aegypti 0.3.8

Compute the Approximate Clique for undirected graph encoded in DIMACS format.

Aegypti: Approximate Clique Solver

This work builds upon The Aegypti Algorithm.

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The Maximum Clique Problem: Overview

Description

The Maximum Clique Problem (MCP) is a classic NP-hard problem in graph theory and computer science. Given an undirected graph $G = (V, E)$, a clique is a subset of vertices $C \subseteq V$ where every two distinct vertices are connected by an edge. The goal of MCP is to find the largest possible clique in $G$.

Key Definitions

• Clique: A complete subgraph (all possible edges exist between vertices).
• Maximum Clique: The largest clique in the graph.
• Clique Number ($\omega(G)$): The size of the maximum clique in $G$.

Theoretical Background

• MCP is NP-Hard, meaning no known polynomial-time algorithm solves all cases unless $P = NP$.
• It is closely related to other problems like the Independent Set Problem (complement graph) and Graph Coloring.
• Decision version: "Does a clique of size $k$ exist?" is NP-Complete.

Approaches to Solve MCP

Exact Algorithms

1. Brute Force: Check all possible subsets (exponential time $O(2^n)$).
2. Branch and Bound: Prune search space by eliminating branches where clique size cannot exceed the current maximum.
3. Integer Programming (IP): Formulate as an optimization problem with binary variables and constraints.
4. Bron-Kerbosch Algorithm: A recursive backtracking method for listing all maximal cliques.

Heuristic & Approximation Methods

1. Greedy Algorithms: Iteratively add vertices with the highest degree or most connections to the current clique.
2. Local Search: Improve existing solutions via vertex swaps or perturbations.
3. Metaheuristics:
   • Genetic Algorithms: Evolve candidate solutions via selection, crossover, and mutation.
   • Simulated Annealing: Probabilistic technique inspired by thermodynamics.
   • Tabu Search: Avoid revisiting solutions using a "tabu list."

Advanced Techniques

• Reduction Rules: Simplify the graph by removing vertices that cannot be part of the maximum clique.
• Parallel & GPU Computing: Speed up exhaustive searches using parallel processing.
• Machine Learning: Learn graph features to guide heuristic choices (emerging area).

Applications

1. Social Network Analysis: Identifying tightly connected groups (communities).
2. Bioinformatics: Protein interaction networks, gene regulatory networks.
3. Computer Vision: Object recognition, pattern matching.
4. Wireless Networks: Resource allocation, interference modeling.
5. Combinatorial Optimization: Scheduling, coding theory, cryptography.

Challenges & Open Problems

• Scalability for large graphs (millions of vertices).
• Improving approximation guarantees (best-known is $O(n / \log^2 n)$).
• Hybrid approaches combining exact and heuristic methods.

Conclusion

The Maximum Clique Problem remains a fundamental challenge in computational complexity with broad practical implications. While exact methods are limited to small graphs, heuristic and hybrid approaches enable solutions for real-world applications.

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Problem Statement

Input: A Boolean Adjacency Matrix $M$.

Answer: Find a Maximum Clique.

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:

Clique Found 1, 3, 5: Nodes 1, 3, and 5 constitute an optimal solution.

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Compile and Environment

Prerequisites

• Python ≥ 3.12

Installation

pip install aegypti

Execution

1. Clone the repository:

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

2. Run the script:

   clique -i ./benchmarks/testMatrix1
   

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

   Example Output:

   testMatrix1: Clique Found 1, 3, 5
   

   This indicates nodes 1, 3, 5 form a clique.

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Clique Size

Use the -c flag to count the nodes in the clique:

clique -i ./benchmarks/testMatrix2 -c

Output:

testMatrix2: Clique Size 4

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Command Options

Display help and options:

clique -h

Output:

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

Compute the Approximate Clique 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 polynomial factor
  -b, --bruteForce      enable comparison with the exponential-time brute-force approach
  -c, --count           calculate the size of the clique
  -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_clique command, use the following in your terminal or command prompt:

batch_clique -h

This will display the following help information:

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

Compute the Approximate Clique 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 polynomial factor
  -b, --bruteForce      enable comparison with the exponential-time brute-force approach
  -c, --count           calculate the size of the clique
  -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_clique is provided for evaluating the Algorithm using randomly generated, large sparse matrices. It supports the following options:

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

The Aegypti 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 polynomial factor
  -b, --bruteForce      enable comparison with the exponential-time brute-force approach
  -c, --count           calculate the size of the clique
  -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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License

• MIT License.