BiCM package
This is a Python package for the computation of the maximum entropy bipartite configuration model (BiCM) and the projection of bipartite networks on one layer. It was developed with Python 3.5.
You can install this package via pip:
pip install bicm
Documentation is available at https://bipartite-configuration-model.readthedocs.io/en/latest/ .
This package is also a module of NEMtropy that you can find at https://github.com/nicoloval/NEMtropy .
For more solvers of maximum entropy configuration models visit https://meh.imtlucca.it/ .
NOTE of the developer: there was an error in the projection threshold, validating less links than it should have. Please re-run your analysis after updating to the last version (>=3.1)
Basic functionalities
To install:
pip install bicm
To import the module:
import bicm
To generate a Graph object and initialize it (with a biadjacency matrix, edgelist or degree sequences):
from bicm import BipartiteGraph
myGraph = BipartiteGraph()
myGraph.set_biadjacency_matrix(my_biadjacency_matrix)
myGraph.set_adjacency_list(my_adjacency_list)
myGraph.set_edgelist(my_edgelist)
myGraph.set_degree_sequences((first_degree_sequence, second_degree_sequence))
Or alternatively, with the respective data structure as input:
from bicm import BipartiteGraph
myGraph = BipartiteGraph(biadjacency=my_biadjacency_matrix, adjacency_list=my_adjacency_list, edgelist=my_edgelist, degree_sequences=((first_degree_sequence, second_degree_sequence)))
To compute the BiCM probability matrix of the graph or the relative fitnesses coefficients as dictionaries containing the nodes names as keys:
my_probability_matrix = myGraph.get_bicm_matrix()
my_x, my_y = myGraph.get_bicm_fitnesses()
This will solve the bicm using recommended settings for the solver. To customize the solver you can alternatively use (in advance) the following method:
myGraph.solve_tool(light_mode=False, method='newton', initial_guess=None, tolerance=1e-8, max_steps=None, verbose=False, linsearch=True, regularise=False, print_error=True, exp=False)
To get the rows or columns projection of the graph:
myGraph.get_rows_projection()
myGraph.get_cols_projection()
Alternatively, to customize the projection:
myGraph.compute_projection(rows=True, alpha=0.05, method='poisson', threads_num=4, progress_bar=True)
Now version 3 is online, and you can use the package with weighted networks as well using the BiWCM models!
See a more detailed walkthrough in tests/bicm_test or tests/biwcm_test notebooks, or check out the API in the documentation.
How to cite
If you use the bicm module, please cite its location on Github
https://github.com/mat701/BiCM and the
original articles [Vallarano2021], [Saracco2015] and [Saracco2017].
If you use the weighted models BiWCM_c or BiMCM you might consider citing also the paper introducing the solvers of this package [Bruno2023].
References
Author:
Matteo Bruno (BiCM) (a.k.a. mat701)
1 maintainer
Release files for bicm 3.4.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| bicm-3.4.0.tar.gz | 32.7 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| bicm-3.4.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 65.5 kB
Release files / bicm-3.4.0.tar.gz
| Download URL | bicm-3.4.0.tar.gz |
|---|---|
| Size | 32.7 kB |
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| Size | 32.8 kB |
| Tags | Python 3 |
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