graphkit-learn/gklearn/gedlib/lib/libsvm.3.22/tools/README

This directory includes some useful codes:

1. subset selection tools.
2. parameter selection tools.
3. LIBSVM format checking tools

Part I: Subset selection tools

Introduction
============

Training large data is time consuming. Sometimes one should work on a
smaller subset first. The python script subset.py randomly selects a
specified number of samples. For classification data, we provide a
stratified selection to ensure the same class distribution in the
subset.

Usage: subset.py [options] dataset number [output1] [output2]

This script selects a subset of the given data set.

options:
-s method : method of selection (default 0)
     0 -- stratified selection (classification only)
     1 -- random selection

output1 : the subset (optional)
output2 : the rest of data (optional)

If output1 is omitted, the subset will be printed on the screen.

Example
=======

> python subset.py heart_scale 100 file1 file2

From heart_scale 100 samples are randomly selected and stored in
file1. All remaining instances are stored in file2.


Part II: Parameter Selection Tools

Introduction
============

grid.py is a parameter selection tool for C-SVM classification using
the RBF (radial basis function) kernel. It uses cross validation (CV)
technique to estimate the accuracy of each parameter combination in
the specified range and helps you to decide the best parameters for
your problem.

grid.py directly executes libsvm binaries (so no python binding is needed)
for cross validation and then draw contour of CV accuracy using gnuplot.
You must have libsvm and gnuplot installed before using it. The package
gnuplot is available at http://www.gnuplot.info/

On Mac OSX, the precompiled gnuplot file needs the library Aquarterm,
which thus must be installed as well. In addition, this version of
gnuplot does not support png, so you need to change "set term png
transparent small" and use other image formats. For example, you may
have "set term pbm small color".

Usage: grid.py [grid_options] [svm_options] dataset

grid_options :
-log2c {begin,end,step | "null"} : set the range of c (default -5,15,2)
    begin,end,step -- c_range = 2^{begin,...,begin+k*step,...,end}
    "null"         -- do not grid with c
-log2g {begin,end,step | "null"} : set the range of g (default 3,-15,-2)
    begin,end,step -- g_range = 2^{begin,...,begin+k*step,...,end}
    "null"         -- do not grid with g
-v n : n-fold cross validation (default 5)
-svmtrain pathname : set svm executable path and name
-gnuplot {pathname | "null"} :
    pathname -- set gnuplot executable path and name
    "null"   -- do not plot 
-out {pathname | "null"} : (default dataset.out)
    pathname -- set output file path and name
    "null"   -- do not output file
-png pathname : set graphic output file path and name (default dataset.png)
-resume [pathname] : resume the grid task using an existing output file (default pathname is dataset.out)
    Use this option only if some parameters have been checked for the SAME data.

svm_options : additional options for svm-train

The program conducts v-fold cross validation using parameter C (and gamma)
= 2^begin, 2^(begin+step), ..., 2^end.

You can specify where the libsvm executable and gnuplot are using the
-svmtrain and -gnuplot parameters.

For windows users, please use pgnuplot.exe. If you are using gnuplot
3.7.1, please upgrade to version 3.7.3 or higher. The version 3.7.1
has a bug. If you use cygwin on windows, please use gunplot-x11.

If the task is terminated accidentally or you would like to change the
range of parameters, you can apply '-resume' to save time by re-using
previous results.  You may specify the output file of a previous run
or use the default (i.e., dataset.out) without giving a name. Please
note that the same condition must be used in two runs. For example,
you cannot use '-v 10' earlier and resume the task with '-v 5'.

The value of some options can be "null." For example, `-log2c -1,0,1
-log2 "null"' means that C=2^-1,2^0,2^1 and g=LIBSVM's default gamma
value. That is, you do not conduct parameter selection on gamma.

Example
=======

> python grid.py -log2c -5,5,1 -log2g -4,0,1 -v 5 -m 300 heart_scale

Users (in particular MS Windows users) may need to specify the path of
executable files. You can either change paths in the beginning of
grid.py or specify them in the command line. For example,

> grid.py -log2c -5,5,1 -svmtrain "c:\Program Files\libsvm\windows\svm-train.exe" -gnuplot c:\tmp\gnuplot\binary\pgnuplot.exe -v 10 heart_scale

Output: two files
dataset.png: the CV accuracy contour plot generated by gnuplot
dataset.out: the CV accuracy at each (log2(C),log2(gamma))

The following example saves running time by loading the output file of a previous run.

> python grid.py -log2c -7,7,1 -log2g -5,2,1 -v 5 -resume heart_scale.out heart_scale

Parallel grid search
====================

You can conduct a parallel grid search by dispatching jobs to a
cluster of computers which share the same file system. First, you add
machine names in grid.py:

ssh_workers = ["linux1", "linux5", "linux5"]

and then setup your ssh so that the authentication works without
asking a password.

The same machine (e.g., linux5 here) can be listed more than once if
it has multiple CPUs or has more RAM. If the local machine is the
best, you can also enlarge the nr_local_worker. For example:

nr_local_worker = 2

Example:

> python grid.py heart_scale
[local] -1 -1 78.8889  (best c=0.5, g=0.5, rate=78.8889)
[linux5] -1 -7 83.3333  (best c=0.5, g=0.0078125, rate=83.3333)
[linux5] 5 -1 77.037  (best c=0.5, g=0.0078125, rate=83.3333)
[linux1] 5 -7 83.3333  (best c=0.5, g=0.0078125, rate=83.3333)
.
.
.

If -log2c, -log2g, or -v is not specified, default values are used.

If your system uses telnet instead of ssh, you list the computer names
in telnet_workers.

Calling grid in Python
======================

In addition to using grid.py as a command-line tool, you can use it as a
Python module. 

>>> rate, param = find_parameters(dataset, options)

You need to specify `dataset' and `options' (default ''). See the following example.

> python

>>> from grid import *
>>> rate, param = find_parameters('../heart_scale', '-log2c -1,1,1 -log2g -1,1,1')
[local] 0.0 0.0 rate=74.8148 (best c=1.0, g=1.0, rate=74.8148)
[local] 0.0 -1.0 rate=77.037 (best c=1.0, g=0.5, rate=77.037)
.
.
[local] -1.0 -1.0 rate=78.8889 (best c=0.5, g=0.5, rate=78.8889)
.
.
>>> rate
78.8889
>>> param
{'c': 0.5, 'g': 0.5}


Part III: LIBSVM format checking tools

Introduction
============

`svm-train' conducts only a simple check of the input data. To do a
detailed check, we provide a python script `checkdata.py.'

Usage: checkdata.py dataset

Exit status (returned value): 1 if there are errors, 0 otherwise.

This tool is written by Rong-En Fan at National Taiwan University.

Example
=======

> cat bad_data
1 3:1 2:4
> python checkdata.py bad_data
line 1: feature indices must be in an ascending order, previous/current features 3:1 2:4
Found 1 lines with error.