canns-ripser 0.4.4

Rust implementation of Ripser for topological data analysis, optimized for CANNS library

CANNs-Ripser

High-performance Rust implementation of Ripser for topological data analysis, optimized for the CANNS library.

🚀 Performance Highlights

CANNs-Ripser delivers significant performance improvements over the original ripser.py:

• Mean speedup: 1.13x across 54 benchmarks
• Peak speedup: Up to 1.82x on certain datasets
• Memory efficiency: 1.01x memory ratio (stable usage)
• Perfect accuracy: 100% match with ripser.py results

Top Performing Scenarios

Dataset Type	Configuration	Speedup
Random N(0,I)	d=2, n=500, maxdim=2	1.82x
Two moons	n=400, noise=0.08, maxdim=2	1.77x
Random N(0,I)	d=2, n=200, maxdim=2	1.72x
Random N(0,I)	d=3, n=500, maxdim=2	1.72x
Random N(0,I)	d=3, n=200, maxdim=2	1.66x

Overview

CANNs-Ripser is a high-performance Rust implementation of the Ripser algorithm for computing Vietoris-Rips persistence barcodes. It provides a Python interface that's fully compatible with the original ripser.py package, making it a drop-in replacement with significantly improved performance.

Features

🔥 Performance Optimizations (v0.4.0)

• Algorithmic improvements: Row-by-row edge generation, binary search for sparse matrices
• Memory optimization: Structure-of-Arrays layout, intelligent buffer reuse
• Parallel processing: Multi-threading with Rayon (enabled by default)
• Cache efficiency: K-major binomial coefficient layout, aggressive inlining
• Zero-copy operations: Minimized allocations in hot paths

🔧 Core Features

• Full Compatibility: Drop-in replacement for ripser.py with identical API
• Multiple Metrics: Support for Euclidean, Manhattan, Cosine, and custom distance metrics
• Sparse Matrices: Efficient handling of sparse distance matrices with neighbor intersection algorithms
• Cocycle Computation: Optional computation of representative cocycles
• Progress Tracking: Built-in progress bars and verbose output
• CANNs Integration: Optimized for use with the CANNs Python Library for Continuous Attractor Neural Networks

Installation

From PyPI (Recommended)

pip install canns-ripser

From Source

git clone https://github.com/Routhleck/canns-ripser.git
cd canns-ripser
pip install maturin
maturin develop --release

Quick Start

Basic Usage

import numpy as np
from canns_ripser import ripser

# Generate sample data
data = np.random.rand(100, 3)

# Compute persistence diagrams
result = ripser(data, maxdim=2)
diagrams = result['dgms']

print(f"H0: {len(diagrams[0])} features")
print(f"H1: {len(diagrams[1])} features") 
print(f"H2: {len(diagrams[2])} features")

Advanced Options

# High-performance computation with progress tracking
result = ripser(
    data, 
    maxdim=2,
    thresh=1.0,                    # Distance threshold
    coeff=2,                       # Coefficient field Z/2Z  
    do_cocycles=True,              # Compute representative cycles
    verbose=True,                  # Detailed output
    progress_bar=True,             # Show progress
    progress_update_interval=1.0   # Update every second
)

# Access results
diagrams = result['dgms']          # Persistence diagrams
cocycles = result['cocycles']      # Representative cocycles  
num_edges = result['num_edges']    # Number of edges in complex

Sparse Matrix Support

from scipy import sparse

# Create sparse distance matrix
row = [0, 1, 2]
col = [1, 2, 0] 
data = [1.0, 1.5, 2.0]
sparse_dm = sparse.coo_matrix((data, (row, col)), shape=(3, 3))

# Compute with sparse matrix (automatically detected)
result = ripser(sparse_dm, distance_matrix=True, maxdim=1)

Performance Guide

When to Expect Best Performance

• Medium to large datasets (n > 200 points)
• Higher-dimensional homology (maxdim ≥ 2)
• Moderately dense point clouds (not extremely sparse)
• Random or structured data (vs. adversarial/pathological cases)

Optimization Tips

# Enable all performance features
result = ripser(
    data,
    maxdim=2,
    thresh=2.0,        # Set reasonable threshold to limit complex size
    coeff=2,           # Z/2Z is fastest (default)
    progress_bar=False # Disable for batch processing
)

Compatibility

CANNs-Ripser maintains 100% API compatibility with ripser.py:

# These work identically
import ripser              # Original
from canns_ripser import ripser as ripser_fast  # CANNS-Ripser

result1 = ripser.ripser(data, maxdim=2)
result2 = ripser_fast(data, maxdim=2)

# Results are numerically identical
assert np.allclose(result1['dgms'][0], result2['dgms'][0])

Technical Details

Algorithmic Optimizations

• Dense edge enumeration: O(n²) row-by-row generation vs O(n³) vertex decoding
• Sparse queries: O(log k) binary search vs O(k) linear scan
• Cache-friendly data structures: SoA matrix layout, k-major binomial tables
• Zero-apparent pairs: Skip redundant column reductions in higher dimensions

Implementation Features

• Memory allocator: mimalloc for efficient small allocations
• Compilation: Link-time optimization, target-specific vectorization
• Parallel execution: Rayon-based work-stealing parallelism
• Error handling: Comprehensive validation with helpful error messages

Development

Building from Source

# Prerequisites
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
pip install maturin

# Build and install
git clone https://github.com/Routhleck/canns-ripser.git
cd canns-ripser
maturin develop --release --features parallel

# Run tests
python -m pytest tests/ -v

Running Benchmarks

cd benchmarks
python compare_ripser.py --n-points 100 --maxdim 2 --trials 5

License

Licensed under the Apache License, Version 2.0. See LICENSE for details.

Citation

If you use CANNS-Ripser in your research, please cite:

@software{canns_ripser,
  title={CANNS-Ripser: High-Performance Rust Implementation of Ripser},
  author={He, Sichao},
  url={https://github.com/Routhleck/canns-ripser},
  year={2025}
}

Acknowledgments

• Ulrich Bauer: Original Ripser algorithm and C++ implementation
• Christopher Tralie & Nathaniel Saul: ripser.py Python implementation
• Rust community: Amazing ecosystem of high-performance libraries

Related Projects

• Ripser: Original C++ implementation
• ripser.py: Python bindings for Ripser
• CANNS: Continuous Attractor Neural Networks
• scikit-tda: Topological Data Analysis in Python