magpie.models.regression.crystal

Class CoulombSineMatrixRegression

java.lang.Object

magpie.models.BaseModel

magpie.models.regression.BaseRegression

magpie.models.regression.crystal.StructureKRRBasedRegression

magpie.models.regression.crystal.CoulombSineMatrixRegression

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, AbstractRegressionModel, Citable, Commandable, Options, Printable, Savable

public class CoulombSineMatrixRegression
extends StructureKRRBasedRegression

Perform regression based on the Coulomb Sine Matrix approach of Faber et al..

LW 1Apr15: This method does not appear to be insensitive to basis cell selection.

Usage: <lambda> <sigma>
lambda: Regularization parameter
sigma: Normalization parameter in kernel function.

See Also:

Serialized Form

Field Summary

Fields inherited from class magpie.models.BaseModel

AttributeSelector, trained, TrainingStats, validated, ValidationStats

Constructor Summary

Constructors

Constructor and Description
CoulombSineMatrixRegression()

Method Summary

Modifier and Type	Method and Description
protected org.apache.commons.math3.linear.RealMatrix	computeCoulombMatrix(vassal.data.Cell strc) Computes the Coulomb sine matrix.
java.lang.Object	computeRepresentation(vassal.data.Cell strc) Given a structure, compute representation of the structure.
protected double	computeSimiliarity(java.lang.Object strc1, java.lang.Object strc2) Compute similarity between two crystal structures.
java.util.List<org.apache.commons.lang3.tuple.Pair<java.lang.String,Citation>>	getCitations() Return a list of citations for this object and any underlying objects.
java.lang.String	printUsage() Print out required format for options.
void	setOptions(java.util.List<java.lang.Object> Options) Set any options for this object.
void	setSigma(double Sigma) Set the normalization parameter in the kernel function.

Methods inherited from class magpie.models.regression.crystal.StructureKRRBasedRegression

clone, findClosestEntries, getNFittingParameters, printModel_protected, run_protected, runCommand, setLambda, train_protected

Methods inherited from class magpie.models.regression.BaseRegression

doRobustRegression, getRobustRegressionQ, robustTraining, setRobustRegressionQ

Methods inherited from class magpie.models.BaseModel

about, crossValidate, crossValidate, crossValidate, done, externallyValidate, getAttributeSelector, getFilter, getTrainTime, getValidationMethod, handleSetCommand, isTrained, isValidated, loadState, printCommand, printDescription, printModel, printModelDescriptionDetails, resetModel, run, saveCommand, saveState, setAttributeSelector, setComponent, setFilter, train, train

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

CoulombSineMatrixRegression

public CoulombSineMatrixRegression()

Method Detail

setSigma

public void setSigma(double Sigma)

Set the normalization parameter in the kernel function.

Parameters:

Sigma - Desired normalization parameter.

setOptions

public void setOptions(java.util.List<java.lang.Object> Options)
                throws java.lang.Exception

Description copied from interface: Options

Set any options for this object. If parsing the options fails, return an Exception with the usage as its message.

Parameters:

Options - Array of options as Objects - can be null

Throws:

java.lang.Exception - if problem with inputs

printUsage

public java.lang.String printUsage()

Description copied from interface: Options

Print out required format for options. For consistency, should start with "Usage: ".

Returns:

Usage for this function

computeSimiliarity

protected double computeSimiliarity(java.lang.Object strc1,
                                    java.lang.Object strc2)

Description copied from class: StructureKRRBasedRegression

Compute similarity between two crystal structures.

Specified by:

computeSimiliarity in class StructureKRRBasedRegression

Parameters:

strc1 - Representation of structure #1

strc2 - Representation of structure #2

Returns:

Similarity between two structures

computeRepresentation

public java.lang.Object computeRepresentation(vassal.data.Cell strc)

Description copied from class: StructureKRRBasedRegression

Given a structure, compute representation of the structure. For instance, this code could be used to compute the RDF or Coulomb matrix.

Specified by:

computeRepresentation in class StructureKRRBasedRegression

Parameters:

strc - Structure

Returns:

Representation of the structure

computeCoulombMatrix

protected org.apache.commons.math3.linear.RealMatrix computeCoulombMatrix(vassal.data.Cell strc)

Computes the Coulomb sine matrix. Equation 24 of the paper describing this method.

Parameters:

strc - Structure to be evaluated

Returns:

Coulomb sine matrix

getCitations

public java.util.List<org.apache.commons.lang3.tuple.Pair<java.lang.String,Citation>> getCitations()

Description copied from interface: Citable

Return a list of citations for this object and any underlying objects.

Specified by:

getCitations in interface Citable

Overrides:

getCitations in class BaseModel

Returns:

List of pairs: [Reason for Citation], [Citation]