evaluation.comparison
Class BroheeSimilarity

java.lang.Object
  extended by evaluation.comparison.BroheeSimilarity

public class BroheeSimilarity
extends Object

Contains similarity comparison results of two complex sets after

Brohée, S. & van Helden, J.
Evaluation of clustering algorithms for protein-protein interaction networks.
BMC Bioinformatics, 2006, 7, 488
Pubmed: 17087821

This measure is assymetrical and provides a similarity measure of a given candidate complex set with respect to a reference complex set.

The sensitivity describes how much of the reference complex sets are also contained in the candidate complex set, where as the positive predictive value (PPV) is a measure how much of the prediction in the candidate set is correct. The accuracy is then the geometric mean of sensitivity and PPV.

All three measures range between a minimum value of 0.0 and a maximum value of 1.0. Note that for complex sets where proteins occur in multiple complexes it might not be possible for the PPV to reach the maximum of 1.0.

This class is not instantiatable from outside of the package.

Author:
Jan Krumsiek

Constructor Summary
BroheeSimilarity(float sens, float PPV)
          Creates a new similarity object.
 
Method Summary
 float getAccuracy()
          Return the accuracy of the candidate set regarding the reference complex set.
 float getPPV()
          Returns the positive predictive value (PPV) of the candidate set regarding the reference complex set.
 float getSensitivity()
          Returns the sensitivity of the candidate complex set regarding the reference complex set.
 String toString()
          Returns a string representation of the comparison results
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

BroheeSimilarity

public BroheeSimilarity(float sens,
                        float PPV)
Creates a new similarity object. Accuracy is calculated as the geometric mean of sensitivity and PPV.

Parameters:
sens - sensitivity
PPV - positive predictive value
Method Detail

getSensitivity

public float getSensitivity()
Returns the sensitivity of the candidate complex set regarding the reference complex set.

Returns:
the sensitivity

getPPV

public float getPPV()
Returns the positive predictive value (PPV) of the candidate set regarding the reference complex set.

Returns:
the PPV

getAccuracy

public float getAccuracy()
Return the accuracy of the candidate set regarding the reference complex set. Accuracy is defined as the geometric mean of sensitivity and PPV.

Returns:
the accuracy

toString

public String toString()
Returns a string representation of the comparison results

Overrides:
toString in class Object