magpie.models.classification

Class CumulantExpansionClassifier

java.lang.Object

magpie.models.BaseModel

magpie.models.classification.BaseClassifier

magpie.models.classification.CumulantExpansionClassifier

All Implemented Interfaces:

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

public class CumulantExpansionClassifier
extends BaseClassifier
implements Savable

Predict whether instance of a prototype structure will be a member of one of several mutually-exclusive classes. For example, predict whether it will have a negative or positive formation energy. Uses the cumulant-expansion method originally demonstrated by Fisher et al, which is described in more detail in the documentation PhaseDiagramStatistics.

Requires that dataset be a PrototypeDataset.

Usage: <filename> <order>
filename: Path to a file that contains all known compounds.
order: Number sites in prototype

Implemented Print Commands

cumulants [<toPrint>] - Print out the most important cumulant functions for each class
toPrint: Number of top cumulants to print (default 10)

Implemented Save Formats:

cumulants - Print the value of the cumulant between each variable and each class
Writes a file for each possible value of the class variable

See Also:

Serialized Form

Field Summary

Fields inherited from class magpie.models.classification.BaseClassifier

ClassNames, NClasses

Fields inherited from class magpie.models.BaseModel

AttributeSelector, trained, TrainingStats, validated, ValidationStats

Constructor Summary

Constructors

Constructor and Description
CumulantExpansionClassifier()

Method Summary

Modifier and Type	Method and Description
void	defineKnownCompounds(java.lang.String filename) Define compositions of all known compounds.
java.lang.String	printCommand(java.util.List<java.lang.String> Command) Handles more complicated printing commands.
protected java.lang.String	printModel_protected() Internal method that handles printing the model as a string.
java.util.List<java.lang.String>	printModelDescriptionDetails(boolean htmlFormat) Print details of the model.
java.lang.String	printUsage() Print out required format for options.
void	run_protected(Dataset TrainData) Run a model without checking if stuff is trained (use carefully)
java.lang.String	saveCommand(java.lang.String Basename, java.lang.String Command) Handles complicated saving commands.
void	setNBins(int[] NBins) Define number of desired bins of common compositions.
void	setNComponents(int n) Set the number of components in the material being considered.
void	setOptions(java.util.List<java.lang.Object> Options) Set any options for this object.
void	setPhaseDiagramStats(PhaseDiagramStatistics PhaseDiagramStats) Define the phase diagram statistics object used to make predictions.
protected void	train_protected(Dataset TrainData) Train a model without evaluating performance

Methods inherited from class magpie.models.classification.BaseClassifier

clone, getClassNames, getNClasses, run, train

Methods inherited from class magpie.models.BaseModel

about, crossValidate, crossValidate, crossValidate, done, externallyValidate, getAttributeSelector, getCitations, getFilter, getTrainTime, getValidationMethod, handleSetCommand, isTrained, isValidated, loadState, printDescription, printModel, resetModel, runCommand, saveState, setAttributeSelector, setComponent, setFilter, train

Methods inherited from class java.lang.Object

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

Constructor Detail

CumulantExpansionClassifier

public CumulantExpansionClassifier()

Method Detail

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.

Specified by:

setOptions in interface Options

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: ".

Specified by:

printUsage in interface Options

Returns:

Usage for this function

defineKnownCompounds

public void defineKnownCompounds(java.lang.String filename)

Define compositions of all known compounds. This data forms the basis of all inferences made by this model

Parameters:

filename - Path to file containing known compounds

setNBins

public void setNBins(int[] NBins)

Define number of desired bins of common compositions. Default is 30 bins of binary compositions, 100

Parameters:

NBins - Number of compositions to store for each number of compounds. x[0] is for binaries, x[1] is for ternaries, ...

setNComponents

public void setNComponents(int n)

Set the number of components in the material being considered.

Parameters:

n - Number of elements

setPhaseDiagramStats

public void setPhaseDiagramStats(PhaseDiagramStatistics PhaseDiagramStats)

Define the phase diagram statistics object used to make predictions.

NOTE: Also sets NComponents.

Parameters:

PhaseDiagramStats -

printModel_protected

protected java.lang.String printModel_protected()

Description copied from class: BaseModel

Internal method that handles printing the model as a string. Should end with a "\n"

Specified by:

printModel_protected in class BaseModel

Returns:

String representation of model

train_protected

protected void train_protected(Dataset TrainData)

Description copied from class: BaseModel

Train a model without evaluating performance

Specified by:

train_protected in class BaseModel

Parameters:

TrainData - Training data

run_protected

public void run_protected(Dataset TrainData)

Description copied from class: BaseModel

Run a model without checking if stuff is trained (use carefully)

Specified by:

run_protected in class BaseModel

Parameters:

TrainData - Training data

printCommand

public java.lang.String printCommand(java.util.List<java.lang.String> Command)
                              throws java.lang.Exception

Description copied from interface: Printable

Handles more complicated printing commands.

Specified by:

printCommand in interface Printable

Overrides:

printCommand in class BaseModel

Parameters:

Command - Command specifying what to print

Returns:

String formatted as requested

Throws:

java.lang.Exception - If command not understood

saveCommand

public java.lang.String saveCommand(java.lang.String Basename,
                                    java.lang.String Command)
                             throws java.lang.Exception

Description copied from interface: Savable

Handles complicated saving commands.

Dev Note: Make sure to add save format to Javadoc. See Dataset as an example. Required format:

<save><p><b>format<b> - Description
<br>Optional room to talk more about format </save>

Specified by:

saveCommand in interface Savable

Overrides:

saveCommand in class BaseModel

Parameters:

Basename - Name of file without extension

Command - Command specifying format in which to print

Returns:

Filename Path to output file

Throws:

java.lang.Exception - If command not understood

printModelDescriptionDetails

public java.util.List<java.lang.String> printModelDescriptionDetails(boolean htmlFormat)

Description copied from class: BaseModel

Print details of the model. Used by BaseModel.printDescription(boolean).

Implementation note: No not add indentation for details. That is handled by BaseModel.printDescription(boolean). You should also call the super operation to get the Normalizer and Attribute selector settings

Overrides:

printModelDescriptionDetails in class BaseModel

Parameters:

htmlFormat - Whether to use HTML format

Returns:

List describing model details. Each entry is a different line of the description (i.e., in place of newline characters).