Sally - A Tool for Embedding Strings in Vector Spaces

This software belongs to the publication

Konrad Rieck, Christian Wressnegger, and Alexander Bikadorov. Sally: A Tool for Embedding Strings in Vector Spaces Journal of Machine Learning Research (JMLR), 13(Nov):3247-3251, 2012. http://www.jmlr.org/papers/volume13/rieck12a/rieck12a.pdf

Introduction

Sally is a small tool for mapping a set of strings to a set of vectors. This mapping is referred to as embedding and allows for applying techniques of machine learning and data mining for analysis of string data. Sally can be applied to several types of strings, such as text documents, DNA sequences or log files, where it can handle common formats such as directories, archives and text files of string data.

Sally implements a standard technique for mapping strings to a vector space that can be referred to as generalized bag-of-words model. The strings are characterized by a set of features, where each feature is associated with one dimension of the vector space. The following types of features are supported by Sally: bytes, tokens (words), n-grams of bytes and n-grams of tokens.

Sally proceeds by counting the occurrences of the specified features in each string and generating a sparse vector of count values. Alternatively, binary or TF-IDF values can be computed and stored in the vectors. Sally then normalizes the vector, for example using the L1 or L2 norm, and outputs it in a specified format, such as plain text or in LibSVM or Matlab format.

Consult the manual page of Sally for more information.

Dependencies

• zlib >= 1.2.1, http://www.zlib.net/
• libconfig >= 1.3.2, http://www.hyperrealm.com/libconfig/
• libarchive >= 3.1.2, http://libarchive.github.com/

Debian & Ubuntu Linux

The following packages need to be installed for compiling Sally on Debian and Ubuntu Linux

gcc 
libz-dev
libconfig8-dev
libarchive-dev 

The following packages need to be installed for compiling Sally on Centos and RHEL Linux

gcc 
zlib-devel
libconfig-devel
libarchive-devel 

For bootstrapping Sally from the GIT repository or manipulating the automake/autoconf configuration, the following additional packages are necessary.

automake 
autoconf 
libtool

Mac OS X

For compiling Sally on Mac OS X a working installation of Xcode is required including gcc. Additionally, the following packages need to be installed via Homebrew

libconfig   
libarchive (from homebrew-alt) 

OpenBSD

For compiling Sally on OpenBSD the following packages are required. Note that you need to use gmake instead of make for building Sally.

gmake
libconfig
libarchive

For bootstrapping Sally from the GIT repository, the following packages need be additionally installed

autoconf
automake
libtool

Compilation & Installation

From GIT repository, run:

$ ./bootstrap
$ ./configure [options]
$ make
$ make check
$ make install

From tarball, run:

$ ./configure [options]
$ make
$ make check
$ make install

Options for configure

This option sets the prefix of the installation path.

--prefix=PATH           Set directory prefix for installation

This option enables support for OpenMP in Sally. It is still experimental. Sally will execute certain parts of the processing in parallel making use of multi-core architectures where possible.

--enable-md5hash        Enable MD5 as alternative hash

Sally uses a hash function for mapping different features to different dimensions in the vector space. By default the very efficient Murmur hash is used for this task. In certain critical cases it may be useful to use a cryptographic hash as MD5.

Copyright (C) 2010-2015 Konrad Rieck ([email protected]); Christian Wressnegger ([email protected]); Alexander Bikadorov ([email protected])