Dynamic Two-Way Seriation

Two-way Incremental Seriation based on Hamiltonian Path is a package that takes a sparse term-document matrix provided in libsvm format, and calculates the seriation of the term space. Several distance functions are available.

Usage

Given an input matrix in sparse libsvm format, the class DynamicBiseriation will calculate the biseriation of the matrix. Given a sequence of matrices, it will calculate the updates to the biseration. Different distance functions and biseriation heuristics are available.

Usage:

$ java -jar DynamicBiseriation.jar [options] collection_file [update_files]

Arguments:

-d Distance   Distance function (default: Euclidean):
                 Correlation
                 Cosine
                 Euclidean
                 Manhattan
                 MutualInformation
-h heuristic  Heuristic type (default: leftright):
                 leftright
                 insert

Examples:

$ java -jar DynamicBiseriation.jar test_data/collection.dat
$ java -jar -d Correlation -h insert DynamicBiseriation.jar \
    test_data/collection.dat test_data/collection-update.dat

Compilation

Issuing ant jar should compile the classes and create the jar file in build/jar.

Citation

If you use this code, please cite:

Wittek, P. (2013). Two-Way Incremental Seriation in the Temporal Domain with Three-dimensional Visualization: Making Sense of Evolving High-Dimensional Data Sets. Computational Statistics and Data Analysis.

A preprint of the manuscript is available for download here:

http://hdl.handle.net/2320/12278