RDyn: graph benchmark handling community dynamics
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README.md

RDyn: graph benchmark handling community dynamics

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Graph models provide an understanding of the dynamics of network formation and evolution; as a direct consequence, synthesizing graphs having controlled topology and planted partitions has been often identified as a strategy to describe benchmarks able to assess the performances of community discovery algorithm. However, one relevant aspect of real-world networks has been ignored by benchmarks proposed so far: community dynamics. As time goes by network communities rise, fall and may interact with each other generating merges and splits. Indeed, during the last decade dynamic community discovery has become a very active research field: in order to provide a coherent environment to test novel algorithms aimed at identifying mutable network partitions we introduce RDyn, an approach able to generates dynamic networks along with time-dependent ground-truth partitions having tunable quality.

Citation

If you use our algorithm please cite the following works:

Giulio Rossetti "RDyn: graph benchmark handling community dynamics." Journal of Complex Networks 2017. doi:10.1093/comnet/cnx016

Installation

In order to install the package just download (or clone) the current project and copy the demon folder in the root of your application.

Alternatively use pip:

sudo pip install rdyn

Generator Characteristics

For the main specifics of the RDyn algorithm please refer to the original publication. The current release is shipped with only conductance as community quality function.

In order to speed up the computation a simplified flag has been introduced: setting it to True community quality is checked incrementally only on communities selected for merge/split operations.

NB: when set the simplified=True an approximation of the original process is executed: some network characteristics can be not preserved (e.g. degree distribution, interactions time to live).

Execution

The algorithm can be used as standalone program as well as integrated in python scripts.

Standalone

RDyn can be executed as standalone script with the following parameters:

Positional arguments

Name Type Description Default
nodes Integer Number of nodes 1000
iterations Integer Number of iterations 1000
simplified Boolean Simplified execution True

Optional arguments

Flag Extended Name Type Description Default
-d --avg_degree Integer Average node degree 15
-s --sigma Float Percentage of node's edges within a community .7
-l --lbd Float Lambda community size distribution 1
-a --alpha Float Alpha degree distribution 3
-p --prob_action Float Probability of node action 1
-r --prob_renewal Float Probability of edge renewal .8
-q --quality_threshold Float Conductance quality threshold .3
-n --new_nodes Float Probability of node appearance 0
-j --delete_nodes Float Probability of node vanishing 0
-e --max_events Integer Max number of community events for stable iteration 1

All parameters have a default value. In order to generate a dynamic graph of 1000 nodes for 1000 iterations applying the simplified version of the algorithm just use:

python rdyn 1000 1000 True

As python library

RDyn can be also executed within a python program. In order to generate a dynamic network with the default parameter values just use the following snippet

from rdyn import RDyn
rdb = RDyn()
rdb.execute(simplified=True)

To custumize the execution specify the usual parameters during object instantiation.

Output

RDyn generates a folder named results and, for each specific model configuration a subfolder having the following naming convention:

  • nodes_iterations_avgDegree_sigma_renewal_qualityThreshold_maxEvts
  • Example (default parameters): results/1000_1000_15_0.7_0.8_0.3_1

Within such folder the following files are generated:

  • graph-*.txt: Edgelist representation of the generated graph. One file for stable iteration.
  • communities-*.txt: community description. One file for stable iteration.
  • events.txt: summary of merge\split action per stable iteration.
  • interaction.txt: dynamic graph description as edge stream.

The syntax of each class of output files is the following:

Communities

A community per line descibed as:

community_id	[node1, node2, node3, ..., nodeN]

Events

An block of events per stable iteration descibed as:

iteration_id:
 	Event1
 	Event2
 	...
 	EventN

Where the available events are:

  • START, used for the first stable iteration
  • SPLIT id_origina_community [id_new_com1, id_new_com2]
  • MERGE [id_old_com1, id_old_com2] the new com will inherit id_old_com_1

Interactions

One interaction per line with the syntax:

iteration_id interaction_seq operation node1 node2

Where:

  • iteration_id identify the iteration in which the interaction occurs
  • interaction_seq describe an absolute ordering among all the interactions
  • operation define if the interaction produces a new edge + or destroy an existing one -
  • node1 and node2 are interaction endpoints

Example:

123	5361	+	385	390
123	5362	-	385	379

Dependencies

RDyn is written in python and requires the following package to run:

  • python>=2.7.11
  • networkx==1.11
  • numpy==1.11.1
  • tqdm
  • six
  • future