https://github.com/kojix2/ruby-umappp
Uniform Manifold Approximation and Projection for Ruby
https://github.com/kojix2/ruby-umappp
ruby umap
Last synced: about 1 year ago
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Uniform Manifold Approximation and Projection for Ruby
- Host: GitHub
- URL: https://github.com/kojix2/ruby-umappp
- Owner: kojix2
- License: bsd-2-clause
- Created: 2022-01-24T13:36:58.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2025-01-17T03:53:52.000Z (over 1 year ago)
- Last Synced: 2025-03-21T03:47:08.534Z (over 1 year ago)
- Topics: ruby, umap
- Language: C++
- Homepage: https://kojix2.github.io/ruby-umappp
- Size: 1.44 MB
- Stars: 8
- Watchers: 3
- Forks: 2
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- Funding: .github/FUNDING.yml
- License: LICENSE.txt
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README
# Umappp - UMAP for Ruby
[](https://github.com/kojix2/ruby-umappp/actions/workflows/ci.yml)
[](https://badge.fury.io/rb/umappp)
🗺️ [Umappp](https://github.com/LTLA/umappp) - Uniform Manifold Approximation and Projection - for Ruby
> Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique that can be used for visualisation similarly to t-SNE, but also for general non-linear dimension reduction.
> ([original UMAP documentation](https://umap-learn.readthedocs.io/en/latest/index.html))
* Ruby Umappp is a wrapper library for [C++ Umappp library](https://github.com/LTLA/umappp) created by Aaron Lun
* Compatible with [yaumap](https://github.com/LTLA/yaumap)
* Support [Numo::NArray](https://github.com/ruby-numo/numo-narray)
## Installation
```
gem install umappp
```
* [OpenMP](https://www.openmp.org) is required for multithreading.
## Usage
This Gem provides the module `Umappp` and its singular method `Umappp.run()`. The first argument of `Umappp.run()` is a two-dimensional Ruby array or a two-dimensional Numo array. [Numo](https://github.com/ruby-numo/numo-narray) is a library for performing N-dimensional array computing like NumPy. The argument is converted to `Numo::SFloat`. SFloat is a single precision floating point number type of Numo::NArray.
```ruby
# The embedding is two-dimensional Ruby array or Numo array
# Returns Numo::SFloat
r = Umappp.run(embedding)
# Run with parameters
r = Umappp.run(pixels, num_threads: 8, a: 1.8956, b: 0.8006)
```
Available parameters and their default values
| parameters | default value |
|----------------------|------------------------------------|
| method | :annoy (another option is :vptree) |
| ndim | 2 |
| local_connectivity | 1.0 |
| bandwidth | 1 |
| mix_ratio | 1 |
| spread | 1 |
| min_dist | 0.01 |
| a | 0 |
| b | 0 |
| repulsion_strength | 1 |
| initialize | Umappp::InitMethod::SPECTRAL |
| num_epochs | 500 |
| learning_rate | 1 |
| negative_sample_rate | 5 |
| num_neighbors | 15 |
| seed | 1234567890 |
| num_threads | 1 (OpenMP required) |
## Development
```
git clone https://github.com/kojix2/ruby-umappp
cd umap
bundle exec rake compile
bundle exec rake test
```
Update LTLA/umappp
Requires cmake to run
```
cd script
./vendor.sh
```
### Ruby dependencies
* [rice](https://github.com/jasonroelofs/rice) - Ruby Interface for C++ Extensions
* [numo.hpp](https://github.com/ankane/numo.hpp) - C++ header for Numo and Rice
### Umappp dependencies
This Gem is a wrapper for [Umappp](https://github.com/LTLA/umappp). We store and distribute Umappp and other dependent C++ code in the Vendor directory. Umappp is compiled when the Gem is installed. Umappp's C++ modules have complex dependencies as shown in the figure below. It is not a good idea to manage them manually. Use `script/vendor.sh` to update them automatically. This actually runs cmake and moves the required directories to the vendor directory.
```mermaid
graph TD;
id1(eigen)-->CppIrlba;
aarand-->CppIrlba;
Annoy-->knncolle;
hnswlib-->knncolle;
CppKmeans-->knncolle;
aarand-->CppKmeans;
powerit-->CppKmeans;
aarand-->powerit;
knncolle-->umappp;
aarand-->umappp;
CppIrlba-->umappp;
style id1 fill:#f9f,stroke:#333
```
All modules except eigen are the work of Aaron Lun.
## Contributing
Welcome!
Do you need commit rights to my repository?
Do you want to get admin rights and take over the project?
If so, please feel free to contact us @kojix2.
## License
* As for the code I wrote, it is BSD 2-Clause (or MIT).
* The license of Umappp for C++ by Aaron Lun is BSD 2-Clause.
* For other codes, please check on your own. (There are many dependencies)