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view ch5ex6.py @ 32:a13c00c0dfe5
Chapter 5, exercise 6, #1: Barab?si and Albert.
author | Brian Neal <bgneal@gmail.com> |
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date | Wed, 09 Jan 2013 20:09:19 -0600 |
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children | 66a5e7f7c10f |
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# -*- coding: utf-8 -*- """Chapter 5.5, exercise 6 in Allen Downey's Think Complexity book. 1. Read Barabási and Albert’s paper and implement their algorithm for generating graphs. See if you can replicate their Figure 2(A), which shows P(k) versus k for a graph with 150 000 vertices. """ import collections import random import sys from matplotlib import pyplot from Graph import Graph, Vertex, Edge class BAGraph(Graph): """BAGraph implements the algorithm described in the Barabási and Albert paper "Emergence of Scaling in Random Networks" from Science Magazine Vol. 286, 15 October 1999. """ def __init__(self, m0, m): """Create a graph with m0 vertices and m connecting edges. """ self.m0 = m0 self.m = m self.histogram = [] initial_vertices = [Vertex() for i in xrange(m0)] super(BAGraph, self).__init__(vs=initial_vertices) # Add initial edges between nodes randomly n = 0 while n != m: # pick two vertices at random v = random.choice(initial_vertices) w = random.choice(initial_vertices) # if they aren't the same and don't already have an edge, add one if v is not w and not self.get_edge(v, w): self.add_edge(Edge(v, w)) n += 1 def add_edge(self, edge): """Our version of add_edge() adds the two vertices on either end of the edge to a histogram. This allows us to more easily pick popular vertices when adding edges as part of the step() method. """ super(BAGraph, self).add_edge(edge) # invoke base class version v, w = edge self.histogram.append(v) self.histogram.append(w) def step(self): """This method adds a new vertex to the graph, then adds m edges that link the new vertex to m different vertices already present in the graph. Preferential treatment is given towards vertices that already have high connectivity. The paper describes this preferential choosing as creating a probability P that a new vertex will be connected to vertex i depends on the connectivity ki of that vertex, so that P(ki) = ki / sum(kj). We implement that by keeping a list of vertices (histogram), where we insert a vertex into this list whenever it gets an edge added to it. We then randomly choose a vertex from this list. Thus the vertices with more edges will be more likely chosen. """ # pick m unique vertices to attach to the new vertex vs = set() while len(vs) < self.m: w = random.choice(self.histogram) if w not in vs: vs.add(w) # Add the new vertex to the graph and create edges v = Vertex() self.add_vertex(v) for w in vs: self.add_edge(Edge(v, w)) def get_p(self): """This method returns a dictionary of probabilities where each key is the connectivity k and the value is the probability [0-1] for this graph. """ # First, for each vertex, count up how many neighbors it has vs = self.vertices() c = collections.Counter() for v in vs: n = len(self.out_vertices(v)) c[n] += 1 n = len(vs) if n > 0: for k in c: c[k] = float(c[k]) / n return c def main(script, m0, m, n): # create a BAGraph with parameters m0 & m: m0, m, n = int(m0), int(m), int(n) g = BAGraph(m0, m) # step the graph n times: for i in xrange(n): g.step() # retrieve probabilities p = g.get_p() # plot P(k) versus k on a log-log scale vals = p.items() vals.sort(key=lambda t: t[0]) x, y = zip(*vals) pyplot.clf() pyplot.xscale('log') pyplot.yscale('log') pyplot.title('P(k) versus k') pyplot.xlabel('k') pyplot.ylabel('P(k)') pyplot.plot(x, y, label='P(k) vs. k', color='green', linewidth=3) pyplot.legend(loc='upper right') pyplot.show() if __name__ == '__main__': main(*sys.argv)