lzcomplexity 0.9.13

LempelZiv-76 complexity engine

lzcomplexity: an entropy measures library

lzcomplexity

lzcomplexity is a high-performance C++ library developed for complexity analysis using entropic metrics such as entropy density, effective measure complexity, and informational distance. The algorithms used to estimate the metrics employing Lempel-Ziv factorization (LZ76) [1]. The library provides efficient implementations for analyzing time series data, with applications in information theory, signal processing, and neuroscience.

Overview

The Lempel-Ziv complexity is a non-parametric measure of algorithmic complexity that quantifies the rate at which new patterns appear in a sequence. Unlike Shannon entropy, which assumes statistical stationarity and independence, LZ complexity captures the sequential structure and can estimate the entropy rate of ergodic sources asymptotically [2].

Key Features

• LZ76 Factorization: Efficient computation of Lempel-Ziv complexity using the CaPS (Cache-friendly Parallel Suffix array) algorithm [3]
• Entropy Density: Normalized entropy rate estimation based on LZ factorization
• Effective Complexity: Effective measure complexity measures quantifying statistical dependencies between sequence halves
• Information Distance: Normalized compression-based distance metrics for sequence comparison
• Parallel Processing: Multi-threaded computation with support for multiple backends (OpenMP, Intel TBB, Cilk, or sequential fallback)

Theoretical Background

The LZ76 complexity c(S) of a sequence S of length n is defined as the minimum number of factors in a factorization where each factor is either:

1. A symbol not previously seen, or
2. The longest substring that has appeared earlier in the sequence

For a random sequence over an alphabet of size k, the expected complexity grows as n / log_k(n). The normalized entropy density h is estimated as:

h ≈ c(S) · log_k(n) / n

which converges to the true entropy rate for ergodic sources as $n → \infty$ [2].

Prerequisites

• CMake version >= 3.5
• C++20 compatible compiler:
  • apple-clang >= 14
  • clang >= 17
  • GNU >= 9.4
• At least one parallel backend (optional but recommended):
  • OpenMP (default, widely available)
  • Intel oneTBB (bundled or system installation)
  • OpenCilk or Intel Cilk Plus
  • Falls back to sequential execution if none available

Prepare the Local Workspace

The project uses external submodules:

• oneTBB: Intel's Threading Building Blocks for parallel computation (optional)
• nanobind: Small binding library for C++/Python interoperability for the Python bindings

1. Initialize the submodules:

git submodule init

2. Clone the submodules into your local directory:

git submodule update --recursive

3. Apply the oneTBB patch:

patch external/tbb/CMakeLists.txt patches/tbb.patch 

Build and Install

1. Create a build directory and navigate to it:

mkdir build && cd build

2. Configure the build process using CMake:

cmake -DCMAKE_BUILD_TYPE=Release ..

3. Build and install the library:

make install

Documentation

After installation, access the command-line documentation via man pages:

man lzcomplexity
man lzdistance

To disable man page installation, use -DLZ_INSTALL_MAN=OFF during CMake configuration.

CMake Options

Build Configuration

Option	Default	Description
LZ_SHARE	ON	Build as shared library (.so/.dylib)
LZ_ONLY_LIBS	OFF	Build only libraries (lzcore, lzapp, lzdist) without executables
LZ_ONLY_CORE	OFF	Build only the core library
LZ_APP	ON	Build the lzcomplexity standalone application
LZ_DISTANCE	ON	Build the lzdistance standalone application
LZ_INSTALL_MAN	ON	Install man pages for command-line tools
BUILD_PYTHON	OFF	Enable Python bindings via nanobind

Parallel Backend Configuration

The library supports multiple parallel computing backends. By default, it auto-detects the best available backend.

Option	Default	Description
LZ_PARALLEL_BACKEND	AUTO	Parallel backend selection: AUTO, OPENMP, TBB, CILK, THREADS
LZ_PARALLEL_FORCE	OFF	Force the selected backend (fail if not found)
BUILTIN_TBB	OFF	Use bundled oneTBB instead of system installation

Backend Priority (AUTO mode):

1. OpenMP - Default choice, widely available on most systems
2. TBB - Intel Threading Building Blocks, excellent for fine-grained parallelism
3. Cilk - OpenCilk or Intel Cilk Plus, good for divide-and-conquer algorithms
4. Threads - Sequential fallback using std::thread utilities only

Examples:

# Auto-detect best available backend (default)
cmake -B build

# Force OpenMP backend
cmake -B build -DLZ_PARALLEL_BACKEND=OPENMP

# Force TBB with bundled version
cmake -B build -DLZ_PARALLEL_BACKEND=TBB -DBUILTIN_TBB=ON

# Force Cilk backend (requires OpenCilk compiler)
cmake -B build -DLZ_PARALLEL_BACKEND=CILK

# Sequential only (no parallelism)
cmake -B build -DLZ_PARALLEL_BACKEND=THREADS

macOS Note: For OpenMP on macOS, install libomp via Homebrew:

brew install libomp

Debug and Sanitizer Options

Option	Default	Description
ASAN	OFF	Enable sanitizers for debugging (Clang only)
ENABLE_ADDRESS_SANITIZER	OFF	Detect memory errors (buffer overflows, use-after-free)
ENABLE_MEMORY_SANITIZER	OFF	Detect uninitialized memory reads
ENABLE_UNDEFINED_SANITIZER	OFF	Detect undefined behavior

Example Usage

C++ Example

#include <lz/lempelziv.h>
#include <iostream>

int main() {
    // Create a symbolic sequence
    lz::sequence seq = "ABRACADABRA";
    
    // Compute LZ76 complexity (number of factors)
    auto complexity = lz::lz76Factorization(seq);
    
    // Compute normalized entropy density
    auto entropy = lz::lz76EntropyDensity(seq);
    
    // Compute effective complexity (excess entropy)
    auto effective = lz::lz76EffectiveComplexity(seq);
    
    std::cout << "LZ76 Complexity: " << complexity << std::endl;
    std::cout << "Entropy density: " << entropy << std::endl;
    std::cout << "Effective complexity: " << effective << std::endl;
    
    return 0;
}

Python Example

import lzcomplexity as lz

# Analyze a symbolic sequence
seq = "ABRACADABRA"
result = lz.lz76(seq)

print(f"LZ76 Complexity: {result.complexity}")
print(f"Entropy density: {result.entropy}")
print(f"Effective complexity: {result.effective_complexity}")

References

1. Lempel, A., & Ziv, J. (1976). On the complexity of finite sequences. IEEE Transactions on Information Theory, 22(1), 75-81.

2. Kontoyiannis, I., Algoet, P. H., Suhov, Y. M., & Wyner, A. J. (1998). Nonparametric entropy estimation for stationary processes and random fields, with applications to English text. IEEE Transactions on Information Theory, 44(3), 1319-1327.

3. Khan, J., Rubel, T., Dhulipala, L., Molloy, E., & Patro, R. (2023). Fast, Parallel, and Cache-Friendly Suffix Array Construction. arXiv preprint arXiv:2305.07024.

Citation

If you use this library in your research, please cite:

@software{lzcomplexity_2025, 
  title={lzcomplexity: an entropy measurement library},
  author={Efren Aragon-Perez},
  url={https://github.com/efrenaragon96/LempelZiv}, 
  year={2025} 
}

License

This project is licensed under the MIT License - see the LICENSE file for details.

Contributing

Contributions are welcome! Please feel free to submit issues, feature requests, or pull requests.