinearMap() [2/2]

LocalLinearMap ( LocalLinearMap rhs)
private

Copy constructor not implemented => private.

Member Function Documentation

◆ dist_()

double dist_ ( const Matrix< UInt > &  u,
const Matrix< UInt > &  v,
Size  a,
Size  b 
)
private

calculate distance between two prototypes

◆ genCord_()

Matrix<UInt> genCord_ ( Size  xdim,
Size  ydim 
)
private

needed to store prototype coordinates

◆ getCodebooks()

const Matrix<double>& getCodebooks ( ) const

return position of the codebook vectors (18-dim)

◆ getCord()

const Matrix<UInt>& getCord ( ) const

return coordinates of codebook vectors on the 2-d grid

◆ getLLMParam()

const LLMParam& getLLMParam ( ) const

return parameters of the LocalLinearMap model

◆ getMatrixA()

const Matrix<double>& getMatrixA ( ) const

return linear mappings of the codebooks

◆ getVectorWout()

const std::vector<double>& getVectorWout ( ) const

return linear bias

◆ neigh()

std::vector<double> neigh ( const Matrix< UInt > &  cord,
Size  win,
double  radius 
)

calculate neighborhood function based on distance of prototypes to winner prototype on two-dimensional grid structure and neighborhood width.

◆ normalizeVector()

void normalizeVector ( std::vector< double > &  aaIndexVariables)

calculate and return normalized amino acid index variables from string representation of peptide

◆ operator=()

LocalLinearMap& operator= ( const LocalLinearMap llm)
private

Assignment operator not implemented => private.

Member Data Documentation

◆ A_

Matrix<double> A_
private

linear mappings

◆ code_

Matrix<double> code_
private

codebook vectors

◆ cord_

Matrix<UInt> cord_
private

coordinates of codebooks on grid

◆ param_

LLMParam param_
private

parameters of the model

◆ wout_

std::vector<double> wout_
private

linear bias