# Varela: Minimum Vertex Cover Solver

![Honoring the Memory of Felix Varela y Morales (Cuban Catholic priest and independence leader)](docs/varela.jpg)

This work builds upon [New Insights and Developments on the Unique Games Conjecture](https://www.researchgate.net/publication/389326369_New_Insights_and_Developments_on_the_Unique_Games_Conjecture).

---

# The Minimum Vertex Cover Problem

The **Minimum Vertex Cover (MVC)** problem is a classic optimization problem in computer science and graph theory. It involves finding the smallest set of vertices in a graph that **covers** all edges, meaning at least one endpoint of every edge is included in the set.

## Formal Definition

Given an undirected graph $G = (V, E)$, a **vertex cover** is a subset $V' \subseteq V$ such that for every edge $(u, v) \in E$, at least one of $u$ or $v$ belongs to $V'$. The MVC problem seeks the vertex cover with the smallest cardinality.

## Importance and Applications

- **Theoretical Significance:** MVC is a well-known NP-hard problem, central to complexity theory.
- **Practical Applications:**
  - **Network Security:** Identifying critical nodes to disrupt connections.
  - **Bioinformatics:** Analyzing gene regulatory networks.
  - **Wireless Sensor Networks:** Optimizing sensor coverage.

## Related Problems

- **Maximum Independent Set:** The complement of a vertex cover.
- **Set Cover Problem:** A generalization of MVC.

---

## Problem Statement

Input: A Boolean Adjacency Matrix $M$.

Answer: Find a Minimum Vertex Cover.

### 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](http://dimacs.rutgers.edu/Challenges) 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:_

Vertex Cover Found `1, 2, 3`: Nodes `1`, `2`, and `3` constitute an optimal solution.

---

# Approximate Vertex Cover Algorithm Analysis

## Overview

This algorithm computes an approximate vertex cover for an undirected graph in polynomial time. It utilizes edge covers, bipartite matching, and König's theorem to achieve an approximation ratio of at most 1.75. The algorithm is implemented using the NetworkX library in Python.

## Runtime Analysis

The runtime complexity of this algorithm can be broken down as follows:

1. Removing isolated nodes: $O(n)$, where $n$ is the number of nodes.
2. Finding minimum edge cover: $O(n^3)$, using the Edmonds-Gallai decomposition.
3. Creating subgraph: $O(m)$, where $m$ is the number of edges in the minimum edge cover.
4. Finding connected components: $O(n + m)$.
5. For each connected component:
   - Creating subgraph: $O(n_i + m_i)$, where $n_i$ and $m_i$ are the number of nodes and edges in the component.
   - Finding maximum matching (Hopcroft-Karp): $O(\sqrt{n_i} * m_i)$.
   - Computing vertex cover from matching: $O(n_i + m_i)$.

The dominant factor in the runtime is the minimum edge cover computation, which has a cubic time complexity. Therefore, the overall time complexity of the algorithm is $O(n^3)$.

## Correctness

The algorithm's correctness is based on the following principles:

1. It handles edge cases (empty graph or no edges) correctly.
2. Isolated nodes are removed as they don't contribute to the vertex cover.
3. The minimum edge cover ensures that all edges are covered.
4. König's theorem guarantees that for bipartite graphs, the size of a maximum matching equals the size of a minimum vertex cover.
5. The algorithm processes each connected component separately, ensuring correctness for disconnected graphs.
6. The algorithm concludes with a verification of the calculated vertex cover. If the cover is invalid, a 2-approximation algorithm is executed on the uncovered portion of the graph.

While this algorithm doesn't guarantee an optimal solution, it provides an approximation with a ratio of at most 1.75, which is theoretically sound for the vertex cover problem.

---

# Compile and Environment

## Prerequisites

- Python ≥ 3.10

## Installation

```bash
pip install varela
```

## Execution

1. Clone the repository:

   ```bash
   git clone https://github.com/frankvegadelgado/varela.git
   cd varela
   ```

2. Run the script:

   ```bash
   approx -i ./benchmarks/testMatrix1
   ```

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

   **Example Output:**

   ```
   testMatrix1: Vertex Cover Found 1, 2, 3
   ```

   This indicates nodes `1, 2, 3` form a vertex cover.

---

## Vertex Cover Size

Use the `-c` flag to count the nodes in the vertex cover:

```bash
approx -i ./benchmarks/testMatrix2 -c
```

**Output:**

```
testMatrix2: Vertex Cover Size 7
```

---

# Command Options

Display help and options:

```bash
approx -h
```

**Output:**

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

Estimating the Minimum Vertex Cover with an approximation factor of at most 1.75 encoded for undirected graph in DIMACS format.

options:
  -h, --help            show this help message and exit
  -i INPUTFILE, --inputFile INPUTFILE
                        input file path
  -a, --approximation   enable comparison with another polynomial-time approximation approach within a factor of at most 2
  -b, --bruteForce      enable comparison with the exponential-time brute-force approach
  -c, --count           calculate the size of the vertex cover
  -v, --verbose         anable verbose output
  -l, --log             enable file logging
  --version             show program's version number and exit
```

---

# 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:

```bash
batch_approx -h
```

This will display the following help information:

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

Estimating the Minimum Vertex Cover with an approximation factor of at most 1.75 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 another polynomial-time approximation approach within a factor of at most 2
  -b, --bruteForce      enable comparison with the exponential-time brute-force approach
  -c, --count           calculate the size of the vertex cover
  -v, --verbose         anable verbose output
  -l, --log             enable file logging
  --version             show program's version number and exit
```

---

# 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:

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

The Varela 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 another polynomial-time approximation approach within a factor of at most 2
  -b, --bruteForce      enable comparison with the exponential-time brute-force approach
  -c, --count           calculate the size of the vertex cover
  -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
```

---

# Code

- Python implementation by **Frank Vega**.

---

# Complexity

```diff
+ This result contradicts the Unique Games Conjecture, suggesting that many optimization problems may admit better solutions, revolutionizing theoretical computer science.
```

---

# License

- MIT License.
