Biorithm  1.1
Public Member Functions | Protected Member Functions
Vanilla Class Reference

This class implements the Vanilla algorithm. More...

#include <reconciliation-algorithms.h>

Inheritance diagram for Vanilla:
AbstractSingleReconciliation

List of all members.

Public Member Functions

 Vanilla (MyGraph &graph, MyPointSet &weights, double q, double maxIters, double epsilon, string output)
 Vanilla (vector< MyGraph > &graphs, double q, double maxIters, double epsilon, string outputPrefix)
virtual ~Vanilla ()
 Destructor.
virtual string getName ()
 Return the name of the Vanilla algorithm.

Protected Member Functions

virtual void _updateNodeWeightA (MyNode node)
 Update the weight of a node in the current graph according to the Vanilla update function.
virtual pair< double, double > _computeEnergy ()
 Compute the node sum and edge sum from the Vanilla energy function.

Detailed Description

This class implements the Vanilla algorithm.


Constructor & Destructor Documentation

Vanilla::Vanilla ( MyGraph graph,
MyPointSet weights,
double  q,
double  maxIters,
double  epsilon,
string  output 
) [inline]

Constructor for running the algorithm on a single network with multiple initial weights samples.

Parameters:
[in]graphThe network on which to operate.
[in]weightsThe samples containing initial node weights.
[in]qThe parameter q used by the algorithm.
[in]maxItersThe maximum number of iterations to run the iterative reconciliation algorithms.
[in]epsilonA small value that defines part of the convergence criteria.
[in]outputPrefixA string to prepend to all output files.
Vanilla::Vanilla ( vector< MyGraph > &  graphs,
double  q,
double  maxIters,
double  epsilon,
string  outputPrefix 
) [inline]

Constructor for running the algorithm on multiple networks with no initial weights.

Parameters:
[in]graphsThe networks on which to operate.
[in]qThe parameter q used by the algorithm.
[in]maxItersThe maximum number of iterations to run the iterative reconciliation algorithms.
[in]epsilonA small value that defines part of the convergence criteria.
[in]outputPrefixA string to prepend to all output files.

Member Function Documentation

void Vanilla::_updateNodeWeightA ( MyNode  v) [protected, virtual]

Update the weight of a node in the current graph according to the Vanilla update function.

In order to compute the state of any node in the network, GeneMANIA solves the following equation where f_{i} is the node score for gene i, y_{i} is the inital bias vale for gene i, and w_{ij} is the association weight between genes i and j. $f=min({i}{}(f_{i}-y_{i})^{2}+{i}{}{j}{}w_{ij}(f_{i}-f_{j})^{2}) This equation reduces down to $f(u)={y(u)+ w_{u}f(u)}{1+ w_{v}f(v)}$ For more information about this formula, see the paper (cited in the class documentation).

Implements AbstractSingleReconciliation.


The documentation for this class was generated from the following files:
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