@ladybugmem/icebug 0.1.0 → 0.1.2

package/vendor/include/networkit/scoring/ModularityScoring.hpp

@@ -1,79 +0,0 @@
-/*
- * ModularityScoring.hpp
- *
- *  Created on: 15.10.2012
- *      Author: Christian Staudt
- */
-
-#ifndef NETWORKIT_SCORING_MODULARITY_SCORING_HPP_
-#define NETWORKIT_SCORING_MODULARITY_SCORING_HPP_
-
-#include <networkit/scoring/EdgeScoring.hpp>
-#include <networkit/structures/Partition.hpp>
-
-namespace NetworKit {
-
-// TODO: implement modularity as in Python prototype
-
-/**
- * @ingroup scoring
- */
-template <typename T>
-class ModularityScoring final : public EdgeScoring<T> {
-
-    double totalEdgeWeight; //!< total weight of the graph
-
-public:
-    /**
-     * @param[in]  G  a graph instance
-     *
-     * Do not modify the graph while using this instance of ModularityScoring.
-     */
-    ModularityScoring(Graph &G, double gTotalEdgeWeight = 0.0);
-
-    /** Default destructor */
-    ~ModularityScoring() override = default;
-
-    void scoreEdges(int attrId) override;
-
-    /**
-     * Returns an edge score for an edge (u,v) which expresses the
-     * modularity increase which can be gained by merging
-     * the clusters of u and v.
-     *
-     * $$\\Delta mod(c, d) := \\frac{1}{2 \\omega(E)} \\left ( 2 \\omega(E) \\omega(c,d) -
-     * \\omega(c) \\omega(d) \\right ) $$
-     *
-     * @param[in]  u  source node id
-     * @param[out]  v  target node id
-     *
-     */
-    T edgeScore(node u, node v) const override;
-};
-
-template <typename T>
-ModularityScoring<T>::ModularityScoring(Graph &G, double gTotalEdgeWeight)
-    : EdgeScoring<T>(G), totalEdgeWeight(gTotalEdgeWeight) {
-    if (gTotalEdgeWeight == 0.0) {
-        this->totalEdgeWeight = this->G->totalEdgeWeight();
-    }
-}
-
-template <typename T>
-inline T ModularityScoring<T>::edgeScore(node u, node v) const {
-    assert(totalEdgeWeight != 0.0);
-    double volume = 2.0 * totalEdgeWeight;
-    double nom1 = (this->G->weightedDegree(u) / volume);
-    double nom2 = (this->G->weightedDegree(v) / volume);
-    double deltaMod = (this->G->weight(u, v) / totalEdgeWeight) - (nom1 * nom2);
-    return deltaMod;
-}
-
-template <typename T>
-void ModularityScoring<T>::scoreEdges(int) {
-    // TODO: rewrite with new edge attribute system
-}
-
-} /* namespace NetworKit */
-
-#endif // NETWORKIT_SCORING_MODULARITY_SCORING_HPP_

package/vendor/include/networkit/simulation/EpidemicSimulationSEIR.hpp

@@ -1,59 +0,0 @@
-/*
- * EpidemicSimulationSEIR.hpp
- *
- *  Created on: 20.11.2015
- *      Author: Christian Staudt
- */
-
-#ifndef NETWORKIT_SIMULATION_EPIDEMIC_SIMULATION_SEIR_HPP_
-#define NETWORKIT_SIMULATION_EPIDEMIC_SIMULATION_SEIR_HPP_
-
-#include <networkit/base/Algorithm.hpp>
-#include <networkit/graph/Graph.hpp>
-
-namespace NetworKit {
-
-/**
- * @ingroup simulation
- * Node centrality index which ranks nodes by their degree.
- * Optional normalization by maximum degree.
- */
-class EpidemicSimulationSEIR final : public Algorithm {
-public:
-    /**
-     * Simulates an epidemic spread using the Susceptible-Exposed-Infectious-Removed (SEIR) model.
-     * @param G The network.
-     * @param tMax Max. number of timesteps.
-     * @param transP Transmission probability.
-     * @param eTime Exposed time.
-     * @param iTime Infectious time.
-     * @param zero Starting node.
-     */
-    EpidemicSimulationSEIR(const Graph &G, count tMax, double transP, count eTime, count iTime,
-                           node zero);
-
-    void run() override;
-
-    /**
-     * Returns the data from the simulation (only valid after run() was called).
-     * @return Vector of vectors, containing "zero", "time", "state" and "count" values for each
-     * node.
-     */
-    const std::vector<std::vector<count>> &getData() const;
-
-private:
-    const Graph *G;
-    count tMax;
-    double transP;
-    count eTime;
-    count iTime;
-    node zero;
-    enum class State { S, E, I, R, U }; // Susceptible, Exposed, Infectious, Removed, Undefined
-    std::vector<State> state;
-    std::vector<index> timestamp;
-    std::vector<std::vector<count>> stats;
-};
-
-} /* namespace NetworKit */
-
-#endif // NETWORKIT_SIMULATION_EPIDEMIC_SIMULATION_SEIR_HPP_

package/vendor/include/networkit/sparsification/ChanceCorrectedTriangleScore.hpp

@@ -1,28 +0,0 @@
-/*
- * ChangeCorrectedTriangleScore.hpp
- *
- *  Created on: 20.11.2014
- *      Author: Michael Hamann
- */
-
-#ifndef NETWORKIT_SPARSIFICATION_CHANCE_CORRECTED_TRIANGLE_SCORE_HPP_
-#define NETWORKIT_SPARSIFICATION_CHANCE_CORRECTED_TRIANGLE_SCORE_HPP_
-
-#include <networkit/edgescores/EdgeScore.hpp>
-
-namespace NetworKit {
-
-class ChanceCorrectedTriangleScore final : public EdgeScore<double> {
-
-public:
-    ChanceCorrectedTriangleScore(const Graph &graph, const std::vector<count> &triangles);
-    double score(edgeid eid) override;
-    double score(node u, node v) override;
-    void run() override;
-
-private:
-    const std::vector<count> *triangles;
-};
-
-} // namespace NetworKit
-#endif // NETWORKIT_SPARSIFICATION_CHANCE_CORRECTED_TRIANGLE_SCORE_HPP_

package/vendor/include/networkit/sparsification/ForestFireScore.hpp

@@ -1,34 +0,0 @@
-/*
- * ForestFireScore.hpp
- *
- *  Created on: 26.08.2014
- *      Author: Gerd Lindner
- */
-
-#ifndef NETWORKIT_SPARSIFICATION_FOREST_FIRE_SCORE_HPP_
-#define NETWORKIT_SPARSIFICATION_FOREST_FIRE_SCORE_HPP_
-
-#include <networkit/edgescores/EdgeScore.hpp>
-
-namespace NetworKit {
-
-/**
- * Based on the Forest Fire algorithm introduced by Leskovec et al.
- * The burn frequency of the edges is used as edge score.
- */
-class ForestFireScore final : public EdgeScore<double> {
-
-public:
-    ForestFireScore(const Graph &graph, double pf, double targetBurntRatio);
-    double score(edgeid eid) override;
-    double score(node u, node v) override;
-    void run() override;
-
-private:
-    double pf;
-    double targetBurntRatio;
-};
-
-} // namespace NetworKit
-/* namespace NetworKit */
-#endif // NETWORKIT_SPARSIFICATION_FOREST_FIRE_SCORE_HPP_

package/vendor/include/networkit/sparsification/GlobalThresholdFilter.hpp

@@ -1,40 +0,0 @@
-/*
- * GlobalThresholdFilter.hpp
- *
- *  Created on: 23.07.2014
- *      Author: Gerd Lindner
- */
-
-#ifndef NETWORKIT_SPARSIFICATION_GLOBAL_THRESHOLD_FILTER_HPP_
-#define NETWORKIT_SPARSIFICATION_GLOBAL_THRESHOLD_FILTER_HPP_
-
-#include <networkit/graph/Graph.hpp>
-
-namespace NetworKit {
-
-/**
- * Calculates a sparsified graph by applying a global threshold to an edge score.
- */
-class GlobalThresholdFilter {
-    const Graph *graph;
-    const std::vector<double> &attribute;
-    const double threshold;
-    const bool above;
-
-public:
-    /**
-     * Creates a new instance of a global threshold filter.
-     * @param threshold the threshold
-     * @param above if set to true, edges with a score above or equal to the threshold remain in
-     * the filtered graph. If set to false, edges with a score below or equal to the threshold
-     * remain in the filtered graph.
-     */
-    GlobalThresholdFilter(const Graph &graph, const std::vector<double> &attribute,
-                          double threshold, bool above);
-
-    GraphW calculate();
-    GraphW calculateUndirected();
-};
-
-} // namespace NetworKit
-#endif // NETWORKIT_SPARSIFICATION_GLOBAL_THRESHOLD_FILTER_HPP_

package/vendor/include/networkit/sparsification/LocalDegreeScore.hpp

@@ -1,30 +0,0 @@
-/*
- * LocalDegreeScore.hpp
- *
- *  Created on: 28.08.2014
- *      Author: Gerd Lindner
- */
-
-#ifndef NETWORKIT_SPARSIFICATION_LOCAL_DEGREE_SCORE_HPP_
-#define NETWORKIT_SPARSIFICATION_LOCAL_DEGREE_SCORE_HPP_
-
-#include <networkit/edgescores/EdgeScore.hpp>
-
-namespace NetworKit {
-
-/**
- * Local Degree sparsification method.
- * See 'Structure-Preserving Sparsification of Social Networks' by Lindner, Staudt, Hamann.
- */
-class LocalDegreeScore final : public EdgeScore<double> {
-
-public:
-    LocalDegreeScore(const Graph &G);
-    void run() override;
-    double score(edgeid eid) override;
-    double score(node u, node v) override;
-};
-
-} // namespace NetworKit
-/* namespace NetworKit */
-#endif // NETWORKIT_SPARSIFICATION_LOCAL_DEGREE_SCORE_HPP_

package/vendor/include/networkit/sparsification/LocalFilterScore.hpp

@@ -1,124 +0,0 @@
-/*
- * LocalFilterScore.hpp
- *
- *  Created on: 20.11.2014
- *      Author: Michael Hamann, Gerd Lindner
- */
-
-#ifndef NETWORKIT_SPARSIFICATION_LOCAL_FILTER_SCORE_HPP_
-#define NETWORKIT_SPARSIFICATION_LOCAL_FILTER_SCORE_HPP_
-
-#include <atomic>
-#include <memory>
-
-#include <networkit/auxiliary/Parallel.hpp>
-#include <networkit/edgescores/EdgeScore.hpp>
-
-namespace NetworKit {
-
-/**
- * Local filtering edge scoring. Edges with high score are more important.
- *
- * Edges are ranked locally, the top d^e (logarithmic, default) or 1+e*(d-1) edges (non-logarithmic)
- * are kept. For equal attribute values, neighbors of low degree are preferred.
- */
-template <typename InType>
-class LocalFilterScore final : public EdgeScore<double> {
-
-public:
-    /**
-     * Initialize the local edge filtering score.
-     *
-     * @param G The graph for which the score shall be.
-     * @param attribute The input attribute according to which the edges shall be filtered locally.
-     * @param logarithmic If the score shall be logarithmic in the rank (then d^e edges are kept).
-     * Linear otherwise.
-     */
-    LocalFilterScore(const Graph &G, const std::vector<InType> &attribute, bool logarithmic = true)
-        : EdgeScore<double>(G), attribute(&attribute), logarithmic(logarithmic) {}
-
-    /**
-     * Execute the algorithm.
-     */
-    void run() override {
-        if (!G->hasEdgeIds()) {
-            throw std::runtime_error("edges have not been indexed - call indexEdges first");
-        }
-
-        /*
-         * For each edge, we calculate the minimum required sparsification exponent e
-         * such that the edge is contained in the sparse graph.
-         */
-
-        std::unique_ptr<std::atomic<double>[]> sparsificationExp(
-            new std::atomic<double>[G->upperEdgeIdBound()] {});
-
-        G->balancedParallelForNodes([&](node i) {
-            count d = G->degree(i);
-
-            /*
-             * The top d^e edges (sorted by similarity in descending order)
-             * are to be kept in the sparse graph.
-             */
-
-            std::vector<edgeid> neighbors;
-            neighbors.reserve(d);
-            G->forNeighborsOf(i, [&](node _i, node j, edgeid eid) { neighbors.emplace_back(eid); });
-
-            std::sort(neighbors.begin(), neighbors.end(), [&](const edgeid &e1, const edgeid &e2) {
-                return (*attribute)[e1] > (*attribute)[e2];
-            });
-
-            count rank = 0;
-            count numSame = 1;
-            InType oldValue = std::numeric_limits<InType>::lowest();
-
-            for (edgeid eid : neighbors) {
-                if ((*attribute)[eid] != oldValue) {
-                    rank += numSame;
-                    numSame = 1;
-                } else {
-                    ++numSame;
-                }
-
-                double e = 1.0;
-
-                if (d > 1) {
-                    if (logarithmic) {
-                        e = 1.0 - log(rank) / log(d);
-                    } else {
-                        e = 1.0 - (rank - 1) * 1.0 / (d - 1); // Keep top 1 + e * (d-1) edges
-                    }
-                }
-
-                Aux::Parallel::atomic_max(sparsificationExp[eid], e);
-            }
-        });
-
-        scoreData.clear();
-        scoreData.resize(G->upperEdgeIdBound());
-
-#pragma omp parallel for
-        for (omp_index i = 0; i < static_cast<omp_index>(scoreData.size()); ++i) {
-            scoreData[i] = sparsificationExp[i];
-        }
-
-        hasRun = true;
-    }
-
-    double score(node u, node v) override {
-        throw std::runtime_error("Not implemented: Use scores() instead.");
-    }
-
-    double score(edgeid eid) override {
-        throw std::runtime_error("Not implemented: Use scores() instead.");
-    }
-
-private:
-    const std::vector<InType> *attribute;
-    bool logarithmic;
-};
-
-} // namespace NetworKit
-
-#endif // NETWORKIT_SPARSIFICATION_LOCAL_FILTER_SCORE_HPP_

package/vendor/include/networkit/sparsification/LocalSimilarityScore.hpp

@@ -1,63 +0,0 @@
-/*
- * LocalSimilarityScore.hpp
- *
- *  Created on: 26.07.2014
- *      Author: Gerd Lindner
- */
-
-#ifndef NETWORKIT_SPARSIFICATION_LOCAL_SIMILARITY_SCORE_HPP_
-#define NETWORKIT_SPARSIFICATION_LOCAL_SIMILARITY_SCORE_HPP_
-
-#include <networkit/edgescores/EdgeScore.hpp>
-
-namespace NetworKit {
-
-template <typename T>
-struct AttributizedEdge {
-    node ego;
-    node alter;
-    edgeid eid;
-    T value;
-
-    AttributizedEdge(node ego, node alter, edgeid eid, T v)
-        : ego(ego), alter(alter), eid(eid), value(v) {}
-
-    bool operator<(const AttributizedEdge<T> &other) const {
-        return (value > other.value) || (value == other.value && alter < other.alter);
-    }
-
-    bool operator>(const AttributizedEdge<T> &other) const {
-        return (value < other.value) || (value == other.value && alter > other.alter);
-    }
-
-    bool operator==(const AttributizedEdge<T> &other) const {
-        return ego == other.ego && alter == other.alter && value == other.value;
-    }
-};
-
-struct greater {
-    template <class T>
-    bool operator()(T const &a, T const &b) const {
-        return a > b;
-    }
-};
-
-/**
- * Implementation of the Local Sparsification Algorithm by Sataluri et al.
- */
-class LocalSimilarityScore final : public EdgeScore<double> {
-
-public:
-    LocalSimilarityScore(const Graph &G, const std::vector<count> &triangles);
-    double score(edgeid eid) override;
-    double score(node u, node v) override;
-    void run() override;
-
-private:
-    const std::vector<count> *triangles;
-};
-
-} // namespace NetworKit
-/* namespace NetworKit */
-
-#endif // NETWORKIT_SPARSIFICATION_LOCAL_SIMILARITY_SCORE_HPP_

package/vendor/include/networkit/sparsification/MultiscaleScore.hpp

@@ -1,38 +0,0 @@
-/*
- * MultiscaleScore.hpp
- *
- *  Created on: 20.06.2014
- *      Author: Gerd Lindner
- */
-
-#ifndef NETWORKIT_SPARSIFICATION_MULTISCALE_SCORE_HPP_
-#define NETWORKIT_SPARSIFICATION_MULTISCALE_SCORE_HPP_
-
-#include <networkit/edgescores/EdgeScore.hpp>
-
-namespace NetworKit {
-
-/**
- * Calculates the multiscale edge score for a given graph. Each edge is
- * assigned the maximum filter value in [0,1] for which the edge will be contained
- * in the multiscale backbone.
- *
- * See "Extracting the multiscale backbone of complex weighted networks" by Serrano et al.
- */
-class MultiscaleScore final : public EdgeScore<double> {
-
-public:
-    MultiscaleScore(const Graph &graph, const std::vector<double> &attribute);
-    double score(edgeid eid) override;
-    double score(node u, node v) override;
-    void run() override;
-    double getProbability(count degree, edgeweight normalizedWeight);
-
-private:
-    const std::vector<double> *attribute;
-};
-
-} // namespace NetworKit
-/* namespace NetworKit */
-
-#endif // NETWORKIT_SPARSIFICATION_MULTISCALE_SCORE_HPP_

package/vendor/include/networkit/sparsification/RandomEdgeScore.hpp

@@ -1,33 +0,0 @@
-/*
- * RandomEdgeScore.hpp
- *
- *  Created on: 11.08.2014
- *      Author: Gerd Lindner
- */
-
-#ifndef NETWORKIT_SPARSIFICATION_RANDOM_EDGE_SCORE_HPP_
-#define NETWORKIT_SPARSIFICATION_RANDOM_EDGE_SCORE_HPP_
-
-#include <networkit/edgescores/EdgeScore.hpp>
-
-namespace NetworKit {
-
-/**
- * Generates a random edge attribute. Each edge is assigned a random value in [0,1].
- */
-class RandomEdgeScore final : public EdgeScore<double> {
-
-public:
-    /**
-     * Creates a new instance of the Random edge score.
-     */
-    RandomEdgeScore(const Graph &G);
-
-    double score(edgeid eid) override;
-    double score(node u, node v) override;
-    void run() override;
-};
-
-} // namespace NetworKit
-/* namespace NetworKit */
-#endif // NETWORKIT_SPARSIFICATION_RANDOM_EDGE_SCORE_HPP_

package/vendor/include/networkit/sparsification/RandomNodeEdgeScore.hpp

@@ -1,29 +0,0 @@
-/*
- * RandomNodeEdgeScore.hpp
- *
- *  Created on: 20.11.2014
- *      Author: Michael Hamann
- */
-
-#ifndef NETWORKIT_SPARSIFICATION_RANDOM_NODE_EDGE_SCORE_HPP_
-#define NETWORKIT_SPARSIFICATION_RANDOM_NODE_EDGE_SCORE_HPP_
-
-#include <networkit/edgescores/EdgeScore.hpp>
-
-namespace NetworKit {
-
-class RandomNodeEdgeScore final : public EdgeScore<double> {
-
-public:
-    RandomNodeEdgeScore(const Graph &graph, double rneRatio = 0.8);
-    void run() override;
-    double score(edgeid eid) override;
-    double score(node u, node v) override;
-
-private:
-    double rneRatio;
-};
-
-} /* namespace NetworKit */
-
-#endif // NETWORKIT_SPARSIFICATION_RANDOM_NODE_EDGE_SCORE_HPP_

package/vendor/include/networkit/sparsification/SCANStructuralSimilarityScore.hpp

@@ -1,23 +0,0 @@
-
-#ifndef NETWORKIT_SPARSIFICATION_SCAN_STRUCTURAL_SIMILARITY_SCORE_HPP_
-#define NETWORKIT_SPARSIFICATION_SCAN_STRUCTURAL_SIMILARITY_SCORE_HPP_
-
-#include <networkit/edgescores/EdgeScore.hpp>
-
-namespace NetworKit {
-
-class SCANStructuralSimilarityScore final : public EdgeScore<double> {
-
-public:
-    SCANStructuralSimilarityScore(const Graph &G, const std::vector<count> &triangles);
-    void run() override;
-    double score(edgeid eid) override;
-    double score(node u, node v) override;
-
-private:
-    const std::vector<count> *triangles;
-};
-
-} // namespace NetworKit
-
-#endif // NETWORKIT_SPARSIFICATION_SCAN_STRUCTURAL_SIMILARITY_SCORE_HPP_

package/vendor/include/networkit/sparsification/SimmelianOverlapScore.hpp

@@ -1,35 +0,0 @@
-/*
- * SimmelianOverlapScore.hpp
- *
- *  Created on: 22.07.2014
- *      Author: Gerd Lindner
- */
-
-#ifndef NETWORKIT_SPARSIFICATION_SIMMELIAN_OVERLAP_SCORE_HPP_
-#define NETWORKIT_SPARSIFICATION_SIMMELIAN_OVERLAP_SCORE_HPP_
-
-#include <set>
-#include <networkit/sparsification/SimmelianScore.hpp>
-
-namespace NetworKit {
-
-/**
- * Calculates the Simmelian backbone (paramaetric variant) for a given input graph.
- */
-class SimmelianOverlapScore final : public SimmelianScore {
-
-public:
-    /**
-     * Creates a new instance of the parametric variant of the Simmelian Backbone calculator.
-     * @param maxRank     the maximum rank that is considered for overlap calculation
-     */
-    SimmelianOverlapScore(const Graph &graph, const std::vector<count> &triangles, count maxRank);
-    void run() override;
-
-private:
-    count maxRank;
-};
-
-} // namespace NetworKit
-/* namespace NetworKit */
-#endif // NETWORKIT_SPARSIFICATION_SIMMELIAN_OVERLAP_SCORE_HPP_