megaman: Manifold Learning for Millions of Points
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Bugs fixed and enhancement in riemannian relaxation and plotter.
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megaman: Manifold Learning for Millions of Points

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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

If you use our software please cite the following JMLR paper:

McQueen, Meila, VanderPlas, & Zhang, "Megaman: Scalable Manifold Learning in Python", Journal of Machine Learning Research, Vol 17 no. 14, 2016.

You can also find our arXiv paper at


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 megaman --channel=conda-forge

Currently builds are available for OSX and Linux, 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:

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
  • h5py for reading testing .mat files

These requirements can be installed on Linux and MacOSX using the following conda command:

$ conda install --channel=conda-forge pip nose coverage gcc cython numpy scipy scikit-learn pyflann pyamg h5py plotly

Finally, within the source repository, run this command to install the megaman package itself:

$ python install

Unit Tests

megaman uses 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.


Other Contributors

  • Xiao Wang: lazy rmetric, Nystrom Extension

Future Work

See this issues list for what we have planned for upcoming releases:

Future Work