magpie.csp

Class DMSPEngine

java.lang.Object

magpie.csp.CSPEngine

magpie.csp.DMSPEngine

All Implemented Interfaces:

Commandable, Options, Printable

public class DMSPEngine
extends CSPEngine

Data-Mining Structure Predictor (DMSP) from Fisher et al.

Usage: *No options*

Method: Uses strategy described in PhaseDiagramStatistics to calculate probabilities of each prototype appearing at a certain composition. Using the notation from the that documentation, the goal is to calculate:

P(C_j = y | C₁ = a₁ ∩ ... ∩ C_j-1 = a_j-1 ∩ C_j+1 = a_j+1 ∩ ... ∩ E_N = Z_N)

Field Summary

Fields inherited from class magpie.csp.CSPEngine

DiagramStatistics, KnownCompounds, LastCompositionBin, LastNComponents, PerformanceStats

Constructor Summary

Constructors

Constructor and Description
DMSPEngine()

Method Summary

Modifier and Type	Method and Description
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.
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, getProbabilities, getTrainingSet, importKnownCompounds, makeSiteInfo, predictStructure, predictStructure, printCommand, printDescription, removeKnownCompoundsContainingElements, runCommand, setKnownCompounds

Methods inherited from class java.lang.Object

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

Constructor Detail

DMSPEngine

public DMSPEngine()

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

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