magpie.csp

Class CompositionBasedCSPEngine

java.lang.Object

magpie.csp.CSPEngine

magpie.csp.CompositionBasedCSPEngine

All Implemented Interfaces:

Commandable, Options, Printable

public class CompositionBasedCSPEngine
extends CSPEngine

Use machine learning model trained on the composition of the entries. Usage: $<model template>
model template: Template of a BaseClassifier used to predict which structure is most likely

Implemented Commands:

attributes [<command...>] - Configure how attributes are generated
command: Attribute command from PrototypeDataset

Field Summary

Fields inherited from class magpie.csp.CSPEngine

DiagramStatistics, KnownCompounds, LastCompositionBin, LastNComponents, PerformanceStats

Constructor Summary

Constructors

Constructor and Description
CompositionBasedCSPEngine()

Method Summary

Modifier and Type	Method and Description
protected double[]	getProbabilities(BaseClassifier classifier, java.util.List<java.lang.String> knownPrototypes, PrototypeSiteInformation siteInfo, PrototypeEntry entryToPredict) Calculate probability that a compound will form as each of the known prototypes.
protected BaseClassifier	makeClassifier(PhaseDiagramStatistics statistics, PrototypeDataset trainData) Given the dataset of training examples, make a classifier to predict the probability that a prototype will form at a certain composition.
java.lang.String	printUsage() Print out required format for options.
java.lang.Object	runCommand(java.util.List<java.lang.Object> Command) Process some command described by a list of Objects.
void	setClassifierTempate(BaseClassifier ClfrTempate) Define a template for the classifier used by this class
void	setOptions(java.util.List<java.lang.Object> Options) Set any options for this object.

Methods inherited from class magpie.csp.CSPEngine

about, crossvalidate, fillPrototypeEntry, getComponent, getPossibleStructures, getPossibleStructures, getTrainingSet, importKnownCompounds, makeSiteInfo, predictStructure, predictStructure, printCommand, printDescription, removeKnownCompoundsContainingElements, setKnownCompounds

Methods inherited from class java.lang.Object

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

Constructor Detail

CompositionBasedCSPEngine

public CompositionBasedCSPEngine()

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.

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

setClassifierTempate

public void setClassifierTempate(BaseClassifier ClfrTempate)

Define a template for the classifier used by this class

Parameters:

ClfrTempate -

makeClassifier

protected BaseClassifier makeClassifier(PhaseDiagramStatistics statistics,
                                        PrototypeDataset trainData)

Description copied from class: CSPEngine

Given the dataset of training examples, make a classifier to predict the probability that a prototype will form at a certain composition.

Specified by:

makeClassifier in class CSPEngine

Parameters:

statistics - Statistics about all known phase diagrams (could be used predictively)

trainData - Training data, where each entry maps

Returns:

Classifier fitting the specifications above

getProbabilities

protected double[] getProbabilities(BaseClassifier classifier,
                                    java.util.List<java.lang.String> knownPrototypes,
                                    PrototypeSiteInformation siteInfo,
                                    PrototypeEntry entryToPredict)

Description copied from class: CSPEngine

Calculate probability that a compound will form as each of the known prototypes.

Overrides:

getProbabilities in class CSPEngine

Parameters:

classifier - Model trained to predict which prototype will form, given composition.

knownPrototypes - List of known prototypes

siteInfo - Information about the prototypes

entryToPredict - Entry to predict

Returns:

List of probabilities (that add to 1) in same order as knownPrototypes

runCommand

public java.lang.Object runCommand(java.util.List<java.lang.Object> Command)
                            throws java.lang.Exception

Description copied from interface: Commandable

Process some command described by a list of Objects.

Specified by:

runCommand in interface Commandable

Overrides:

runCommand in class CSPEngine

Parameters:

Command - Command as a list of objects

Returns:

Any output (null if no output generated by command)

Throws:

java.lang.Exception - If something goes wrong