higorsmonteiro / fast_fibrationp

graph fibrations on julia

Fibrations symmetries on Julia

Implementation in Julia for the fast fibration partitioning (FFP) algorithm on directed networks. The algorithm is presented in the paper of Monteiro et. al. (link for the draft to be available soon). In this paper we use the codes in this repo for proper perfomance comparison between the FFP algorithm and other common methods for the identification of fibration symmetries. Here, we give general guidance on how to obtain the fibration partitioning, or minimal balanced coloring, of any directed network parsed through a CSV file.

Fibration symmetries in context of complex networks are introduced in the recent work of Morone et. al..

Importing

To use the julia package of name 'FastFibration' in the command line, it is necessary first to access the package command line of julia (accessed via ']' in the julia REPL) and use the following command inside the fast_fibration/ folder:

pkg> activate .
julia> using FastFibration

The activate command above is not necessary if the package is used in jupyter notebooks.

Usage

To find the fibration partitioning of a given directed network it is necessary only the information of the network structure (nodes and edges) and the types of each edge (in case the edges are multidimensional). For this, the network must be parsed as an CSV file following the structure of an edgelist containing two essential informations (source and target) and one optional information (the type of the edge for multiplex scenarios). For instance, let us consider the graph below where the edges can assume two possible values: 'positive' or 'negative'.

The edgefile for this graph, called net.csv should follow the format below:

Source,Target,Type
1,2,positive
2,1,positive
3,1,positive
3,4,positive
4,2,negative
4,3,positive
4,5,positive
6,3,negative
7,4,negative
8,6,positive
8,7,positive

In this file, the third column refers to the possible values of each edge. There is no restriction on the specific format of its values as long as each different string represent a different edge type. For the first (source) and second (target) columns the node labels must be inside the interval [1,N] where N is the total number of nodes in the graph.

Thus, to extract the fibers of the network provided by this edgefile, we run the following

    graph = FastFibration.graph_from_csv("path/to/edgefile", true)
    fiber_partition = FastFibration.fast_fibration(graph)
    number_nontrivial_fibers, total_fibers, fiber_map = FastFibration.extract_fiber_groups(fiber_partition)

Where fiber_partition is a container or array holding Fiber structures. To access the nodes belonging to a specific fiber, we can check .nodes, like in fiber_partition[1].nodes for the first element of the container returned. To get the information about the number of fibers, total number of partition elements and which nodes inside each partition element, we can use the results obtained from extract_fiber_groups function, which returns the number of fibers containing more than one node (nontrivial), the total number of fibers (including single node fibers) and a julia dictionary fiber_map. The dictionary fiber_map has as keys the indexes of fiber_partition and as values the array of node labels belonging to each fiber of fiber_partition.

Tests

In the folder fast_fibration/data/ there are 7 seven different networks which provides basic example networks to test the code. All these files represent simple circuits on which is easy to check the correctness of the algorithm, with exception the file test_Ecoli.csv, which represents the main dataset used in the previous work of Morone et. al..

License

MIT License

Copyright (c) 2021 higorsmonteiro [email protected] and contributors

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

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