manifolds-rs

Dimensionality reduction for single-cell and computational biology. The Rust crate does the work; this is a scikit-learn shaped layer over it.

Eight algorithms on the CPU, three of them with GPU variants where the neighbour search and the optimiser (UMAP's Adam, t-SNE's three-kernel FFT) move to the device. Scanpy-style mf.umap(adata) and mf.tsne(adata) for AnnData. No CUDA runtime to install: the GPU backend is wgpu, so it runs on Metal, Vulkan or DX12 and ships in the ordinary wheel.

Documentation: https://gregorlueg.github.io/manifolds-rs/

This package versions separately from the Rust crate. Changes here are in python/CHANGELOG.md; the crate's are in CHANGELOG.md.

Install

uv pip install manifolds-rs

Wheels are built for Linux x86_64 and macOS on both architectures, against Python 3.10 and up.

Thirty seconds

import manifolds_rs as mf

X, labels = mf.datasets.clustered(20_000, dim=50, n_clusters=12)

embedding = mf.UMAP(n_neighbors=15, min_dist=0.1).fit_transform(X)

Every estimator takes its parameters in the constructor, its data in fit, and hands back an (n_samples, n_components) array. get_params and set_params are there, so clone and Pipeline work without scikit-learn being an install requirement.

What's here

AnnData

With uv pip install 'manifolds-rs[anndata]', mf.umap and mf.tsne drop in for sc.tl.umap and sc.tl.tsne: same slots, so sc.pl.umap just works.

import scanpy as sc
import manifolds_rs as mf

sc.pp.pca(adata)
sc.pp.neighbors(adata)
mf.umap(adata)  # obsm["X_umap"], uns["umap"]
mf.tsne(adata)  # obsm["X_tsne"], uns["tsne"]
sc.pl.umap(adata, color="leiden")

device="gpu" switches to the GPU estimators. On 25,000 cells on an M1 Max, mf.umap ran in 1.5s against 10.6s for sc.tl.umap, and mf.tsne in 9.7s (4.9s with device="gpu", approx="fft_3k_gpu") against 47.2s for a 10-thread sc.tl.tsne. The AnnData page has the full table, cluster separation included, and the caveats.

Parameters

The knobs people actually turn are ordinary constructor arguments. The rest live in frozen dataclasses, one per group, and anything you leave alone keeps the crate's default:

mf.UMAP(
    n_neighbors=30,
    ann="hnsw",
    nn_params=mf.NeighbourParams(m=32, ef_search=200),
    optim_params=mf.UmapOptim(gamma=1.5, neg_sample_rate=10),
)

Every parameter has exactly one home. If it is a constructor argument it is not in the group, so there is never a question of which wins.

Reusing the neighbour graph

Running several embeddings over the same data? Build the graph once. On anything large the search is most of the runtime.

ind, dist = mf.knn_graph(X, k=15, ann="hnsw")

a = mf.UMAP().fit_transform(X, knn_indices=ind, knn_distances=dist)
b = mf.PaCMAP().fit_transform(X, knn_indices=ind, knn_distances=dist)

No transform

None of these projects new points, so there is no transform. That is the crate's position rather than a gap in the bindings: embedding new data means refitting on the combined set, which moves the existing coordinates too. Anyone telling you otherwise is doing something to the new points that is not the same operation the old ones went through.

Precision

float32 in, float32 throughout; float64 in, float64 throughout. Anything else is promoted to float64 rather than narrowed, so precision is never lost by accident. The GPU estimators are the exception and cast to float32, because WGSL has no float64 and the alternative is a failure inside a kernel.

What is not in the wheel

CPU FFT-accelerated t-SNE. It needs FFTW, which is GPL-2.0-or-later and would be linked statically, turning the whole wheel GPL. So the CPU estimators take Barnes-Hut only. On a GPU, TSNEGpu(approx="fft_3k_gpu") gives you FFT-interpolated repulsion without FFTW.

Parametric UMAP is in the crate but not yet bound.