SHOGUN
5.0.0

SHOGUN's "modular" interfaces to Python, Octave, Java, Lua, Ruby and C# give intuitive and easy access to the shogun's functionality. Compared to the static interfaces (Static Interfaces), the modular ones are much more flexible and allow for nearly unlimited extensibility.
If this is your first time using shogun, you've found the right place to start!
In this tutorial, we demonstrate how to use shogun to create a simple Gaussian kernel based Support Vector Machine (SVM) classifier, but first things first. Let's fire up python, octave, java, lua, ruby or C#, and load the modular shogun environment.
To load all of shogun's modules under octave start octave and issue
init_shogun
Under python we have to specify what we'd like to import. For this example, we will need features and labels to represent our input data, a classifier, a kernel to compare the similarity of features and some evaluation procedures.
from shogun.Features import * from shogun.Kernel import * from shogun.Classifier import * from shogun.Evaluation import *
Under java we need import shogun package and jblas package.
import org.shogun.*; import org.jblas.*;
Under lua We need set LUA_PATH and LUA_CPATH to find the *.lua lib and *.so lib that lua_modular requires. For instance, if current dir is examples/undocumented /lua_modular, we need set the path as the following when we want to test the examples:
export LUA_PATH=../../../src/interfaces/lua_modular/?.lua\;?.lua export LUA_CPATH=../../../src/interfaces/lua_modular/?.so
Under ruby we need import shogun package and narray package.
require 'modshogun' require 'narray'
Under c# we need import system package.
using System;
we need import shogun package, which includes all the sub package, such as kernel, classifier, distance and so on.
require('shogun')
we also have to specify what we'd like to load. For this example, we will need features and labels to represent our input data, a classifier, a kernel to compare the similarity of features
System.loadLibrary("Features"); System.loadLibrary("Classifier"); System.loadLibrary("Kernel");
We also need use the method of Features to init shogun as the following:
Features.init_shogun_with_defaults();
(Note here that the module shogun.Features contains the class Labels).
If you would like to get an overview of the classes in shogun or if you are looking for the documentation of a particular class, use the "Classes" tab above and browse through the class list. All classes are rather well documented (if documentation is not good enough in a particular class, please notify us). Note that all classes in the classes list (classes tab above) are all prefixed with a 'C'  that really is the only difference to using them from within the python or octave modular interfaces (where the C prefix is missing).
Alternatively, under python the same documentation is available via python help strings, so you may issue
help(<classname>)
for example
from shogun.Kernel import GaussianKernel help(GaussianKernel)
or
import shogun.Kernel help(shogun.Kernel)
To start with, we will generate a small toy dataset. In python, we need to import numpy to do this. We will generate real valued training (and testing) data drawn from Gaussians distribution. We will generate two Gauss bumps that are "dist" apart. The data is in matrix shape with each column describing an object and as many columns as we have examples. Additionally, we need a vector of labels (that is a vector of ones or minus ones) that indicates the class of each example.
from numpy import * from numpy.random import randn dist=0.5 traindata_real = concatenate((randn(2,100)dist, randn(2,100)+dist), axis=1) testdata_real = concatenate((randn(2,100)dist, randn(2,100)+dist), axis=1) train_labels = concatenate((ones(100), ones(100))) test_labels = concatenate((ones(100), ones(100)))
In octave, this is is done as follows:
dist=0.5 traindata_real = [randn(2,100)dist, randn(2,100)+dist]; testdata_real = [randn(2,100)dist, randn(2,100)+dist]; train_labels = [ones(1,100), ones(1,100)]; test_labels = [ones(1,100), ones(1,100)];
In java, this is is done as follows:
dist=0.5 int num = 1000; double dist = 1.0; DoubleMatrix offs=ones(2, num).mmul(dist); DoubleMatrix x = randn(2, num).sub(offs); DoubleMatrix y = randn(2, num).add(offs); DoubleMatrix traindata_real = concatHorizontally(x, y); DoubleMatrix m = randn(2, num).sub(offs); DoubleMatrix n = randn(2, num).add(offs); DoubleMatrix testdata_real = concatHorizontally(m, n); DoubleMatrix o = ones(1,num); DoubleMatrix trainlab = concatHorizontally(o.neg(), o); DoubleMatrix testlab = concatHorizontarily(o.neg(), o)
In lua, this is is done as follows:
require 'shogun' require 'load' function concatenate(...) local result = ... for _,t in ipairs{select(2, ...)} do for row,rowdata in ipairs(t) do for col,coldata in ipairs(rowdata) do table.insert(result[row], coldata) end end end return result end function rand_matrix(rows, cols, dist) local matrix = {} for i = 1, rows do matrix[i] = {} for j = 1, cols do matrix[i][j] = math.random() + dist end end return matrix end function ones(num) r={} for i=1,num do r[i]=1 end return r end num=1000 dist=1 width=2.1 C=1 traindata_real=concatenate(rand_matrix(2,num, dist),rand_matrix(2,num,dist)) testdata_real=concatenate(rand_matrix(2,num,dist), rand_matrix(2,num, dist)) trainlab={} for i = 1, num do trainlab[i] = 1 trainlab[i + num] = 1 end testlab={} for i = 1, num do testlab[i] = 1 testlab[i + num] = 1 end
In ruby, this is is done as follows:
@num = 1000 @dist = 1 @width = 2.1 C = 1 def gen_rand_ary ary = [[],[]] ary.each do p p << ary_fill( @dist ) + ary_fill( @dist ) p.flatten! end return ary end def gen_ones_vec ary = [] @num.times do ary << 1 end @num.times do ary << 1 end return ary end puts "generating training data" traindata_real = gen_rand_ary testdata_real = gen_rand_ary puts "generating labels" trainlab = gen_ones_vec testlab = gen_ones_vec
In C#, this is is done as follows: int num = 1000; double dist = 1.0; double width = 2.1; double C = 1.0;
Random RandomNumber = new Random();
double[,] traindata_real = new double[2, num * 2]; for (int i = 0; i < num; i ++) { traindata_real[0, i] = RandomNumber.NextDouble()  dist; traindata_real[0, i + num] = RandomNumber.NextDouble() + dist; traindata_real[1, i] = RandomNumber.NextDouble()  dist; traindata_real[1, i + num] = RandomNumber.NextDouble() + dist; }
double[,] testdata_real = new double[2, num * 2]; for (int i = 0; i < num; i ++) { testdata_real[0, i] = RandomNumber.NextDouble()  dist; testdata_real[0, i + num] = RandomNumber.NextDouble() + dist; testdata_real[1, i] = RandomNumber.NextDouble()  dist; testdata_real[1, i + num] = RandomNumber.NextDouble() + dist; }
double[] trainlab = new double[num * 2]; for (int i = 0; i < num; i ++) { trainlab[i] = 1; trainlab[i + num] = 1; }
double[] testlab = new double[num * 2]; for (int i = 0; i < num; i ++) { testlab[i] = 1; testlab[i + num] = 1; }
The rest of this tutorial below will now work the same (identical syntax) for python, octave (when using a trailing semicolon for each command, which is optional in python), lua(we use colon to get the method of an object), ruby and C#
For java, we use DoubleMatrix to represent most of the types. If shogun C++ class need a int Vector/Matrix, we convert the DoubleMatrix into int Vector/Matrix and when returned from the function, we convert the int Vector/Matrix into DoubleMatrix again.
To process the above toy data in shogun, we need to create a shogun feature object, here RealFeatures (for dense real valued feature matrices, see also shogun::CSimpleFeatures) like this
feats_train = RealFeatures(traindata_real); feats_test = RealFeatures(testdata_real);
Using the above feature object we can now create a kernel object. Here, we create a Gaussian kernel of a certain width (see also shogun::CGaussianKernel) based on our training features
width = 2; kernel = GaussianKernel(feats_train, feats_train, width);
and can now compute the kernel matrix
km = kernel.get_kernel_matrix();
To train an SVM, we need labeled examples, which is a vector of ones and minus ones, such as the one we have previously stored in the variable train_labels. We now create a shogun label object from it (the same goes for our test labels, which we'll use later):
labels = Labels(train_labels); labels_test = Labels(test_labels);
Given the labels object and the kernel all that is left to do is to specify a cost parameter C (used to control generalization performance) and we can construct an SVM object. To start the training, we simply invoke the train method of the SVM object. Quiet easy, isn't it?
C = 1.0; svm = LibSVM(C, kernel, labels); svm.train();
To apply the SVM to unseen test data, we simply need to pass a feature object to the SVM's apply method, which returns a shogun Label object (note that we could alternatively initialize the kernel object with the train and test data manually and then call apply without arguments, which is done in some of the other example scripts). If we would like to analyze the outputs directly in python/octave, we can obtain the vector of outputs in native python/octave representation via get_labels().
output = svm.apply(feats_test); output_vector = output.get_labels();
Given the output and the test labels, we can now assess the prediction performance. For this, we create an instance of the class PerformanceMeasures, which provides a convenient way of obtaining various performance measures, such as accuracy (acc), area under the receiver operator characteristic curve (auROC), Fscore and others:
pm = PerformanceMeasures(labels_test, output); acc = pm.get_accuracy(); roc = pm.get_auROC(); fms = pm.get_fmeasure();
That's really it. For any of the advanced topics please have a look one of the many selfexplanatory examples in
A full, working example similar to the one presented above is shown below:
For octave:
For java:
For lua:
For ruby:
For csharp:
For python: