mendive 0.0.7

Solve the Claw-Free Problem for an undirected graph encoded in DIMACS format.

Mendive: Claw-Free Solver

This work builds upon Mendive: Fast Claw Detection in Sparse Graphs.

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Claw-Free Graph Problem

The Claw-Free Graph Problem is a fundamental decision problem in graph theory. Given an undirected graph, the problem asks whether the graph is claw-free – meaning it contains no induced subgraph isomorphic to a claw (the complete bipartite graph $K_{1,3}$). A claw consists of:

• A central vertex connected to three independent vertices (leaves)
• No edges between the leaves (forming a star with three rays)

This problem is important for various reasons:

• Graph Analysis: Serves as a foundation for complex graph algorithms with applications in network analysis, combinatorial optimization, and scheduling.
• Computational Complexity: A benchmark for efficient graph property verification. The brute-force approach checks all vertex quadruplets ($O(n^4)$), while optimized algorithms:
  • Achieve $O(n^{3})$ via neighbor independence checks
  • Reach subcubic time ($O(n^{ω})$) using matrix multiplication (where $ω < 2.373$)
• Structural Implications: Claw-free graphs exhibit special properties (e.g., perfect graph connections, polyhedral characterization).

Understanding this problem is essential for graph algorithm design and complexity theory.

Problem Statement

Input: A Boolean Adjacency Matrix $M$.

Question: Does $M$ contain no claws?

Answer: True / False

Example Instance: 5 x 5 matrix

	c1	c2	c3	c4	c5
r1	0	0	1	1	1
r2	0	0	0	0	0
r3	1	0	0	0	1
r4	1	0	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 1 4
e 2 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:

Claw Found (1, {3, 4, 5}): In Column 1 (Center) and Rows 3 & 4 & 5 (Leaves)

Claw Detection Algorithm Overview

Algorithm Description

This algorithm, implemented as find_claw_coordinates, detects claws (a $K_{1,3}$ subgraph with one central vertex connected to three non-adjacent leaf vertices) in an undirected graph. It leverages the aegypti package (developed by the same author), which provides a linear-time triangle detection algorithm claimed to run in $O(n + m)$ time, where $n$ is the number of nodes and $m$ is the number of edges. The claw detection process adapts this by applying triangle finding to the complement of each node’s neighbor-induced subgraph.

Key Steps:

1. Neighbor Subgraph and Complement:

   • For each node $i$ with degree at least 3, extract the induced subgraph of its neighbors.
   • Compute the complement of this subgraph, where edges represent the absence of connections in the original graph.

2. Triangle Finding with Aegypti:

   • Use the aegypti package’s find_triangle_coordinates function to detect triangles in the complement subgraph.
   • A triangle in the complement indicates three neighbors of $i$ that form an independent set, which, combined with $i$, forms a claw.
   • The aegypti algorithm employs Depth-First Search (DFS) tailored for this subgraph, achieving efficiency based on its claimed $O(n' + m')$ complexity, where $n'$ and $m'$ are the nodes and edges in the complement subgraph.

3. Claw Storage:

   • Store detected claws as frozensets, each containing the center $i$ and the three leaf vertices.
   • The storage time is $O(c)$, where $c$ is the number of claws found.

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Runtime Analysis

The runtime of the find_claw_coordinates algorithm depends on the graph’s structure, particularly the maximum degree $\Delta$, and varies based on the first_claw parameter.

Notation:

• $n = |V|$: Number of vertices.
• $m = |E|$: Number of edges.
• $\text{deg}(i)$: Degree of vertex $i$.
• $\Delta$: Maximum degree in the graph.
• $c$: Number of claws detected.
• For each node $i$, the complement subgraph has $n' = \text{deg}(i)$ vertices and up to $m' \leq {\text{deg}(i) \choose 2}$ edges.

Case 1: first_claw=True (Find One Claw)

• Process: Iterates over nodes until a claw is found, checking each node’s neighbor complement for a triangle.
• Per Node $i$:
  • Subgraph and complement construction: $O(\text{deg}(i)^2)$.
  • aegypti triangle detection: $O(\text{deg}(i)^2)$ for the complement subgraph.
  • Total per node: $O(\text{deg}(i)^2)$.
• Total:
  • Worst case (no claws): $\sum_i O(\text{deg}(i)^2) \leq \Delta \cdot \sum_i \text{deg}(i) = \Delta \cdot 2m = O(m \cdot \Delta)$.
  • Best case (claw found early): $O(\text{deg}(i)^2)$ for the first node with a claw.
• Conclusion: $O(m \cdot \Delta)$, efficient for sparse graphs ($\Delta = O(1)$), but not linear in $n + m$ for dense graphs.

Case 2: first_claw=False (List All Claws)

• Process: Iterates over all nodes, finding all triangles in each complement subgraph.
• Per Node $i$:
  • Same construction cost: $O(\text{deg}(i)^2)$.
  • aegypti lists all triangles: $O(\text{deg}(i)^2)$ plus output time for each triangle.
  • Claw formation: $O(1)$ per triangle, up to ${\text{deg}(i) \choose 3}$ triangles.
• Total:
  • Base cost: $\sum_i O(\text{deg}(i)^2) = O(m \cdot \Delta)$.
  • Output cost: $O(c)$, where $c$ is the number of claws (up to $\sum_i {\text{deg}(i) \choose 3}$, potentially $O(n^3)$ in dense graphs).
• Conclusion: $O(m \cdot \Delta + c)$, output-sensitive, with runtime dominated by $c$ in graphs with many claws.

Special Case: Claw-Free Graphs

• If no claws exist ($c = 0$), the runtime simplifies to $O(m \cdot \Delta)$ for both cases, as no additional output processing is needed.
• This matches the efficiency of triangle detection in the absence of claws.

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Impact of the Algorithm

This claw detection algorithm, built on the aegypti package, has significant implications:

1. Leveraging Aegypti’s Innovation:

   • The aegypti algorithm’s claimed $O(n + m)$ triangle detection (potentially challenging the sparse triangle hypothesis, $O(m^{4/3})$) enables efficient claw finding per node.
   • Its availability via pip install aegypti makes it accessible for practical use.

2. Practical Applications:

   • Useful in network analysis (e.g., social networks, bioinformatics) to identify claw-like structures.
   • Integrates seamlessly with NetworkX, enhancing graph processing workflows.

3. Theoretical Significance:

   • If aegypti’s linear-time claim holds against 3SUM-hard instances, this algorithm could contribute to breakthroughs in graph theory, influencing related problems like independent set detection.
   • The degree-dependent runtime ($O(m \cdot \Delta)$) suggests it’s optimized for sparse graphs, aligning with real-world networks.

4. Limitations:

   • Not strictly linear-time ($O(n + m)$) due to $\Delta$-dependence, limiting scalability in dense graphs.
   • Listing all claws can be slow if $c$ is large, reflecting the output-sensitive nature.

In summary, this algorithm extends the aegypti breakthrough to claw detection, offering a practical tool with theoretical promise. Further testing on diverse graphs could solidify its impact, especially if aegypti’s claims are validated.

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Compile and Environment

Install Python >=3.12.

Install Mendive's Library and its Dependencies with:

pip install mendive

Execute

1. Go to the package directory to use the benchmarks:

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

2. Execute the script:

claw -i .\benchmarks\testMatrix1

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

The console output will display:

testMatrix1: Claw Found (1, {3, 4, 5})

which implies that the Boolean adjacency matrix mendive\benchmarks\testMatrix1 contains a claw combining the nodes (1, {3, 4, 5}) with center 1 and leaves 3, 4, 5.

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Find and Count All Claws

The -a flag enables the discovery of all claws within the graph.

Example:

claw -i .\benchmarks\testMatrix2 -a

Output:

testMatrix2: Claws Found (1, {6, 11, 12}); (1, {8, 9, 11}); (2, {6, 8, 9}); (1, {4, 6, 8}); (9, {2, 3, 5}); (1, {6, 8, 9}); (1, {3, 6, 12}); (1, {8, 9, 12}); (1, {3, 8, 12}); (2, {6, 8, 11}); (11, {2, 3, 5}); (2, {6, 9, 11}); (5, {8, 9, 11}); (1, {2, 3, 12}); (1, {6, 8, 11}); (1, {8, 11, 12}); (1, {9, 11, 12}); (1, {4, 6, 12}); (1, {4, 8, 12}); (1, {6, 9, 12}); (4, {2, 3, 5}); (1, {6, 9, 11}); (2, {8, 9, 11}); (2, {4, 6, 8}); (1, {6, 8, 12}); (1, {3, 6, 8})

When multiple claws exist, the output provides a list of their vertices.

Similarly, the -c flag counts all claws in the graph.

Example:

claw -i .\benchmarks\testMatrix2 -c

Output:

testMatrix2: Claws Count 26

Runtime Analysis:

We employ the same algorithm used to solve the claw-free problem.

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Command Options

To display the help message and available options, run the following command in your terminal:

claw -h

This will output:

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

Solve the Claw-Free Problem for an undirected graph encoded in DIMACS format.

options:
  -h, --help            show this help message and exit
  -i INPUTFILE, --inputFile INPUTFILE
                        input file path
  -a, --all             identify all claws
  -b, --bruteForce      compare with a brute-force approach using matrix multiplication
  -c, --count           count the total amount of claws
  -v, --verbose         anable verbose output
  -l, --log             enable file logging
  --version             show program's version number and exit

This output describes all available options.

The Mendive Testing Application

A command-line tool, test_claw, has been developed for testing algorithms on randomly generated, large sparse matrices. It accepts the following options:

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

The Mendive 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, --all             identify all claws
  -b, --bruteForce      compare with a brute-force approach using matrix multiplication
  -c, --count           count the total amount of claws
  -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

This tool is designed to benchmark algorithms for sparse matrix operations.

It generates random square matrices with configurable dimensions (-d), sparsity levels (-s), and number of tests (-n). While a comparison with a brute-force matrix multiplication approach is available, it's recommended to avoid this for large datasets due to performance limitations. Additionally, the generated matrix can be written to the current directory (-w), and verbose output or file logging can be enabled with the (-v) or (-l) flag, respectively, to record test results.

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Code

• Python code by Frank Vega.

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Complexity

+ This algorithm provides multiple of applications to other computational problems in combinatorial optimization and computational geometry.

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License

• MIT.