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
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.
- 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
gcc. Additionally, the following packages need to be installed
libconfig libarchive (from homebrew-alt)
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.