Tapkee
Efficient dimensionality reduction library with a focus on spectral methods.
Tapkee implements over 20 dimensionality reduction algorithms and provides a simple Python interface to all of them.
Installation
pip install tapkee
Usage
import numpy as np
from matplotlib import pyplot as plt
import tapkee
# Generate a Swiss roll dataset
n = 2000
t = 1.5 * np.pi * (1 + 2 * np.random.rand(n))
x, y, z = t * np.cos(t), 30 * np.random.rand(n), t * np.sin(t)
data = np.vstack([x, y, z]) # 3 features, n samples
# Unroll with Locally Linear Embedding
embedding = tapkee.embed(data, method="lle", num_neighbors=12)
plt.scatter(embedding[:, 0], embedding[:, 1], c=t, cmap="Spectral", s=5)
plt.title("Swiss roll unrolled with LLE")
plt.show()
Supported methods
| Method | method= |
Key parameters |
|---|---|---|
| Isomap | "isomap" |
num_neighbors |
| Landmark Isomap | "l-isomap" |
num_neighbors, landmark_ratio |
| Diffusion Maps | "dm" |
gaussian_kernel_width, diffusion_map_timesteps |
| Laplacian Eigenmaps | "la" |
num_neighbors, gaussian_kernel_width |
| Locally Linear Embedding | "lle" |
num_neighbors |
| Hessian LLE | "hlle" |
num_neighbors |
| Local Tangent Space Alignment | "ltsa" |
num_neighbors |
| Linear LTSA | "lltsa" |
num_neighbors |
| Locality Preserving Projections | "lpp" |
num_neighbors, gaussian_kernel_width |
| Neighborhood Preserving Embedding | "npe" |
num_neighbors |
| PCA | "pca" |
|
| Kernel PCA | "kpca" |
gaussian_kernel_width |
| Factor Analysis | "fa" |
max_iteration, fa_epsilon |
| Random Projection | "ra" |
|
| MDS | "mds" |
|
| Landmark MDS | "l-mds" |
landmark_ratio |
| t-SNE | "t-sne" |
sne_perplexity, sne_theta |
| Stochastic Proximity Embedding | "spe" |
spe_global_strategy, spe_num_updates, spe_tolerance |
| Manifold Sculpting | "manifold_sculpting" |
num_neighbors, squishing_rate, max_iteration |
All methods accept target_dimension (default: 2). Neighbor-based methods accept num_neighbors (default: 5).
Parameters
| Parameter | Type | Description |
|---|---|---|
target_dimension |
int | Output dimensionality |
num_neighbors |
int | Number of neighbors for local methods |
gaussian_kernel_width |
float | Width of the Gaussian kernel |
landmark_ratio |
float | Ratio of landmark points (0 to 1) |
max_iteration |
int | Maximum iterations for iterative methods |
diffusion_map_timesteps |
int | Number of timesteps for Diffusion Maps |
sne_perplexity |
float | Perplexity for t-SNE |
sne_theta |
float | Angle for Barnes-Hut approximation in t-SNE |
squishing_rate |
float | Rate for Manifold Sculpting |
spe_global_strategy |
bool | Use global strategy for SPE |
spe_num_updates |
int | Number of SPE updates |
spe_tolerance |
float | SPE convergence tolerance |
nullspace_shift |
float | Regularizer for eigenproblems |
klle_shift |
float | KLLE regularizer |
fa_epsilon |
float | Factor Analysis convergence epsilon |
check_connectivity |
bool | Check graph connectivity |
Links
Citation
If you use Tapkee in a publication, please cite:
Sergey Lisitsyn, Christian Widmer, Fernando J. Iglesias Garcia. Tapkee: An Efficient Dimension Reduction Library. Journal of Machine Learning Research, 14: 2355-2359, 2013.
License
BSD 3-Clause
1 maintainer
Metadata
1 maintainer
Release files for tapkee 1.4.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| tapkee-1.4.0.tar.gz | 83.4 kB | Details |
Built distributions (wheels)
| File | Reset | |||
|---|---|---|---|---|
| tapkee-1.4.0-cp314-cp314-win_amd64.whl | CPython 3.14 | CPython 3.14 | Windows x86-64 | Details |
| tapkee-1.4.0-cp314-cp314-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl | CPython 3.14 | CPython 3.14 | Linux glibc 2.28+ x86-64, Linux glibc 2.27+ x86-64 | Details |
| tapkee-1.4.0-cp314-cp314-macosx_26_0_arm64.whl | CPython 3.14 | CPython 3.14 | macOS 26.0+ ARM64 | Details |
| tapkee-1.4.0-cp313-cp313-win_amd64.whl | CPython 3.13 | CPython 3.13 | Windows x86-64 | Details |
| tapkee-1.4.0-cp313-cp313-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl | CPython 3.13 | CPython 3.13 | Linux glibc 2.28+ x86-64, Linux glibc 2.27+ x86-64 | Details |
| tapkee-1.4.0-cp313-cp313-macosx_26_0_arm64.whl | CPython 3.13 | CPython 3.13 | macOS 26.0+ ARM64 | Details |
| tapkee-1.4.0-cp312-cp312-win_amd64.whl | CPython 3.12 | CPython 3.12 | Windows x86-64 | Details |
| tapkee-1.4.0-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl | CPython 3.12 | CPython 3.12 | Linux glibc 2.28+ x86-64, Linux glibc 2.27+ x86-64 | Details |
| tapkee-1.4.0-cp312-cp312-macosx_26_0_arm64.whl | CPython 3.12 | CPython 3.12 | macOS 26.0+ ARM64 | Details |
| tapkee-1.4.0-cp311-cp311-win_amd64.whl | CPython 3.11 | CPython 3.11 | Windows x86-64 | Details |
| tapkee-1.4.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl | CPython 3.11 | CPython 3.11 | Linux glibc 2.28+ x86-64, Linux glibc 2.27+ x86-64 | Details |
| tapkee-1.4.0-cp311-cp311-macosx_26_0_arm64.whl | CPython 3.11 | CPython 3.11 | macOS 26.0+ ARM64 | Details |
Total release size: 120.4 MB
Release files / tapkee-1.4.0.tar.gz
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