Umappp - UMAP 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)
- Ruby Umappp is a wrapper library for C++ Umappp library created by Aaron Lun
- Compatible with yaumap
- Support Numo::NArray
Installation
gem install umappp
- OpenMP 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 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.
Umappp.run(embedding) # embedding is two-dimensional Ruby array or Numo array
# with parameters
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 |
tick | 0 (Not yet implemented) |
local_connectivity | 1.0 |
bandwidth | 1 |
mix_ratio | 1 |
spread | 1 |
min_dist | 0.01 |
a | 0 |
b | 0 |
repulsion_strength | 1 |
num_epochs | 500 |
learning_rate | 1 |
negative_sample_rate | 5 |
num_neighbors | 15 |
seed | 1234567890 |
batch | false |
num_threads | 1 (OpenMP required) |
Development
git clone https://github.com/kojix2/umap
cd umap
b ndle dle exec rake compile
bundle exec rake test
Ruby dependencies
Umappp dependencies
This Gem is a wrapper for 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.
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)