clsd

A C++ implementation of the LSD algorithm to detect super bubbles.

Install

To install:

1. Clone git repro.
2. Run configure.
3. Run make.

    git clone [email protected]:Fabianexe/clsd.git
    cd clsd
    ./configure 
    make

Input

clsd needs an edge list as input file. The format is that in every line is one edge, where the labels of the vertices are seperated by a space or tab. As an example, a graph with the directed edges: 1->2, 1->3, 2->4, and 3->4 would have this file:

1 2
1 3
2 4
3 4

The file could contain multi-edges but the parser ignores them because they have no information of superbubbles. Many edgelist writes put properties behind this for example an edge 1->2 with a weight 0.2 would look like:

1 2 0.2

This is also possible but again clsd ignores the weights.

Statistics

clsd can compute different stastistics. Note that clsd ignores multi-edges. Thus every stastistic is done by ignoring multiple appearence of the same edge. The output is a list of numbers sperated by &. Before content line is the header line. The header shorts mean:

Graph Properties

Metric	Short	Paper	Description
Vertices	N	-	Number of Vertices
Edges	M	-	Number of Edges
Multi Edges	ME	-	Fraction of Edges that are multi edges
Max Degree	deg	-	The largest degree
Graph Density	GD	-	(2m)/(n(n-1))
Connected components	CC	-	The number of connected components
Assortativity	R	Mixing patterns in networks	Valiation of euqal degrees on neighbor vertices
Self-Similarity	SS	Towards a Theory of Scale-Free Graphs: Definition, Properties, and Implications	This is maximized when high-degree nodes are connected to other high-degree nodes

Digraph Properties

Metric	Short	Paper	Description
Max in Degree	$deg_\leftarrow$	-	The largest inDegree
Max out Degree	$deg_\rightarrow$	-	The largest outDegree
Strongly connected components	SCC	-	The number of strongly connected components
Bidirectional edges	BE	-	Fraction of the edges that have invertet edge in Each
Directed assortativity	$R_{\leftarrow\leftarrow}$	Edge direction and the structure of networks	Valiation of euqal degrees on neighbor vertices by comparing in- to in-degree
Directed assortativity	$R_{\leftarrow\rightarrow}$	Edge direction and the structure of networks	Valiation of euqal degrees on neighbor vertices by comparing in- to out-degree
Directed assortativity	$R_{\rightarrow\leftarrow}$	Edge direction and the structure of networks	Valiation of euqal degrees on neighbor vertices by comparing out- to in-degree
Directed assortativity	$R_{\rightarrow\rightarrow}$	Edge direction and the structure of networks	Valiation of euqal degrees on neighbor vertices by comparing out- to out-degree
Heterogeneity index	H	Entropy and Heterogeneity Measures for Directed Graphs	Entropy of neighbor degrees

Superbubble Properties

Metric	Short	Description
Number of Superbubbles	S	How many superbubbles in the graph
Vertices Superbubbles	VS	The fraction of vertices that are part of a superbubble
Edges Superbubbles	ES	The fraction of edges that are part of a superbubble
Number of Mini-Superbubbles	MS	How many mini superbubbles in the graph i.e. superbubbles with two vertices
Vertices Complex Superbubbles	VCS	The fraction of vertices that are part of a complex superbubble
Edges Complex Superbubbles	ECS	The fraction of edges that are part of a complex superbubble
Max Vertices	mVS	What is the maximum of vertices in one superbubble
Max Edges	mES	What is the maximum of edges in one superbubble
Superbubble Complex	C	How many non-overlapping superbubble complexes exist
Superbubble Complex size	CS	The maximum number of superbubbles in one complex
Deepest Superbubble	depth	The maximal depth that a superbubble have
maximal paths in Superbubble	P	The maximal number of a paths in one superbubble
longest path in Superbubble	PL	The maximal length of a path in a superbubble

Non-mini Superbubble Properties

Metric	Short	Description
Average number of paths	aP	The average number of paths in non-mini superbubbles
Average path length	aPL	The average path length in non-mini superbubbles
Superbubble Density	SD	The average value of (2m)/(n(n-1)) for all superbubbles in non-mini superbubbles