scvelo-rs 0.1.3

Drop-in Rust acceleration of scVelo for single-cell RNA velocity.

scvelo-rs

A Rust + PyO3 port of scVelo.

Rust implementation of heavy-weight bottlenecks like recover_dynamics & velocity_graph - bit-exact to the original scVelo.

Highlights

• 30–40× faster than the original scVelo on representative atlases (5k–100k cells), and ~2–4× lower peak memory. See Benchmarks.
• Bit-exact equivalence to scVelo on 99.9% of genes — the residual drift is at f64 ULP scale (per-gene Pearson r = 1.0000 across fit_alpha, fit_beta, fit_gamma, fit_t_).
• Drop-in: import scvelo_rs.patch and every downstream call to scv.tl.{recover_dynamics, velocity, velocity_graph} routes to Rust. Or import scvelo_rs as scv for the full API.
• Cross-platform wheels for Linux x86_64/aarch64, macOS arm64, Windows x86_64. Single abi3-py310 wheel covers Python 3.10–3.13.
• CPU-only. Runs anywhere Python runs — laptop, HPC, Docker, ARM. No CUDA. No Numba. No JIT warmup.

# Option 1 — drop-in import.
import scvelo_rs as scv

adata = scv.datasets.pancreas()
scv.pp.filter_and_normalize(adata); scv.pp.moments(adata)
scv.tl.recover_dynamics(adata)            # ~35× faster than the original scvelo
scv.tl.velocity(adata, mode="dynamical")
scv.tl.velocity_graph(adata)
scv.pl.velocity_embedding_stream(adata, basis="umap")

# Option 2 — monkey-patch. Keep your existing `import scvelo as scv`;
# only the three patched hot paths get the Rust kernel.
import scvelo as scv
import scvelo_rs.patch  # noqa: F401   # patches scv.tl.{recover_dynamics, velocity, velocity_graph}

scv.tl.recover_dynamics(adata)         # bit-exact, no other code change needed

Installation

pip install scvelo-rs

scVelo and scanpy are runtime dependencies (used for plotting, dataset I/O, DPT/PAGA pass-through). They are pulled in automatically.

Quick start

Three usage patterns, in order of how invasive the migration is.

1. Monkey-patch (zero code changes)

Add one line at the top of your existing scVelo script:

import scvelo as scv
import scvelo_rs.patch  # noqa: F401   # swaps scv.tl.{recover_dynamics, velocity, velocity_graph}

adata = scv.datasets.pancreas()
scv.pp.filter_and_normalize(adata)
scv.pp.moments(adata)
scv.tl.recover_dynamics(adata)         # now Rust-backed
scv.tl.velocity(adata, mode="dynamical")
scv.tl.velocity_graph(adata)

Originals are preserved at scv.tl.<name>_original for A/B comparison.

2. Drop-in import

Replace import scvelo as scv with import scvelo_rs as scv. The scvelo_rs.{tl, pp, pl, datasets} namespaces expose scVelo's full public API; the hot loops route through Rust, everything else passes through scVelo unchanged.

import scvelo_rs as scv

adata = scv.datasets.pancreas()
scv.pp.filter_and_normalize(adata)
scv.pp.moments(adata)
scv.tl.recover_dynamics(adata)
scv.tl.velocity(adata, mode="dynamical")
scv.tl.velocity_graph(adata)
scv.pl.velocity_embedding_stream(adata, basis="umap")

3. Direct call

import scvelo_rs
scvelo_rs.recover_dynamics(adata)      # same signature as scv.tl.recover_dynamics

See examples/ for runnable end-to-end scripts.

Benchmarks

Measured locally on standard datasets.

Wall time

benchmark	cells	genes	scvelo	scvelo-rs	speedup
recover_dynamics (5k cells, 50 genes)	5,000	50	43.24 s	1.03 s	42.0×
recover_dynamics + velocity (20k, 100)	20,000	100	380.02 s	10.09 s	37.7×
recover_dynamics + velocity + velocity_graph (20k, 100)	20,000	100	389.54 s	10.79 s	36.1×
full pipeline (50k, 100)	50,000	100	1202.26 s	34.35 s	35.0×
recover_dynamics (100k, 30)	100,000	30	671.65 s	22.85 s	29.4×

Peak memory

benchmark	cells	genes	scvelo	scvelo-rs	saved
recover_dynamics (5k, 50)	5,000	50	108.4 MB	35.0 MB	73 MB
velocity_graph (20k, 100)	20,000	100	1727.5 MB	626.5 MB	1,101 MB
steady-state layers (5k, 200)	5,000	200	252.1 MB	66.2 MB	186 MB
full pipeline (50k, 100)	50,000	100	4831.6 MB	1879.3 MB	2,952 MB
recover_dynamics + velocity_graph (100k, 30)	100,000	30	7074.4 MB	2794.9 MB	4,280 MB

Build from source

Requires Rust 1.75+ and Python 3.10+.

git clone https://github.com/ilaykav/scvelo-rs
cd scvelo-rs
python -m venv .venv && source .venv/bin/activate   # or .venv\Scripts\activate on Windows
pip install -e ".[dev]"
maturin develop --release
pytest tests/unit tests/integration

The Rust crates nalgebra (SVD for PCA) and hnsw_rs (HNSW for KNN) are pure-Rust — no OpenBLAS, no vcpkg, no system C libraries. Cross-platform builds work out of the box.

Documentation

A full Sphinx site (Quick start, Installation, Migration from scVelo, Architecture, Numerical parity, Benchmarks) is in the works for v0.2. Until then, this README, the CHANGELOG, and the runnable scripts under examples/ and notebooks/ cover the same ground.

Contributing

Bug reports, PRs, and benchmark contributions welcome. See CONTRIBUTING.md — the short version is:

git clone https://github.com/ilaykav/scvelo-rs
cd scvelo-rs
pip install -e ".[dev]"
maturin develop --release
pytest tests/unit tests/integration

Bit-exact equivalence to scVelo is the contract for every Rust-backed function. PRs that move per-gene drift above 1e-9 need a documented reason.

License

Released under BSD-3-Clause. The Rust kernels are independent reimplementations of theislab's published algorithms — credit for the underlying methods belongs to La Manno et al. 2018 (RNA velocity, Nature, doi:10.1038/s41586-018-0414-6) and Bergen et al. 2020 (scVelo, Nat Biotechnol, doi:10.1038/s41587-020-0591-3).

Citing this work

scvelo-rs is a faithful port: the method is Bergen et al. 2020, the implementation is this repository. Always cite the original scVelo paper as the primary reference; cite the version of scvelo-rs you used as a software dependency (pip show scvelo-rs or scvelo_rs.__version__).

@article{bergen2020generalizing,
  title   = {Generalizing RNA velocity to transient cell states through dynamical modeling},
  author  = {Bergen, Volker and Lange, Marius and Peidli, Stefan and
             Wolf, F. Alexander and Theis, Fabian J.},
  journal = {Nature Biotechnology},
  year    = {2020},
  doi     = {10.1038/s41587-020-0591-3}
}

@software{scvelo_rs,
  title   = {scvelo-rs: a Rust acceleration of scVelo's dynamical model},
  author  = {Kavitzky, Ilay},
  year    = {2026},
  version = {0.1.0},
  url     = {https://github.com/ilaykav/scvelo-rs},
  note    = {Rust + PyO3 port of Bergen et al. 2020 (doi:10.1038/s41587-020-0591-3)}
}

Authored and maintained by Ilay Kavitzky. Contribution guidelines are in CONTRIBUTING.md.

Reporting bugs and feature requests

Open an issue at github.com/ilaykav/scvelo-rs/issues.

Bug reports — include:

• scvelo-rs version (pip show scvelo-rs)
• OS and Python version
• A minimum reproducer (a small .h5ad slice + the calls that fail is usually enough)
• What you expected vs what you got

Parity issues (a fitted parameter or velocity vector differs from the original scvelo): include both runs' values for the affected gene/cell, the relative drift, and which fixture you ran on.

Feature requests — describe the workflow you can't do today, not just the API you'd like. Atlas-scale parity reports are especially welcome.

For anything else, direct mail: [e-mail].