OntologyMeasures (GATE Core 9.1-SNAPSHOT API)

java.lang.Object
- gate.util.OntologyMeasures

```
public class OntologyMeasures
extends Object
```
Modified version of Precision and Recall called BDM that takes into account the distance of two concepts in an ontology.

Field Summary

Fields
Modifier and Type	Field and Description
`protected Map<String,Float>`	`bdmByConceptsMap`
`protected Map<String,Float>`	`bdmByTypeMap`
`protected URL`	`bdmFileUrl`
`protected Map<String,AnnotationDiffer>`	`differByTypeMap`

Constructor Summary

Constructors
Constructor and Description
`OntologyMeasures()`
`OntologyMeasures(Collection<OntologyMeasures> measures)` Constructor to be used when you have a collection of OntologyMeasures and want to consider it as only one OntologyMeasures.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`calculateBdm(Collection<AnnotationDiffer> differs)` For a document get the annotation differs that contain the type to compare and the annotation differs that may have miscategorized annotations for this type.
`Map<String,AnnotationDiffer>`	`getDifferByTypeMap()` Be careful, don't modify it.
`double`	`getFMeasureAverageBdm(double beta)` Gets the average of strict and lenient F-Measure values.
`double`	`getFMeasureAverageBdm(String type, double beta)`
`double`	`getFMeasureLenientBdm(double beta)`
`double`	`getFMeasureLenientBdm(String type, double beta)`
`double`	`getFMeasureStrictBdm(double beta)`
`double`	`getFMeasureStrictBdm(String type, double beta)`
`List<String>`	`getMeasuresRow(Object[] measures, String title)`
`double`	`getPrecisionAverageBdm()` Gets the average of the strict and lenient precision values.
`double`	`getPrecisionAverageBdm(String type)`
`double`	`getPrecisionLenientBdm()`
`double`	`getPrecisionLenientBdm(String type)`
`double`	`getPrecisionStrictBdm()`
`double`	`getPrecisionStrictBdm(String type)` AP = (sum of BDMs for BDM-matching pair spurious/missing + Correct) / (Correct + Spurious)
`double`	`getRecallAverageBdm()` Gets the average of the strict and lenient recall values.
`double`	`getRecallAverageBdm(String type)`
`double`	`getRecallLenientBdm()`
`double`	`getRecallLenientBdm(String type)`
`double`	`getRecallStrictBdm()`
`double`	`getRecallStrictBdm(String type)`
`Map<String,Float>`	`read(URL bdmFile)` Read the BDM scores from a file.
`void`	`setBdmFile(URL url)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - bdmByTypeMap
```
protected Map<String,Float> bdmByTypeMap
```
  - bdmFileUrl
```
protected URL bdmFileUrl
```
  - differByTypeMap
```
protected Map<String,AnnotationDiffer> differByTypeMap
```
  - bdmByConceptsMap
```
protected Map<String,Float> bdmByConceptsMap
```
- Constructor Detail
  - OntologyMeasures
```
public OntologyMeasures()
```
  - OntologyMeasures
```
public OntologyMeasures(Collection<OntologyMeasures> measures)
```
    Constructor to be used when you have a collection of OntologyMeasures and want to consider it as only one OntologyMeasures. Then you can only use the methods getPrecision/Recall/FMeasure...().
    
    Parameters:
    
    measures - collection to be regrouped in one OntologyMeasures
- Method Detail
  - calculateBdm
```
public void calculateBdm(Collection<AnnotationDiffer> differs)
```
    For a document get the annotation differs that contain the type to compare and the annotation differs that may have miscategorized annotations for this type. Then we try to find miscategorized types that are close enough from the main type and use their BDM value to get an augmented precision, recall and fscore.
    
    Parameters:
    
    differs - annotation differ for the type and for possible miscategorized types.
  - getPrecisionStrictBdm
```
public double getPrecisionStrictBdm(String type)
```
    AP = (sum of BDMs for BDM-matching pair spurious/missing + Correct) / (Correct + Spurious)
    
    Parameters:
    
    type - annotation type
    
    Returns:
    
    strict precision with BDM correction
  - getPrecisionStrictBdm
```
public double getPrecisionStrictBdm()
```
  - getRecallStrictBdm
```
public double getRecallStrictBdm(String type)
```
  - getRecallStrictBdm
```
public double getRecallStrictBdm()
```
  - getFMeasureStrictBdm
```
public double getFMeasureStrictBdm(String type,
                                   double beta)
```
  - getFMeasureStrictBdm
```
public double getFMeasureStrictBdm(double beta)
```
  - getPrecisionLenientBdm
```
public double getPrecisionLenientBdm(String type)
```
  - getPrecisionLenientBdm
```
public double getPrecisionLenientBdm()
```
  - getRecallLenientBdm
```
public double getRecallLenientBdm(String type)
```
  - getRecallLenientBdm
```
public double getRecallLenientBdm()
```
  - getFMeasureLenientBdm
```
public double getFMeasureLenientBdm(String type,
                                    double beta)
```
  - getFMeasureLenientBdm
```
public double getFMeasureLenientBdm(double beta)
```
  - getPrecisionAverageBdm
```
public double getPrecisionAverageBdm(String type)
```
  - getPrecisionAverageBdm
```
public double getPrecisionAverageBdm()
```
    Gets the average of the strict and lenient precision values.
    
    Returns:
    
    a double value.
  - getRecallAverageBdm
```
public double getRecallAverageBdm(String type)
```
  - getRecallAverageBdm
```
public double getRecallAverageBdm()
```
    Gets the average of the strict and lenient recall values.
    
    Returns:
    
    a double value.
  - getFMeasureAverageBdm
```
public double getFMeasureAverageBdm(String type,
                                    double beta)
```
  - getFMeasureAverageBdm
```
public double getFMeasureAverageBdm(double beta)
```
    Gets the average of strict and lenient F-Measure values.
    
    Parameters:
    
    beta - The relative weight of precision and recall. A value of 1 gives equal weights to precision and recall. A value of 0 takes the recall value completely out of the equation.
    
    Returns:
    
    a doublevalue.
  - setBdmFile
```
public void setBdmFile(URL url)
```
  - read
```
public Map<String,Float> read(URL bdmFile)
```
    Read the BDM scores from a file.
    
    Parameters:
    
    bdmFile - URL of the BDM file
    
    Returns:
    
    map from a pair of concepts to their BDM score
  - getMeasuresRow
```
public List<String> getMeasuresRow(Object[] measures,
                                   String title)
```
  - getDifferByTypeMap
```
public Map<String,AnnotationDiffer> getDifferByTypeMap()
```
    Be careful, don't modify it. That's not a copy because it would take too much memory.
    
    Returns:
    
    differ by type map

Class OntologyMeasures

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

bdmByTypeMap

bdmFileUrl

differByTypeMap

bdmByConceptsMap

Constructor Detail

OntologyMeasures

OntologyMeasures

Method Detail

calculateBdm

getPrecisionStrictBdm

getPrecisionStrictBdm

getRecallStrictBdm

getRecallStrictBdm

getFMeasureStrictBdm

getFMeasureStrictBdm

getPrecisionLenientBdm

getPrecisionLenientBdm

getRecallLenientBdm

getRecallLenientBdm

getFMeasureLenientBdm

getFMeasureLenientBdm

getPrecisionAverageBdm

getPrecisionAverageBdm

getRecallAverageBdm

getRecallAverageBdm

getFMeasureAverageBdm

getFMeasureAverageBdm

setBdmFile

read

getMeasuresRow

getDifferByTypeMap