Shogun (toolbox)

Shogun machine learning toolbox
Shogun mac os
Original author(s)	Gunnar Rätsch; Soeren Sonnenburg
Developer(s)	Soeren Sonnenburg; Sergey Lisitsyn; Heiko Strathmann; Fernando Iglesias; Viktor Gal
Stable release	6.0.0 / April 25, 2017
Repository	github.com/shogun-toolbox/shogun
Written in	C++
Operating system	Cross-platform
Type	Software library
License	BSD3 with optional GNU GPLv3
Website	www.shogun.ml

Shogun is a free, open-source machine learning software library written in C++. It offers numerous algorithms and data structures for machine learning problems. It offers interfaces for Octave, Python, R, Java, Lua, Ruby and C# using SWIG.

It is licensed under the terms of the GNU General Public License version 3 or later.

Description

The focus of Shogun is on kernel machines such as support vector machines for regression and classification problems. Shogun also offers a full implementation of Hidden Markov models. The core of Shogun is written in C++ and offers interfaces for MATLAB, Octave, Python, R, Java, Lua, Ruby and C#. Shogun has been under active development since 1999. Today there is a vibrant user community all over the world using Shogun as a base for research and education, and contributing to the core package.

A screenshot taken under Mac OS X

Supported algorithms

Currently Shogun supports the following algorithms:

Support vector machines
Dimensionality reduction algorithms, such as PCA, Kernel PCA, Locally Linear Embedding, Hessian Locally Linear Embedding, Local Tangent Space Alignment, Linear Local Tangent Space Alignment, Kernel Locally Linear Embedding, Kernel Local Tangent Space Alignment, Multidimensional Scaling, Isomap, Diffusion Maps, Laplacian Eigenmaps
Online learning algorithms such as SGD-QN, Vowpal Wabbit
Clustering algorithms: k-means and GMM
Kernel Ridge Regression, Support Vector Regression
Hidden Markov Models
K-Nearest Neighbors
Linear discriminant analysis
Kernel Perceptrons.

Many different kernels are implemented, ranging from kernels for numerical data (such as gaussian or linear kernels) to kernels on special data (such as strings over certain alphabets). The currently implemented kernels for numeric data include:

linear
gaussian
polynomial
sigmoid kernels

The supported kernels for special data include:

Spectrum
Weighted Degree
Weighted Degree with Shifts

The latter group of kernels allows processing of arbitrary sequences over fixed alphabets such as DNA sequences as well as whole e-mail texts.

Special features

As Shogun was developed with bioinformatics applications in mind it is capable of processing huge datasets consisting of up to 10 million samples. Shogun supports the use of pre-calculated kernels. It is also possible to use a combined kernel i.e. a kernel consisting of a linear combination of arbitrary kernels over different domains. The coefficients or weights of the linear combination can be learned as well. For this purpose Shogun offers a multiple kernel learning functionality.

gollark: Very shiny.

gollark: I guess they would make nice decorations.

gollark: What would you *use* them for?

gollark: You could probably vaguely look at what it looks like, but NAND flash is just going to be a big grid of capacitors or whatever, and you will know very little about how it's made.

gollark: I doubt you could do anything with them even if you have them.

References

S. Sonnenburg, G. Rätsch, S. Henschel, C. Widmer, J. Behr, A. Zien, F. De Bona, A. Binder, C. Gehl and V. Franc: The SHOGUN Machine Learning Toolbox, Journal of Machine Learning Research, 11:1799−1802, June 11, 2010.
M. Gashler. Waffles: A Machine Learning Toolkit. Journal of Machine Learning Research, 12 (July):2383–2387, 2011.
P. Vincent, Y. Bengio, N. Chapados, and O. Delalleau. Plearn high-performance machine learning library. URL http://plearn.berlios.de/.

External links

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