megaman: Manifold Learning for Millions of Points
megaman is a scalable manifold learning package implemented in python. It has a front-end API designed to be familiar to scikit-learn but harnesses the C++ Fast Library for Approximate Nearest Neighbors (FLANN) and the Sparse Symmetric Positive Definite (SSPD) solver Locally Optimal Block Precodition Gradient (LOBPCG) method to scale manifold learning algorithms to large data sets. On a personal computer megaman can embed 1 million data points with hundreds of dimensions in 10 minutes. megaman is designed for researchers and as such caches intermediary steps and indices to allow for fast re-computation with new parameters.
Package documentation can be found at http://mmp2.github.io/megaman/
You can also find our arXiv paper at http://arxiv.org/abs/1603.02763
Installation with Conda
The easiest way to install
megaman and its dependencies is with conda , the cross-platform package manager for the scientific Python ecosystem.
To install megaman and its dependencies, run
$ conda install --channel=jakevdp megaman
Currently builds are available for OSX-64 and Linux-64, on Python 2.7, 3.4, and 3.5. For other operating systems, see the full install instructions below.
Installation from source
To install megaman from source requires the following:
- python tested with versions 2.7, 3.4, and 3.5
- numpy version 1.8 or higher
- scipy version 0.16.0 or higher
- a C++ compiler such as
Optional requirements include
- pyamg , which allows for faster decompositions of large matrices
- pyflann which offers another method of computing distance matrices (this is bundled with the FLANN source code)
- nose for running the unit tests
These requirements can be installed on Linux and MacOSX using the following conda command:
$ conda install --channel=jakevdp pip nose coverage gcc cython numpy scipy scikit-learn pyflann pyamg
Finally, within the source repository, run this command to install the
megaman package itself:
$ python setup.py install
nose for unit tests. With
nose installed, type
$ make test
to run the unit tests.
megaman is tested on Python versions 2.7, 3.4, and 3.5.
We have the following planned updates for upcoming releases:
- Native support for K-Nearest Neighbors distance (in progress)
- Lazy R-metric (only calcualte on selected points)
- Make cover_plotter.py work more generally with rmetric.py
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