https://github.com/microscopic-image-analysis/geosss
Implementation of the geodesic slice sampling on the sphere
https://github.com/microscopic-image-analysis/geosss
bayesian-inference bioinformatics directional-statistics mcmc shape-analysis
Last synced: 5 months ago
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Implementation of the geodesic slice sampling on the sphere
- Host: GitHub
- URL: https://github.com/microscopic-image-analysis/geosss
- Owner: microscopic-image-analysis
- License: bsd-3-clause
- Created: 2023-07-14T16:11:53.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2025-12-03T13:34:21.000Z (6 months ago)
- Last Synced: 2025-12-06T14:48:46.544Z (6 months ago)
- Topics: bayesian-inference, bioinformatics, directional-statistics, mcmc, shape-analysis
- Language: Jupyter Notebook
- Homepage:
- Size: 18.1 MB
- Stars: 5
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
[](https://pypi.org/project/geosss/)
[](https://opensource.org/licenses/BSD-3-Clause)
# GeoSSS: Geodesic Slice Sampling on the Sphere
This python package implements the novel and efficient tuning-free MCMC based inference methods to sample distributions defined on the sphere as published in JMLR. This includes the two variants GeoSSS (reject) and GeoSSS (shrink), where the latter is much faster and therefore recommended for practical utility.
In addition, the package also provides the implementation of the spherical variants of random-walk Metropolis-Hastings (RWMH) [Lie et al. 2023] and state-of-the-art Hamiltonian Monte Carlo [Lan et al. 2014]. As demonstrated in our [paper](https://doi.org/10.48550/arXiv.2301.08056), the proposed GeoSSS samplers outperform these baseline samplers for several challenging target distributions.
To reproduce the results in the paper, see this [section](#development-and-reproducibility). However, to get started quickly, install the package and follow along with the demo provided below.
## Installation
GeoSSS is available for installation from [PyPI](https://pypi.org/project/geosss/). Therefore, simply type:
```bash
pip install geosss
```
## Minimal Example
As a demo, we consider a target that is a mixture of von Mises-Fisher distributions on $\mathbb{S}^2$ with concentration parameter $\kappa=$ 80. By considering a fixed computational budget of 1000 samples, our samplers manage to explore all modes, whereas RWMH and HMC get stuck in a single mode.
This demo can be created with the below script.
```python
import geosss as gs
import numpy as np
# Create mixture of von Mises-Fisher distributions
mus = np.array([[0.87, -0.37, 0.33],
[-0.20, -0.89, -0.40],
[0.19, 0.22, -0.96]])
vmfs = [gs.VonMisesFisher(80.0 * mu) for mu in mus]
pdf = gs.MixtureModel(vmfs)
# Sampling parameters
n_samples, burnin = 1000, 100
init_state = np.array([-0.86, 0.19, -0.47])
seed = 3521
# Sample with different methods
samplers = {
'sss-reject': gs.RejectionSphericalSliceSampler, # very accurate, but slow
'sss-shrink': gs.ShrinkageSphericalSliceSampler, # reasonably accurate, but fast
'rwmh': gs.MetropolisHastings, # automatically tuned during burnin
'hmc': gs.SphericalHMC, # automatically tuned during burnin
}
samples = {name: cls(pdf, init_state, seed).sample(n_samples, burnin)
for name, cls in samplers.items()}
```
See the notebook [`demo.ipynb`](demo.ipynb) for visualization of the samples.
## Development and Reproducibility
To reproduce results from the numerical illustrations section of the paper, check the [scripts](scripts/) directory. Precomputed results can also be downloaded from the [Science Data Bank](https://doi.org/10.57760/sciencedb.30181) and used with these scripts.
However, first installing the package and it's *locked* dependencies is necessary and can be done as follows:
1. Clone the repository and navigate to the root of the folder,
```bash
git clone https://github.com/microscopic-image-analysis/geosss.git
cd geosss
git checkout v0.3.5 # version (for JMLR paper reprod.)
```
2. You can now create a virtual environment (with `conda` for example),
```bash
conda create --name geosss-venv python=3.12 # or python >= 3.10, < 3.13
conda activate geosss-venv
```
3. The dependencies can now be installed in this environment as,
```bash
pip install -r requirements.txt
pip install -e . --no-deps
```
## References
[Lie et al. 2023](https://doi.org/10.48550/arXiv.2112.12185): Lie, H. C., Rudolf, D., Sprungk, B., and Sullivan, T. J. (2023). “Dimension-independent Markov
chain Monte Carlo on the sphere”. *Scandinavian Journal of Statistics* 5:4, pp. 1818–1858.
[Lan et al. 2014](https://doi.org/10.48550/arXiv.1309.4289): Lan, S., Zhou, B., and Shahbaba, B. (2014). “Spherical Hamiltonian Monte Carlo for constrained
target distributions”. In: *Proceedings of the 31st International Conference on Machine Learning.* Vol. 32.
PMLR, pp. 629–637.
## Citation
If you use this package or ideas from the paper, please consider citing us.
```bash
@misc{habeck2023,
title={Geodesic slice sampling on the sphere},
author={Michael Habeck and Mareike Hasenpflug and Shantanu Kodgirwar and Daniel Rudolf},
year={2023},
eprint={2301.08056},
archivePrefix={arXiv},
primaryClass={stat.ME}
}
```