MultiXrank - heterogeneous MULTIlayer eXploration by RANdom walK with restart. MultiXrank is a Python package for the exploration of heterogeneous multilayer networks, with random walk with restart method. It permits prioritization of nodes between full heterogeneous networks, whatever their complexities.
Project description
MultiXrank is a Python package for the exploration of heterogeneous multilayer networks, with random walk with restart method. It permits prioritization of nodes between full heterogeneous networks, whatever their complexities. If you use MultiXrank in scientific works, please cite the following article:
Baptista, A., González, A., Baudot, A.. Universal Multilayer Network Exploration by Random Walk with Restart, arXiv:2107.04565.
Commands for a quick installation:
conda create --name multixrank python=3.10 -y
python3 -m pip install multixrank
Commands for a quick working example in the python console:
import multixrank
multixrank.Example().write(path="airport")
This generates a working example based on the “airport” multiplex:
`-- airport
|-- bipartite
| |-- 1_2.tsv
| |-- 1_3.tsv
| `-- 2_3.tsv
|-- config_minimal.yml
|-- multiplex
| |-- 1
| | |-- FR26.tsv
| | |-- FR3.tsv
| | |-- FR3_2.tsv
| | `-- FR7.tsv
| |-- 2
| | |-- UK15.tsv
| | |-- UK26.tsv
| | `-- UK3.tsv
| `-- 3
| |-- G1.tsv
| |-- G24.tsv
| `-- G6.tsv
`-- seeds.txt
The minimal configuration file ‘config.yml’ looks like this.
multiplex:
1:
layers:
- multiplex/1/FR26.tsv
- multiplex/1/FR3.tsv
- multiplex/1/FR7.tsv
2:
layers:
- multiplex/2/UK15.tsv
- multiplex/2/UK26.tsv
- multiplex/2/UK3.tsv
3:
layers:
- multiplex/3/G1.tsv
- multiplex/3/G24.tsv
- multiplex/3/G6.tsv
bipartite:
bipartite/1_2.tsv:
source: 1
target: 2
bipartite/1_3.tsv:
source: 1
target: 3
bipartite/2_3.tsv:
source: 2
target: 3
seed:
seeds.txt
import multixrank
multixrank_obj = multixrank.Multixrank(config="airport/config_minimal.yml", wdir="airport")
ranking_df = multixrank_obj.random_walk_rank()
multixrank_obj.write_ranking(ranking_df, path="output_airport")
multixrank_obj.to_sif(ranking_df, path="output_airport/airport_seed7_top3.sif", top=3)
This runs the software and writes the results to the output_airport folder:
$ ls output_airport/
airport_seed7_top3.sif multiplex_1.tsv multiplex_2.tsv multiplex_3.tsv
There is a ranking file for each multiplex:
$ head -n 4 output_airport/multiplex_1.tsv
multiplex node score
1 7 0.250002565842259
1 169 0.0025983048938841304
1 199 0.0018837852068513332
The MultiXrank documentation is hosted at ReadTheDocs.
MultiXrank is maintained by Anthony Baptista (anthony dot baptista at univ-amu dot fr) and Aitor González (aitor dot gonzalez at univ-amu dot fr)
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.