NetworkX

Source code for networkx.algorithms.core

"""
Find the k-cores of a graph.

The k-core is found by recursively pruning nodes with degrees less than k. 

See the following reference for details:

An O(m) Algorithm for Cores Decomposition of Networks
Vladimir Batagelj and Matjaz Zaversnik, 2003.
http://arxiv.org/abs/cs.DS/0310049 

"""
__author__ = "\n".join(['Dan Schult (dschult@colgate.edu)',
                        'Jason Grout (jason-sage@creativetrax.com)',
                        'Aric Hagberg (hagberg@lanl.gov)'])

#    Copyright (C) 2004-2010 by 
#    Aric Hagberg <hagberg@lanl.gov>
#    Dan Schult <dschult@colgate.edu>
#    Pieter Swart <swart@lanl.gov>
#    All rights reserved.
#    BSD license.
__all__ = ['core_number','k_core','k_shell','k_crust','k_corona','find_cores']

import networkx as nx

[docs]def core_number(G): """Return the core number for each vertex. A k-core is a maximal subgraph that contains nodes of degree k or more. The core number of a node is the largest value k of a k-core containing that node. Parameters ---------- G : NetworkX graph A graph or directed graph Returns ------- core_number : dictionary A dictionary keyed by node to the core number. Raises ------ NetworkXError The k-core is not defined for graphs with self loops or parallel edges. Notes ----- Not implemented for graphs with parallel edges or self loops. For directed graphs the node degree is defined to be the in-degree + out-degree. References ---------- .. [1] An O(m) Algorithm for Cores Decomposition of Networks Vladimir Batagelj and Matjaz Zaversnik, 2003. http://arxiv.org/abs/cs.DS/0310049 """ if G.is_multigraph(): raise nx.NetworkXError( 'MultiGraph and MultiDiGraph types not supported.') if G.number_of_selfloops()>0: raise nx.NetworkXError( 'Input graph has self loops; the core number is not defined.', 'Consider using G.remove_edges_from(G.selfloop_edges()).') if G.is_directed(): import itertools def neighbors(v): return itertools.chain.from_iterable([G.predecessors_iter(v), G.successors_iter(v)]) else: neighbors=G.neighbors_iter degrees=G.degree() # sort nodes by degree nodes=sorted(degrees,key=degrees.get) bin_boundaries=[0] curr_degree=0 for i,v in enumerate(nodes): if degrees[v]>curr_degree: bin_boundaries.extend([i]*(degrees[v]-curr_degree)) curr_degree=degrees[v] node_pos = dict((v,pos) for pos,v in enumerate(nodes)) # initial guesses for core is degree core=degrees nbrs=dict((v,set(neighbors(v))) for v in G) for v in nodes: for u in nbrs[v]: if core[u] > core[v]: nbrs[u].remove(v) pos=node_pos[u] bin_start=bin_boundaries[core[u]] node_pos[u]=bin_start node_pos[nodes[bin_start]]=pos nodes[bin_start],nodes[pos]=nodes[pos],nodes[bin_start] bin_boundaries[core[u]]+=1 core[u]-=1 return core
find_cores=core_number
[docs]def k_core(G,k=None,core_number=None): """Return the k-core of G. A k-core is a maximal subgraph that contains nodes of degree k or more. Parameters ---------- G : NetworkX graph A graph or directed graph k : int, optional The order of the core. If not specified return the main core. core_number : dictionary, optional Precomputed core numbers for the graph G. Returns ------- G : NetworkX graph The k-core subgraph Raises ------ NetworkXError The k-core is not defined for graphs with self loops or parallel edges. Notes ----- The main core is the core with the largest degree. Not implemented for graphs with parallel edges or self loops. For directed graphs the node degree is defined to be the in-degree + out-degree. Graph, node, and edge attributes are copied to the subgraph. See Also -------- core_number References ---------- .. [1] An O(m) Algorithm for Cores Decomposition of Networks Vladimir Batagelj and Matjaz Zaversnik, 2003. http://arxiv.org/abs/cs.DS/0310049 """ if core_number is None: core_number=nx.core_number(G) if k is None: k=max(core_number.values()) # max core nodes=(n for n in core_number if core_number[n]>=k) return G.subgraph(nodes).copy()
[docs]def k_shell(G,k=None,core_number=None): """Return the k-shell of G. The k-shell is the subgraph of nodes in the k-core containing nodes of exactly degree k. Parameters ---------- G : NetworkX graph A graph or directed graph. k : int, optional The order of the shell. If not specified return the main shell. core_number : dictionary, optional Precomputed core numbers for the graph G. Returns ------- G : NetworkX graph The k-shell subgraph Raises ------ NetworkXError The k-shell is not defined for graphs with self loops or parallel edges. Notes ----- Not implemented for graphs with parallel edges or self loops. For directed graphs the node degree is defined to be the in-degree + out-degree. Graph, node, and edge attributes are copied to the subgraph. See Also -------- core_number References ---------- .. [1] A model of Internet topology using k-shell decomposition Shai Carmi, Shlomo Havlin, Scott Kirkpatrick, Yuval Shavitt, and Eran Shir, PNAS July 3, 2007 vol. 104 no. 27 11150-11154 http://www.pnas.org/content/104/27/11150.full """ if core_number is None: core_number=nx.core_number(G) if k is None: k=max(core_number.values()) # max core nodes=(n for n in core_number if core_number[n]==k) return G.subgraph(nodes).copy()
[docs]def k_crust(G,k=None,core_number=None): """Return the k-crust of G. The k-crust is the graph G with the k-core removed. Parameters ---------- G : NetworkX graph A graph or directed graph. k : int, optional The order of the shell. If not specified return the main crust. core_number : dictionary, optional Precomputed core numbers for the graph G. Returns ------- G : NetworkX graph The k-crust subgraph Raises ------ NetworkXError The k-crust is not defined for graphs with self loops or parallel edges. Notes ----- This definition of k-crust is different than the definition in [1]_. The k-crust in [1]_ is equivalent to the k+1 crust of this algorithm. Not implemented for graphs with parallel edges or self loops. For directed graphs the node degree is defined to be the in-degree + out-degree. Graph, node, and edge attributes are copied to the subgraph. See Also -------- core_number References ---------- .. [1] A model of Internet topology using k-shell decomposition Shai Carmi, Shlomo Havlin, Scott Kirkpatrick, Yuval Shavitt, and Eran Shir, PNAS July 3, 2007 vol. 104 no. 27 11150-11154 http://www.pnas.org/content/104/27/11150.full """ if core_number is None: core_number=nx.core_number(G) if k is None: k=max(core_number.values())-1 nodes=(n for n in core_number if core_number[n]<=k) return G.subgraph(nodes).copy()
[docs]def k_corona(G, k, core_number=None): """Return the k-crust of G. The k-corona is the subset of vertices in the k-core which have exactly k neighbours in the k-core. Parameters ---------- G : NetworkX graph A graph or directed graph k : int The order of the corona. core_number : dictionary, optional Precomputed core numbers for the graph G. Returns ------- G : NetworkX graph The k-corona subgraph Raises ------ NetworkXError The k-cornoa is not defined for graphs with self loops or parallel edges. Notes ----- Not implemented for graphs with parallel edges or self loops. For directed graphs the node degree is defined to be the in-degree + out-degree. Graph, node, and edge attributes are copied to the subgraph. See Also -------- core_number References ---------- .. [1] k -core (bootstrap) percolation on complex networks: Critical phenomena and nonlocal effects, A. V. Goltsev, S. N. Dorogovtsev, and J. F. F. Mendes, Phys. Rev. E 73, 056101 (2006) http://link.aps.org/doi/10.1103/PhysRevE.73.056101 """ if core_number is None: core_number = nx.core_number(G) nodes = (n for n in core_number if core_number[n] >= k and len([v for v in G[n] if core_number[v] >= k]) == k) return G.subgraph(nodes).copy()