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A GraphML file consists of an XML file containing a graph element, within which is an unordered sequence of node and edge elements. Each node element should have a distinct id attribute, and each edge element has source and target attributes that identify the endpoints of an edge by having the same value as the id attributes of those endpoints.
Cytoscape, an open source bioinformatics software platform for visualizing molecular interaction networks, loads and save previously-constructed interaction networks in GML. igraph, an open source network analysis library with interfaces to multiple programming languages. Gephi, an open source graph visualization and manipulation software.
DOT is a graph description language, developed as a part of the Graphviz project. DOT graphs are typically stored as files with the .gv or .dot filename extension — .gv is preferred, to avoid confusion with the .dot extension used by versions of Microsoft Word before 2007.
MATLAB (an abbreviation of "MATrix LABoratory" [22]) is a proprietary multi-paradigm programming language and numeric computing environment developed by MathWorks.MATLAB allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages.
Older (.OPJ), but not newer (.OPJU), Origin project files can be read by the open-source LabPlot or SciDAVis software. The files can also be read by QtiPlot but only with a paid "Pro" version. Finally the liborigin [1] library can also read .OPJ files such as by using the opj2dat script, which exports the data tables contained in the file.
The slope number of a graph is the minimum number of distinct edge slopes needed in a drawing with straight line segment edges (allowing crossings). Cubic graphs have slope number at most four, but graphs of degree five may have unbounded slope number; it remains open whether the slope number of degree-4 graphs is bounded. [12]
Wolfram Mathematica is a software system with built-in libraries for several areas of technical computing that allows machine learning, statistics, symbolic computation, data manipulation, network analysis, time series analysis, NLP, optimization, plotting functions and various types of data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in ...
Graph attention network is a combination of a graph neural network and an attention layer. The implementation of attention layer in graphical neural networks helps provide attention or focus to the important information from the data instead of focusing on the whole data.