Description:
pmotiflib 1.0.2
pmotif_lib
Perform motif detection, either with traditional frequency, or with positional metrics for each graphlet occurrence.
This library implements each step of a (p)motif detection pipeline such as
graphlet detection in networks
randomization of networks
frequency comparison of graphlet occurrences
positional metric comparison of graphlet occurrences.
Setup
Install this package:
pip install pmotif-lib
This library relies on the gtrieScanner tool. Please download it, compile it, and add the executable to your path.
Finally, this library loads environment variables. Create an .env file::
export DATASET_DIRECTORY=/path/where/edgelists/are/located
export EXPERIMENT_OUT=/path/where/raw/graphlets/and/pmetric/should/go
export GTRIESCANNER_EXECUTABLE=/path/to/the/gtriescanner/executable
export WORKERS=1 # Optional, controls the max. degree of parallelization
In order to make these variablea available to the library, use source .env before command line usage!
You can also use the python-dotenv package to load the .env file from python code:
from dotenv import load_dotenv
load_dotenv(".env")
Usage
showcase/ contains a number of examples:
graphlet detection
p-graphlet detection
motif detection
p-motif detection
After installing pmotif_lib, navigate into showcase/, run source .showcase_env, and then run python3 graphlet_detection (or one of the other examples).
This expects the gtrieScanner executable to be in your system's path under gtrieScanner!
Glossary
Induced Subgraph: A graph created by cutting out a set of nodes from a graph G, retaining all edges between these nodes
Isomorphic graphs: Graphs, that are structurally the same when ignoring node labels
Isomorphic Classes of Size k: A set of graphs with k nodes, so that every other graph with k nodes is isomorphic to one graph in the set
k-Graphlet: An isomorphic class of size k, so that at least one induced subgraph in a graph G is isomorphic to that class
Graphlet Occurrences: All induced sub-graphs in a graph G that belong to a specific k-Graphlet
Graphlet Frequency: The number of graphlet occurrences of a specific k-graphlet in a graph G
Graph Motif: A k-Graphlet, which has a graphlet frequency which is significantly higher than expected, usually tested against randomized graphs generated based on G
p-Motif: A k-Graphlet, which has graphlet occurrences with a significant expression of a positional metric, when compared against randomized graphs generated based on G
License
For personal and professional use. You cannot resell or redistribute these repositories in their original state.
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