tsne-h2pack: High-Performance t-SNE with H2Pack Acceleration

A high-performance, sklearn-compatible implementation of t-SNE with H2Pack acceleration for large-scale dimensionality reduction.

Features

• Drop-in sklearn replacement: Same API as sklearn.manifold.TSNE
• Fast on large datasets: the repulsive forces are computed in O(N) with an H² matrix (H2Pack). On the same k-NN graph and P matrix, and at matched embedding quality, the optimization phase is 2.0–3.4× faster than FIt-SNE on one thread and 4.3–8.8× faster on eight (Zheng 10x, 50K–1M points; see benchmarks/results/REPORT.md)
• Multiple k-NN methods: PyNNDescent (default), exact, ball tree, FAISS, and Annoy; or pass your own k-NN graph with metric='precomputed'
• Validated at scale: 1M points in 2.5 minutes end-to-end (k-NN included) on an 8-core laptop
• Native performance: OpenMP parallelization on Linux and macOS

Quick Start

Installation

pip install tsne-h2pack

Binary wheels are published for Linux x86-64 (manylinux) and macOS Apple Silicon (macOS 14+), CPython 3.9–3.13. On other platforms pip builds from the source distribution, which needs a C compiler and OpenBLAS — see Prerequisites.

The GitHub repository is not public yet; the complete C and Python source is in the source distribution (pip download --no-binary :all: --no-deps tsne-h2pack). To install from a source checkout:

git clone --recursive https://github.com/xinxing02/tsne-h2pack-python.git
cd tsne-h2pack-python
pip install .

Basic Usage

from tsne_h2pack import TSNE
import numpy as np

# Generate sample data
X = np.random.randn(1000, 50)

# Same API as sklearn
tsne = TSNE(n_components=2, perplexity=30, random_state=42)
Y = tsne.fit_transform(X)

print(f"Embedding shape: {Y.shape}")

Advanced Usage

Large Datasets

from tsne_h2pack import TSNE

# For large datasets (>50K samples)
tsne = TSNE(
    n_components=2,
    perplexity=30,
    method='h2pack',         # Use H2Pack acceleration
    knn_method='pynndescent', # Fast approximate k-NN
    n_jobs=8,                # Use 8 CPU cores
    verbose=1
)

Y = tsne.fit_transform(X_large)

k-NN Methods

Choose the best k-NN method for your dataset size:

# Small datasets (<5K): exact k-NN
tsne = TSNE(knn_method='exact', n_jobs=4)

# Medium datasets (5K-50K): PyNNDescent (default)
tsne = TSNE(knn_method='pynndescent')

# Large datasets (>50K): FAISS
tsne = TSNE(knn_method='faiss')

Available k-NN methods:

• 'pynndescent' - Fast approximate (default, ~96% accuracy)
• 'exact' - sklearn brute-force (100% accurate, slow)
• 'balltree' - sklearn ball tree (100% accurate, medium speed)
• 'faiss' - Facebook FAISS (very fast approximate)
• 'annoy' - Spotify Annoy (memory-efficient approximate)

Install optional k-NN methods as extras:

pip install 'tsne-h2pack[knn]'           # All methods
pip install 'tsne-h2pack[pynndescent]'   # Or a single method
pip install 'tsne-h2pack[faiss]'
pip install 'tsne-h2pack[annoy]'

(From a source checkout, replace tsne-h2pack with ..) Below 10,000 samples the default 'pynndescent' falls back to exact brute-force search automatically.

Parameters

All sklearn.manifold.TSNE parameters are supported:

TSNE(
    n_components=2,          # Output dimensions
    perplexity=30.0,         # Balance local/global structure
    early_exaggeration=12.0, # Exaggeration factor for the first 250 iterations
    learning_rate='auto',    # 'auto' = max(n_samples / 12, 200), or a float
    max_iter=1000,           # Maximum iterations
    random_state=None,       # Random seed
    init='random',           # Initialization ('random' only)
    metric='euclidean',      # 'euclidean', or 'precomputed' (sparse k-NN distances)
    method='h2pack',         # 'h2pack' or 'exact'
    n_jobs=None,             # Number of parallel jobs
    knn_method='pynndescent', # k-NN method (see above)
    verbose=0                # Verbosity level
)

metric='precomputed' takes a SciPy sparse matrix of k-NN distances (as sklearn.manifold.TSNE does) and skips the neighbor search, so several runs or several libraries can share one graph. Each row needs more than perplexity neighbors; 3 * perplexity is the usual choice.

H2Pack-specific parameters:

• h2_tol (float, default=1e-2): relative accuracy of the H² approximation of the repulsive kernel. The default matches FIt-SNE's embedding quality (KL divergence, neighbor preservation); tighter tolerances cost time without measurable gain.
• h2_rebuild_freq (int, default=3): the H² matrix is rebuilt every this many iterations after early exaggeration; the repulsive force is reused in between. 2 is slightly more accurate and slower; 6 and above is visibly less accurate.
• h2_rebuild_freq_early (int, default=10): rebuild frequency during early exaggeration.
• h2_leaf_size (int, default=100): points per leaf of the H² tree. Only for tuning experiments; the default was chosen for the low rank (~10) of the kernel at h2_tol=1e-2.

Installation Details

Prerequisites

macOS (Apple Silicon):

brew install gcc openblas

Linux:

# Ubuntu/Debian
sudo apt-get install gcc libopenblas-dev liblapack-dev liblapacke-dev

# RHEL/CentOS
sudo yum install gcc openblas-devel lapack-devel

Windows: Not supported. Use WSL2 (Windows Subsystem for Linux).

Building from Source

git clone --recursive https://github.com/xinxing02/tsne-h2pack-python.git
cd tsne-h2pack-python
pip install .

If you cloned without --recursive, fetch the H2Pack submodule:

git submodule update --init --recursive

Platform Support

Troubleshooting

Common Issues

ImportError: No module named 'pynndescent'

pip install pynndescent
# or use exact k-NN: TSNE(knn_method='exact')

macOS: Build fails

brew install gcc openblas

Backend not available

pip install --force-reinstall --no-deps .

For more issues, see docs/TROUBLESHOOTING.md.

Documentation

• CHANGELOG.md - Version history
• CLAUDE.md - Development guide (technical details)
• docs/TROUBLESHOOTING.md - Detailed troubleshooting guide
• docs/PACKAGING_GUIDE.md - Package maintainer guide

For Package Maintainers

Building Distribution Packages

# Using automated build script
./build_package.sh

# Or manual build
python -m build

Publishing to PyPI

See docs/PACKAGING_GUIDE.md for the full release workflow.

Examples

See the examples/ directory:

# Basic demo (configurable via --n-samples)
python examples/basic_example.py

# Full MNIST (60K samples)
python examples/basic_example.py --n-samples 60000

# Benchmark suite (tsne-h2pack vs FIt-SNE vs openTSNE vs UMAP): see benchmarks/README.md
python benchmarks/sweep.py --dry-run

Citation & License

Citation

If you use tsne-h2pack in your research, please cite:

@software{tsne_h2pack,
  title = {tsne-h2pack: High-Performance t-SNE with H2Pack Acceleration},
  author = {Xing, Xin},
  year = {2026},
  url = {https://github.com/xinxing02/tsne-h2pack-python}
}

And the H2Pack library:

@article{huang2020toms,
    title = { {H2Pack}: High-performance \textit{{H}} $^{\textrm{2}}$ Matrix Package for Kernel Matrices Using the Proxy Point Method },
    journal = {ACM Transactions on Mathematical Software},
    author = {Huang, Hua and Xing, Xin and Chow, Edmond},
    year = {2020},
    month = {Dec},
    volume = {47},
    pages = {1--29},
    doi = {10.1145/3412850},
    issn = {0098-3500, 1557-7295},
    number = {1},
}

License

MIT License - see LICENSE file for details.

Version: 3.1.0 Status: Production-ready (PyPI release pending)