Harry - A Tool for Measuring String Similarity
This software belongs to the publication
Konrad Rieck and Christian Wressnegger. Harry: A Tool for Measuring String Similarity. Journal of Machine Learning Research (JMLR), 17(9): 1-5, 2016 http://jmlr.org/papers/volume17/rieck16a/rieck16a.pdf
Harry is a small tool for comparing strings. The tool supports several common distance and kernel functions for strings as well as some excotic similarity measures. The focus of Harry lies on implicit similarity measures, that is, comparison functions that do not give rise to an explicit vector space. Examples of such similarity measures are the Levenshtein distance, the Jaro-Winkler distance or the spectrum kernel.
During operation Harry loads a set of strings from input, computes the specified similarity measure and writes a matrix of similarity values to output. The similarity measure can be computed based on the granulartiy of bytes, bits and tokens (words) contained in the strings. The configuration of this process, such as the input format, the similarity measure and the output format, are specified in a configuration file and can be additionally refined using command-line options.
Harry is implemented using OpenMP, such that the computation time for a set of strings scales linear with the number of available CPU cores. Moreover, efficient implementations of several similarity measures, effective caching of similarity values and low-overhead locking further speedup the computation.
Harry complements the tool sally(1) that embeds strings in a vector space and allows computing vectorial similarity measures, such as the cosine distance and the bag-of-words kernel.
The following similarity measures are supported so by Harry
dist_bag Bag distance dist_compression Normalized compression distance (NCD) dist_damerau Damerau-Levenshtein distance dist_hamming Hamming distance dist_jaro Jaro distance dist_jarowinkler Jaro-Winkler distance dist_kernel Kernel-based distance dist_lee Lee distance dist_levenshtein Levenshtein distance dist_osa Optimal string alignment (OSA) distance kern_distance Distance substitution kernel (DSK) kern_spectrum Spectrum kernel kern_subsequence Subsequence kernel (SSK) kern_wdegree Weighted-degree kernel (WDK) sim_braun Braun-Blanquet coefficient sim_dice Soerensen-Dice coefficient sim_jaccard Jaccard coefficient sim_kulczynski second Kulczynski coefficient sim_otsuka Otsuka coefficient sim_simpson Simpson coefficient sim_sokal Sokal-Sneath coefficient
- OpenMP >= 2.5 (need to be supported by the C compiler)
- 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 Harry on Debian and Ubuntu Linux
gcc libz-dev libconfig8-dev libarchive-dev
For bootstrapping Harry from the GIT repository or manipulating the automake/autoconf configuration, the following additional packages are necessary.
automake autoconf libtool
Mac OS X
For compiling Harry on Mac OS X a working installation of Xcode is needed.
Moreover, a C compiler supporting OpenMP is required (
clang from Xcode
currently does not support OpenMP). The following packages need to be
installed from Homebrew.
gcc43 (or download from <http://hpc.sourceforge.net>) libconfig libarchive (from homebrew-alt)
Due to the vague state of OpenBSD multi-threading, neither the default
nor the packaged
gcc seem to correctly support OpenMP. To get Harry to
run you can only try to build gcc from scratch
Compilation & Installation
From GIT repository first run
From tarball run
./configure [options] make make check make install
Options for configure
--prefix=PATH Set directory prefix for installation
By default Harry is installed into /usr/local. If you prefer a different location, use this option to select an installation directory.
--enable-prwlock Enable support for POSIX read-write locks
This feature enables read-write locks (rwlocks) from the POSIX thread library. The locks can accelerate the run-time performance on multi-core systems. However, these POSIX locks are not guaranteed to interplay with OpenMP and thus may not work on all platforms.
--enable-md5hash Enable MD5 as alternative hash
Harry uses a hash function for mapping tokens to symbols. 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.