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134 6 ⋅ software Let us recap. Sparse matrices are the best way to store graphs in Matlab. They provide all the necessary pieces to integrate cleanly with “natural” Matlab syntax and allow us access to their internals to run algorithms efficiently. 6.2.2 Other packages There are other graph packages for Matlab too. One of the first was the meshpart toolkit [Gilbert and Teng, 2002], which focuses on partitioning meshes. A more recent example is Matgraph [Scheinerman, 2009], which con- tains a rich set of graph constructors to create adjacency matrices for standard graphs. It also provides an interface to support graph properties, such as la- bels and weights. Various authors released individual graph theory functions on the Mathworks File Exchange [Various, 2009a, search for dijkstra]. For example, the Exchange contains more than three separate implementations of Dijkstra’s shortest path algorithm. A full comparison of these packages is beyond the scope of this chapter. The only package with the breadth of MatlabBGL is the bioinformatics graph package, which is also based on the Boost graph library. Among the na- tive Matlab packages, only meshpart [Gilbert and Teng, 2002] handles large graphs well. Both MatlabBGL and gaimc are distinguished because they • scaletolargegraphs; • support no-data-copy paths when possible; and • provideasuiteofalgorithms. 6.3 matlabbgl MatlabBGL is the first package we discuss. Its source code lives publicly on LaunchPad, http://launchpad.net/matlab-bgl. As previously mentioned, MatlabBGL is a Matlab package for working with graphs. It uses the Boost graph library to implement the graph algo- rithms efficiently. MatlabBGL is designed to compute on large sparse graphs with hundreds of thousands of nodes. To do so, the library consists of “wrap- pers” for algorithms from the Boost graph library. Each wrapper is a mex function and it is callable directly from Matlab. The goal of the library was to introduce as little new material into Matlab as possible. To facilitate this, MatlabBGL does not introduce a new data structure and uses the Matlab sparse matrix type as the graph type directly.PDF Image | Instagram Cheat Sheet
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