Dimensionality Reduction Python Packages

umap-learn

Uniform Manifold Approximation and Projection

opentsne

Extensible, parallel implementations of t-SNE

minisom

:red_circle: MiniSom is a minimalistic implementation of the Self Organizing Maps

scikit-fda

Functional Data Analysis Python package

pymorton

A lightweight and efficient Python Morton encoder with support for geo-hashing

pymde

Minimum-distortion embedding with PyTorch

phate

PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.

palantir

Single cell trajectory detection

torchdr

TorchDR - PyTorch Dimensionality Reduction

xeofs

Comprehensive EOF analysis in Python with xarray: A versatile, multidimensional, and scalable tool for advanced climate data analysis

sphereql

Project high-dimensional embeddings onto a 3D sphere for fast semantic search, spatial queries, category-aware exploration, and interactive visualization.

ivis

Dimensionality reduction in very large datasets using Siamese Networks

fabba

An efficient symbolic time series approximation with ABBA.

adnmtf

Non-Negative Matrix and Tensor Factorizations

robustmodelmaker

A reproducible model-building pipeline for small-to-medium scientific datasets

driada

Dimensionality Reduction for Integrated Activity Data Analysis

chemplot

A python package for chemical space visualization.

topometry

Systematically learn and evaluate the latent geometry of high-dimensional data, with a focus on scRNAseq analysis

dire-rapids

DiRe accelerated by PyTorch, PyKeOps and cuVS

tsimcne

Visualization tool for unsupervised image visualization (ICLR 2023)

zadu

A Python Library for Evaluating the Reliability of Dimensionality Reduction Embeddings

augmented-pca

Python implementations of supervised and adversarial linear factor models.

simpsom

Python library for Self-Organizing Maps

dpca

Implements Demixed Principal Components Analysis