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java.lang.Objectnct.score.LogLikelihoodScoreModel<NodeType>
public class LogLikelihoodScoreModel<NodeType extends java.lang.Comparable<? super NodeType>>
This class implements the log likelihood edge scoring scheme described in the supplemental to Sharan, et al., 2005, Conserved patterns of protein interaction in multiple species, PNAS, 102(6). As well as: Sharan, et al., "Identification of Protein Complexes by Comparative Analysis of Yeast and Bacterial Protein Interaction Data", JOURNAL OF COMPUTATIONAL BIOLOGY, Volume 12, Number 6, 2005.
Constructor Summary | |
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LogLikelihoodScoreModel(double truthFactor,
double model,
double backgroundProbability)
Sets the truthFactor accordingly (ensures > 0) and initializes the graphMap object. |
Method Summary | |
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double |
scoreEdge(NodeType srcNode,
NodeType destNode,
Graph<NodeType,java.lang.Double> graph)
For the two nodes from the specified graph graph, return the log likelihood score between the complex model and the null model. |
double |
scoreGraph(Graph<NodeType,java.lang.Double> g)
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double |
scoreNode(NodeType node,
Graph<NodeType,java.lang.Double> g)
Given a node from graph, this function will return the score of the node. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public LogLikelihoodScoreModel(double truthFactor, double model, double backgroundProbability)
truthFactor
- factor used to consider the background truth distributionmodel
- Truth for the model (assumed between 0 and 1)Method Detail |
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public double scoreEdge(NodeType srcNode, NodeType destNode, Graph<NodeType,java.lang.Double> graph)
scoreEdge
in interface ScoreModel<NodeType extends java.lang.Comparable<? super NodeType>,java.lang.Double>
srcNode
- node bewteen which it and destNode generates a scoredestNode
- node between which it and srcNode generates a scoregraph
- graph containing both srcNode and destNode
public double scoreNode(NodeType node, Graph<NodeType,java.lang.Double> g)
ScoreModel
scoreNode
in interface ScoreModel<NodeType extends java.lang.Comparable<? super NodeType>,java.lang.Double>
node
- Node to score.g
- The graph that contains the node to score.
public double scoreGraph(Graph<NodeType,java.lang.Double> g)
scoreGraph
in interface ScoreModel<NodeType extends java.lang.Comparable<? super NodeType>,java.lang.Double>
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