siriaisa 0.0.3

Compute the Approximate Independent Dominating Set for an undirected graph encoded in DIMACS format.

Siriaisa: Approximate Independent Dominating Set Solver

This work builds upon A 3-Approximation for Independent Dominating Sets: The Siriaisa Algorithm.

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Overview of the Minimum Independent Dominating Set (MIDS)

Definition:

An independent dominating set in a graph $G = (V, E)$ is a subset $D \subseteq V$ such that no two vertices in $D$ are adjacent and every vertex not in $D$ is adjacent to at least one vertex in $D$. The minimum independent dominating set (MIDS) is the smallest possible independent 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. Independent Dominating Set:

   • A set $D$ where no two vertices in $D$ are adjacent, and for every vertex $v \in V$, either $v \in D$ or $v$ is adjacent to some vertex in $D$.

3. Minimum Independent Dominating Set:

   • The independent 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 independent dominating set is computationally intensive for large graphs.
• Approximation Algorithms: Used to find near-optimal solutions in polynomial time.

Algorithms:

1. Greedy Algorithm:

   • Builds a degree-four auxiliary graph, repairs the two lifted vertex seeds into maximal independent sets, and selects the smallest verified candidate.
   • Provides the implementation studied in the 3-approximation certificate theorem.

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 independent 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 independent 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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Problem Statement

Input: A Boolean Adjacency Matrix $M$.

Answer: Find a Minimum Independent 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:

Independent Dominating Set Found 1, 4: Nodes 1 and 4 constitute an optimal solution.

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Compile and Environment

Prerequisites

• Python >= 3.12

Installation

pip install siriaisa

Execution

1. Clone the repository:

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

2. Run the script:

   iris -i ./benchmarks/testMatrix1
   

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

   Example Output:

   testMatrix1: Independent Dominating Set Found 1, 4
   

   This indicates nodes 1, 4 form an Independent Dominating Set.

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Independent Dominating Set Size

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

iris -i ./benchmarks/testMatrix2 -c

Output:

testMatrix2: Independent Dominating Set Size 2

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Command Options

Display help and options:

iris -h

Output:

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

Solve the Approximate Independent 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 maximum degree factor
  -b, --bruteForce      enable comparison with the exponential-time brute-force approach
  -c, --count           calculate the size of the Independent Dominating Set
  -v, --verbose         enable 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_iris command, use the following in your terminal or command prompt:

batch_iris -h

This will display the following help information:

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

Solve the Approximate Independent 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 maximum degree factor
  -b, --bruteForce      enable comparison with the exponential-time brute-force approach
  -c, --count           calculate the size of the Independent Dominating Set
  -v, --verbose         enable 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_iris is provided for evaluating the Algorithm using randomly generated, large sparse matrices. It supports the following options:

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

The Siriaisa 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 maximum degree factor
  -b, --bruteForce      enable comparison with the exponential-time brute-force approach
  -c, --count           calculate the size of the Independent Dominating Set
  -w, --write           write the generated random matrix to a file in the current directory
  -v, --verbose         enable 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

+ Siriaisa separates feasibility from the approximation certificate: every returned set is verified as independent and dominating, while a universal proof of the 3-approximation certificate would imply P = NP by known MIDS inapproximability results.

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License

• MIT License.