capablanca 3.2

Find a 2-Approximate Dominating Set for undirected graph encoded in DIMACS format.

Capablanca: 2-Approximation Dominating Set Solver

This work builds upon A 2-Approximation Algorithm for Dominating Sets.

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Overview of the Minimum Dominating Set (MDS)

Definition:

A dominating set in a graph $G=(V,E)$ is a subset $D\subseteq V$ such that every vertex not in $D$ is adjacent to at least one vertex in $D$. The minimum dominating set (MDS) is the smallest possible dominating set in terms of the number of vertices.

Key Concepts:

1. Graph Representation:

   • $V$: Set of vertices.
   • $E$: Set of edges connecting the vertices.

2. Dominating Set:

   • A set $D$ where for every vertex $v\in V$, either $v\in D$ or $v$ is adjacent to some vertex in $D$.

3. Minimum Dominating Set:

   • The dominating set with the smallest cardinality (i.e., the fewest number of vertices).

Applications:

• Network Design: Ensuring coverage in wireless sensor networks.
• Social Networks: Identifying influential nodes.
• Game Theory: Strategies in certain types of games.
• Biology: Modeling protein-protein interaction networks.

Computational Complexity:

• NP-Hard: Finding the minimum dominating set is computationally intensive for large graphs.
• Approximation Algorithms: Used to find near-optimal solutions in polynomial time.

Algorithms:

1. Greedy Algorithm:

   • Iteratively selects the vertex that covers the most uncovered vertices.
   • Provides a logarithmic approximation ratio.

2. Integer Linear Programming (ILP):

   • Formulates the problem as an optimization problem.
   • Solvable using ILP solvers for exact solutions, though computationally expensive.

3. Heuristics and Metaheuristics:

   • Genetic algorithms, simulated annealing, etc., for large-scale problems.

Challenges:

• Scalability: Exact algorithms are infeasible for very large graphs.
• Dynamic Graphs: Maintaining a minimum dominating set in graphs that change over time.

Research Directions:

• Parallel Algorithms: Leveraging multi-core processors and distributed computing.
• Machine Learning: Using learning-based approaches to predict dominating sets.
• Hybrid Methods: Combining exact and heuristic methods for better performance.

Conclusion:

The minimum dominating set problem is a fundamental issue in graph theory with wide-ranging applications. While it is computationally challenging, various algorithms and heuristics provide practical solutions for different scenarios. Ongoing research continues to improve the efficiency and applicability of these methods.

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Overview of the find_dominating_set Algorithm and Runtime Analysis

Algorithm Purpose

The find_dominating_set algorithm computes a 2-approximation for the minimum dominating set in a general undirected graph. It transforms the input graph into a chordal structure and leverages the approximate_dominating_set_chordal algorithm, which is proven to provide a 2-approximation for chordal graphs. This approach ensures applicability to any graph while maintaining the approximation guarantee.

Algorithm Structure

approximate_dominating_set_chordal (Inner Algorithm)

• Input: A chordal graph $G$ with $n$ nodes and $m$ edges.
• Process:
  1. Verifies chordality $O(n+m)$.
  2. Computes a perfect elimination ordering (PEO) and reverses it $O(n)$.
  3. Iterates over nodes in reverse PEO:
     • For each undominated node $v$, selects a vertex from $N[v]$ (self and neighbors) that maximizes the number of undominated nodes covered.
     • Updates the dominating set and marks covered nodes as dominated.
• Output: A dominating set $D$ such that $|D|\le 2\cdot |OPT|$, where $OPT$ is the minimum dominating set.
• Key Mechanism: Greedy selection based on undominated coverage, leveraging chordal graph properties (PEO ensures structured neighborhoods).

find_dominating_set (Outer Algorithm)

• Input: A general undirected graph $G$ with $n$ nodes and $m$ edges.
• Process:
  1. Preprocessing:
     • Handles trivial cases (empty graph or no edges): $O(1)$.
     • Identifies and removes isolated nodes, adding them to the dominating set: $O(n+m)$.
  2. Component Processing:
     • Identifies connected components: $O(n+m)$.
     • For each component with $n_i$ nodes and $m_i$ edges:
       • Subgraph Extraction: $O(n_i+m_i)$.
       • Chordal Transformation:
         • Creates a chordal graph with $2n_i$ nodes and $O(n_i^2)$ edges (includes a clique on $n_i$ nodes).
         • Construction time: $O(n_i^2)$.
       • Inner Algorithm Call: Applies approximate_dominating_set_chordal to the chordal graph.
       • Mapping Back: Extracts original node indices: $O(n_i)$.
  3. Output: Combines dominating sets from isolated nodes and components.
• Output: A dominating set for $G$ with size at most twice the minimum dominating set size.

Runtime Analysis

approximate_dominating_set_chordal

• Preprocessing:
  • Chordality check and PEO: $O(n+m)$.
  • Reverse PEO and initialization: $O(n)$.
• Main Loop:
  • Iterates $n$ times, but costly steps occur $|D|\le n$ times.
  • For each selected $v$:
    • Computes $N[v]$: $O(d_v)$.
    • For each $w\in N[v]$ (size $d_v+1$), counts undominated in $N[w]$: $O(d_w)$.
    • Total per $v$: $O(\sum _{w\in N[v]}{d}_w)\le O(m)$.
  • Overall: $O(n\cdot m)$ (e.g., in a clique, $m\approx n^2$).
• Total: $O(n+m)+O(nm)=O(nm)$.

find_dominating_set

• Preprocessing:
  • Isolated nodes and removal: $O(n+m)$.
  • Connected components: $O(n+m)$.
• Component Loop:
  • $k$ components, $\sum n_i=n^{\prime }\le n$, $\sum m_i=m^{\prime }\le m$.
  • Per component:
    • Subgraph: $O(n_i+m_i)$.
    • Chordal graph: $n^{\prime }=2n_i$, $m^{\prime }=n_i+m_i+(\genfrac{}{}{0ex}{}{n_i}{2})=O(n_i^2)$, construction $O(n_i^2)$.
    • Inner call: $O(n^{\prime }{m}^{\prime })=O(2n_i\cdot n_i^2)=O(n_i^3)$.
    • Update: $O(n_i)$.
    • Total per component: $O(n_i^3)$.
  • Across all components: $\sum O(n_i^3)\le O(n^3)$ (worst case: one component with $n$ nodes).
• Total: $O(n+m)+O(n^3)=O(n^3)$.

Summary

• Inner Algorithm: $O(nm)$, efficient for chordal graphs with runtime dependent on edge density.
• Outer Algorithm: $O(n^3)$, dominated by the cubic cost per component due to the dense chordal graph, $O(n_i^2)$ edges, amplifying the inner $O(nm)$ runtime.
• Correctness and Approximation: Both algorithms produce dominating sets, with the outer algorithm preserving the 2-approximation by transforming general graphs into chordal ones, as verified through proofs and examples.

This $O(n^3)$ runtime reflects the current dense clique construction; optimizing the chordal transformation could potentially lower it to $O(n^2)$ or $O(nm)$.

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Problem Statement

Input: A Boolean Adjacency Matrix $M$.

Answer: Find a Minimum Dominating Set.

Example Instance: 5 x 5 matrix

	c1	c2	c3	c4	c5
r1	0	0	1	0	1
r2	0	0	0	1	0
r3	1	0	0	0	1
r4	0	1	0	0	0
r5	1	0	1	0	0

The input for undirected graph is typically provided in DIMACS format. In this way, the previous adjacency matrix is represented in a text file using the following string representation:

p edge 5 4
e 1 3
e 1 5
e 2 4
e 3 5

This represents a 5x5 matrix in DIMACS format such that each edge $(v,w)$ appears exactly once in the input file and is not repeated as $(w,v)$. In this format, every edge appears in the form of

e W V

where the fields W and V specify the endpoints of the edge while the lower-case character e signifies that this is an edge descriptor line.

Example Solution:

Dominating Set Found 1, 2: Nodes 1 and 2 constitute an optimal solution.

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Compile and Environment

Prerequisites

• Python ≥ 3.10

Installation

pip install capablanca

Execution

1. Clone the repository:

   git clone https://github.com/frankvegadelgado/capablanca.git
   cd capablanca
   

2. Run the script:

   approx -i ./benchmarks/testMatrix1
   

   utilizing the approx command provided by Capablanca's Library to execute the Boolean adjacency matrix capablanca\benchmarks\testMatrix1. The file testMatrix1 represents the example described herein. We also support .xz, .lzma, .bz2, and .bzip2 compressed text files.

   Example Output:

   testMatrix1: Dominating Set Found 1, 2
   

   This indicates nodes 1, 2 form a Dominating Set.

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Dominating Set Size

Use the -c flag to count the nodes in the Dominating Set:

approx -i ./benchmarks/testMatrix2 -c

Output:

testMatrix2: Dominating Set Size 2

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Command Options

Display help and options:

approx -h

Output:

usage: approx [-h] -i INPUTFILE [-a] [-b] [-c] [-v] [-l] [--version]

Find a 2-Approximate Dominating Set for undirected graph encoded in DIMACS format.

options:
  -h, --help            show this help message and exit
  -i INPUTFILE, --inputFile INPUTFILE
                        input file path
  -a, --approximation   enable comparison with a polynomial-time approximation approach within a logarithmic factor
  -b, --bruteForce      enable comparison with the exponential-time brute-force approach
  -c, --count           calculate the size of the Dominating Set
  -v, --verbose         anable verbose output
  -l, --log             enable file logging
  --version             show program's version number and exit

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Batch Execution

Batch execution allows you to solve multiple graphs within a directory consecutively.

To view available command-line options for the batch_approx command, use the following in your terminal or command prompt:

batch_approx -h

This will display the following help information:

usage: batch_approx [-h] -i INPUTDIRECTORY [-a] [-b] [-c] [-v] [-l] [--version]

Find a 2-Approximate Dominating Set for all undirected graphs encoded in DIMACS format and stored in a directory.

options:
  -h, --help            show this help message and exit
  -i INPUTDIRECTORY, --inputDirectory INPUTDIRECTORY
                        Input directory path
  -a, --approximation   enable comparison with a polynomial-time approximation approach within a logarithmic factor
  -b, --bruteForce      enable comparison with the exponential-time brute-force approach
  -c, --count           calculate the size of the Dominating Set
  -v, --verbose         anable verbose output
  -l, --log             enable file logging
  --version             show program's version number and exit

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Testing Application

A command-line utility named test_approx is provided for evaluating the Algorithm using randomly generated, large sparse matrices. It supports the following options:

usage: test_approx [-h] -d DIMENSION [-n NUM_TESTS] [-s SPARSITY] [-a] [-b] [-c] [-w] [-v] [-l] [--version]

The Capablanca Testing Application using randomly generated, large sparse matrices.

options:
  -h, --help            show this help message and exit
  -d DIMENSION, --dimension DIMENSION
                        an integer specifying the dimensions of the square matrices
  -n NUM_TESTS, --num_tests NUM_TESTS
                        an integer specifying the number of tests to run
  -s SPARSITY, --sparsity SPARSITY
                        sparsity of the matrices (0.0 for dense, close to 1.0 for very sparse)
  -a, --approximation   enable comparison with a polynomial-time approximation approach within a logarithmic factor
  -b, --bruteForce      enable comparison with the exponential-time brute-force approach
  -c, --count           calculate the size of the Dominating Set
  -w, --write           write the generated random matrix to a file in the current directory
  -v, --verbose         anable verbose output
  -l, --log             enable file logging
  --version             show program's version number and exit

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Code

• Python implementation by Frank Vega.

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Complexity

+ We present a polynomial-time algorithm achieving a 2-approximation ratio for MDS, providing strong evidence that P = NP by efficiently solving a computationally hard problem with near-optimal solutions.

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License

• MIT License.