/** * Copyright (c) 2008, the JUNG Project and the Regents of the University * of California * All rights reserved. * * This software is open-source under the BSD license; see either * "license.txt" or * http://jung.sourceforge.net/license.txt for a description. * Created on Aug 22, 2008 * */ package edu.uci.ics.jung.algorithms.scoring; import org.apache.commons.collections15.Transformer; import edu.uci.ics.jung.algorithms.scoring.util.ScoringUtils; import edu.uci.ics.jung.graph.Hypergraph; /** * A special case of {@code PageRankWithPriors} in which the final scores * represent a probability distribution over position assuming a random (Markovian) * walk of exactly k steps, based on the initial distribution specified by the priors. * *

NOTE: The version of {@code KStepMarkov} in {@code algorithms.importance} * (and in JUNG 1.x) is believed to be incorrect: rather than returning * a score which represents a probability distribution over position assuming * a k-step random walk, it returns a score which represents the sum over all steps * of the probability for each step. If you want that behavior, set the * 'cumulative' flag as follows before calling {@code evaluate()}: *

 *     KStepMarkov ksm = new KStepMarkov(...);
 *     ksm.setCumulative(true);
 *     ksm.evaluate();
 * 
* * By default, the 'cumulative' flag is set to false. * * NOTE: THIS CLASS IS NOT YET COMPLETE. USE AT YOUR OWN RISK. (The original behavior * is captured by the version still available in {@code algorithms.importance}.) * * @see "Algorithms for Estimating Relative Importance in Graphs by Scott White and Padhraic Smyth, 2003" * @see PageRank * @see PageRankWithPriors */ public class KStepMarkov extends PageRankWithPriors { private boolean cumulative; /** * Creates an instance based on the specified graph, edge weights, vertex * priors (initial scores), and number of steps to take. * @param graph the input graph * @param edge_weights the edge weights (transition probabilities) * @param vertex_priors the initial probability distribution (score assignment) * @param steps the number of times that {@code step()} will be called by {@code evaluate} */ public KStepMarkov(Hypergraph graph, Transformer edge_weights, Transformer vertex_priors, int steps) { super(graph, edge_weights, vertex_priors, 0); initialize(steps); } /** * Creates an instance based on the specified graph, vertex * priors (initial scores), and number of steps to take. The edge * weights (transition probabilities) are set to default values (a uniform * distribution over all outgoing edges). * @param graph the input graph * @param vertex_priors the initial probability distribution (score assignment) * @param steps the number of times that {@code step()} will be called by {@code evaluate} */ public KStepMarkov(Hypergraph graph, Transformer vertex_priors, int steps) { super(graph, vertex_priors, 0); initialize(steps); } /** * Creates an instance based on the specified graph and number of steps to * take. The edge weights (transition probabilities) and vertex initial scores * (prior probabilities) are set to default values (a uniform * distribution over all outgoing edges, and a uniform distribution over * all vertices, respectively). * @param graph the input graph * @param steps the number of times that {@code step()} will be called by {@code evaluate} */ public KStepMarkov(Hypergraph graph, int steps) { super(graph, ScoringUtils.getUniformRootPrior(graph.getVertices()), 0); initialize(steps); } private void initialize(int steps) { this.acceptDisconnectedGraph(false); if (steps <= 0) throw new IllegalArgumentException("Number of steps must be > 0"); this.max_iterations = steps; this.tolerance = -1.0; this.cumulative = false; } /** * Specifies whether this instance should assign a score to each vertex * based on the * @param cumulative */ public void setCumulative(boolean cumulative) { this.cumulative = cumulative; } /** * Updates the value for this vertex. Called by step(). */ @Override public double update(V v) { if (!cumulative) return super.update(v); collectDisappearingPotential(v); double v_input = 0; for (E e : graph.getInEdges(v)) { // For graphs, the code below is equivalent to // V w = graph.getOpposite(v, e); // total_input += (getCurrentValue(w) * getEdgeWeight(w,e).doubleValue()); // For hypergraphs, this divides the potential coming from w // by the number of vertices in the connecting edge e. int incident_count = getAdjustedIncidentCount(e); for (V w : graph.getIncidentVertices(e)) { if (!w.equals(v) || hyperedges_are_self_loops) v_input += (getCurrentValue(w) * getEdgeWeight(w,e).doubleValue() / incident_count); } } // modify total_input according to alpha double new_value = alpha > 0 ? v_input * (1 - alpha) + getVertexPrior(v) * alpha : v_input; setOutputValue(v, new_value + getCurrentValue(v)); // FIXME: DO WE NEED TO CHANGE HOW DISAPPEARING IS COUNTED? NORMALIZE? return Math.abs(getCurrentValue(v) - new_value); } }