info.debatty.java.graphs

Class Graph<T>

java.lang.Object

info.debatty.java.graphs.Graph<T>

Type Parameters:

T - The type of nodes value

All Implemented Interfaces:

GraphInterface<T>

public class Graph<T>
extends Object
implements GraphInterface<T>

k-nn graph, represented as a mapping node => neighborlist

Author:

Thibault Debatty

Field Summary

Fields

Modifier and Type	Field and Description
protected int	k
protected HashMap<Node<T>,NeighborList>	map
protected SimilarityInterface<T>	similarity

Constructor Summary

Constructors

Constructor and Description
Graph()
Graph(int k)

Method Summary

Methods

Modifier and Type	Method and Description
ArrayList<Graph<T>>	connectedComponents() Split the graph in connected components (usually you will first prune the graph to remove "weak" edges).
boolean	containsKey(Node node)
Iterable<Map.Entry<Node<T>,NeighborList>>	entrySet()
NeighborList	get(Node node) Get the neighborlist of this node
int	getK()
Iterable<Node<T>>	getNodes()
SimilarityInterface<T>	getSimilarity()
void	prune(double threshold) Remove from the graph all edges with a similarity lower than threshold
NeighborList	put(Node<T> node, NeighborList neighborlist)
NeighborList	search(T query, int K)
NeighborList	search(T query, int K, double speedup) Improved implementation of Graph Nearest Neighbor Search (GNNS) algorithm from paper "Fast Approximate Nearest-Neighbor Search with k-Nearest Neighbor Graph" by Hajebi et al.
NeighborList	search(T query, int K, double speedup, double expansion) Improved implementation of Graph Nearest Neighbor Search (GNNS) algorithm from paper "Fast Approximate Nearest-Neighbor Search with k-Nearest Neighbor Graph" by Hajebi et al.
NeighborList	searchExhaustive(T query, int K)
void	setK(int k)
void	setSimilarity(SimilarityInterface<T> similarity)
int	size()
ArrayList<Graph<T>>	stronglyConnectedComponents() Computes the strongly connected sub-graphs (where every node is reachable from every other node) using Tarjan's algorithm, which has computation cost O(n).
void	writeGEXF(String filename) Writes the graph as a GEXF file (to be used in Gephi, for example)

Methods inherited from class java.lang.Object

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

Field Detail

map

protected HashMap<Node<T>,NeighborList> map

similarity

protected SimilarityInterface<T> similarity

k

protected int k

Constructor Detail

Graph

public Graph(int k)

Graph

public Graph()

Method Detail

getSimilarity

public SimilarityInterface<T> getSimilarity()

Specified by:

getSimilarity in interface GraphInterface<T>

setSimilarity

public void setSimilarity(SimilarityInterface<T> similarity)

Specified by:

setSimilarity in interface GraphInterface<T>

getK

public int getK()

Specified by:

getK in interface GraphInterface<T>

setK

public void setK(int k)

Specified by:

setK in interface GraphInterface<T>

get

public NeighborList get(Node node)

Get the neighborlist of this node

Specified by:

get in interface GraphInterface<T>

Parameters:

node -

Returns:

the neighborlist of this node

prune

public void prune(double threshold)

Remove from the graph all edges with a similarity lower than threshold

Specified by:

prune in interface GraphInterface<T>

Parameters:

threshold -

connectedComponents

public ArrayList<Graph<T>> connectedComponents()

Split the graph in connected components (usually you will first prune the graph to remove "weak" edges).

Specified by:

connectedComponents in interface GraphInterface<T>

Returns:

stronglyConnectedComponents

public ArrayList<Graph<T>> stronglyConnectedComponents()

Computes the strongly connected sub-graphs (where every node is reachable from every other node) using Tarjan's algorithm, which has computation cost O(n).

Specified by:

stronglyConnectedComponents in interface GraphInterface<T>

Returns:

put

public NeighborList put(Node<T> node,
               NeighborList neighborlist)

Specified by:

put in interface GraphInterface<T>

containsKey

public boolean containsKey(Node node)

Specified by:

containsKey in interface GraphInterface<T>

size

public int size()

Specified by:

size in interface GraphInterface<T>

entrySet

public Iterable<Map.Entry<Node<T>,NeighborList>> entrySet()

Specified by:

entrySet in interface GraphInterface<T>

getNodes

public Iterable<Node<T>> getNodes()

Specified by:

getNodes in interface GraphInterface<T>

searchExhaustive

public NeighborList searchExhaustive(T query,
                            int K)
                              throws InterruptedException,
                                     ExecutionException

Specified by:

searchExhaustive in interface GraphInterface<T>

Parameters:

query -

K -

Returns:

Throws:

InterruptedException

ExecutionException

search

public NeighborList search(T query,
                  int K)

Specified by:

search in interface GraphInterface<T>

Returns:

search

public NeighborList search(T query,
                  int K,
                  double speedup)

Improved implementation of Graph Nearest Neighbor Search (GNNS) algorithm from paper "Fast Approximate Nearest-Neighbor Search with k-Nearest Neighbor Graph" by Hajebi et al.

Specified by:

search in interface GraphInterface<T>

Parameters:

query -

K - search K neighbors

speedup - (default: 4)

Returns:

search

public NeighborList search(T query,
                  int K,
                  double speedup,
                  double expansion)

Improved implementation of Graph Nearest Neighbor Search (GNNS) algorithm from paper "Fast Approximate Nearest-Neighbor Search with k-Nearest Neighbor Graph" by Hajebi et al. The algorithm is basically a best-first search method with random starting points.

Specified by:

search in interface GraphInterface<T>

Parameters:

query - query point

K - number of neighbors to find (the K from K-nn search)

expansion - (default: 1.01)

Returns:

writeGEXF

public void writeGEXF(String filename)
               throws FileNotFoundException,
                      IOException

Writes the graph as a GEXF file (to be used in Gephi, for example)

Specified by:

writeGEXF in interface GraphInterface<T>

Parameters:

filename -

Throws:

FileNotFoundException

IOException