Manifold Learning Python Packages

minisom

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

cellrank

CellRank: dynamics from multi-view single-cell data

phate

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

palantir

Single cell trajectory detection

embedding-condensation

[𝗜𝗖𝗠𝗟 𝟮𝟬𝟮𝟲] Dispersion loss counteracts embedding condensation and improves generalization in small language models

torchdr

TorchDR - PyTorch Dimensionality Reduction

pytorch-bsf

PyTorch implementation of Bezier simplex fitting

mlx-vis

Pure MLX implementations of UMAP, t-SNE, PaCMAP, TriMap, DREAMS, CNE, MMAE, and NNDescent for Apple Silicon. Metal GPU for computation and video rendering.

dreimac

Dimensionality Reduction with Eilenberg-MacLane Coordinates

topometry

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

topometry-nosc

An independently maintained, heavily modified fork of TopOMetry: geometry-first topological dimensionality reduction and manifold learning.

cub-tools

Caltech UCSD Birds Database Tools for PyTorch Image Classification

pressio4py

pressio4py: projection-based model reduction for Python

snpmanifold

SNPmanifold: Manifold learning for single-cell SNVs

dse-dsmi

Diffusion spectral entropy and diffusion spectral mutual information (https://arxiv.org/abs/2312.04823).

heatgeo

Heat geodesic embeddings

pamona

manifold alignment method for single-cell multi-omics integration using Pamona

miaaim-python

Multi-omics Image Alignment and Analysis by Information Manifolds