Project details for SHOGUN

Screenshot SHOGUN 0.8.0

by sonne - August 16, 2009, 19:53:50 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ]

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The SHOGUN machine learning toolbox's focus is on large scale kernel methods and especially on Support Vector Machines (SVM). It comes with a generic interface for SVMs, features several SVM and kernel implementations, includes LinAdd optimizations and also Multiple Kernel Learning algorithms. SHOGUN also implements a number of linear methods. It allows the input feature-objects to be dense, sparse or strings and of type int/short/double/char.

The toolbox not only provides efficient implementations of the most common kernels, like the

  • Linear,
  • Polynomial,
  • Gaussian and
  • Sigmoid Kernel

but also comes with a number of recent string kernels as e.g. the

  • Locality Improved,
  • Fischer,
  • TOP,
  • Spectrum,
  • Weighted Degree Kernel (with shifts).

For the latter the efficient LINADD optimizations are implemented. Also SHOGUN offers the freedom of working with custom pre-computed kernels. One of its key features is the combined kernel which can be constructed by a weighted linear combination of a number of sub-kernels, each of which not necessarily working on the same domain. An optimal sub-kernel weighting can be learned using Multiple Kernel Learning. Currently SVM 2-class classification and regression problems can be dealt with. However SHOGUN also implements a number of linear methods like

  • Linear Discriminant Analysis (LDA)
  • Linear Programming Machine (LPM),
  • (Kernel) Perceptrons and features algorithms to train hidden markov models.

The input feature-objects can be

  • dense
  • sparse or
  • strings and of type int/short/double/char

and can be converted into different feature types. Chains of preprocessors (e.g. substracting the mean) can be attached to each feature object allowing for on-the-fly pre-processing.

SHOGUN is implemented in C++ and interfaces to Matlab(tm), R, Octave and Python.

Changes to previous version:

This release contains several cleanups, features and bugfixes:


  • Implements new multiclass svm formulation.
  • 1,2 and general q-norm MKL for classification, regression and one-class for wrapper and chunking algorithm for arbitrary (dual) SVM solvers.
  • Dynamic Programming code is now accessible from python.
  • Implements Regulatory Modules kernel.
  • Documentation updates (Tutorial, improved installation instructions, overview about the implemented algorithms).


  • Correct q-norm MKL for Newton.
  • Upon make install of elwms don't install files into R/octave/python if these interfaces were not configured
  • Svm-nu parameter was not set correctly.
  • Fix custom kernel initialization.
  • Correct get_subkernel_weights.
  • Proper Intel core2 compile flags detection
  • Fix number of outputs for KNN.
  • Run tests with proper LD_LIBRARY_PATH set.
  • Fix several memory leaks.

Cleanup and API Changes

  • Rename svm_one_class_nu to svm_nu.
  • Clean up dynamic programming code.
  • Remove commands from_position_list and slide_window and move functionallity into set/add_features,
  • Remove now obsolete legacy examples.
BibTeX Entry: Download
Corresponding Paper BibTeX Entry: Download
Supported Operating Systems: Cygwin, Linux, Macosx
Data Formats: Plain Ascii, Svmlight
Tags: Bioinformatics, Large Scale, String Kernel, Kernel, Kernelmachine, Lda, Lpm, Matlab, Mkl, Octave, Python, R, Svm
Archive: download here


Soeren Sonnenburg (on September 12, 2008, 16:14:36)
In case you find bugs, feel free to report them at [](
Tom Fawcett (on January 3, 2011, 03:20:48)
You say, "Some of them come with no less than 10 million training examples, others with 7 billion test examples." I'm not sure what this means. I have problems with mixed symbolic/numeric attributes and the training example sets don't fit in memory. Does SHOGUN require that training examples fit in memory?
Soeren Sonnenburg (on January 14, 2011, 18:12:01)
Shogun does not necessarily require examples to be in memory (if you use any of the FileFeatures). However, most algorithms within shogun are batch type - so using the non in-memory FileFeatures would probably be very slow. This does not matter for doing predictions of course, even though the 7 billion test examples above referred to predicting gene starts on the whole human genome (in memory ~3.5GB and a context window of 1200nt was shifted around in that string). In addition one can compute features (or feature space) on-the-fly potentially saving lots of memory. Not sure how big your problem is but I guess this is better discussed on the shogun mailinglist.
Yuri Hoffmann (on September 14, 2013, 17:12:16)
cannot use the java interface in cygwin (already reported on github) nor in debian.

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