directedstructure
Infer communities, hierarchies, and their connection in directed graphs
Maximilian Jerdee, Elizabeth Bruch, Mark Newman
This Python package uses Bayesian inference to identify communities and hierarchies of nodes in a directed network, as well as measure the interaction between those structures.
We model community structure using a stochastic block model, hierarchy structure with a Bradley-Terry model, and their interaction according to our work (link forthcoming).
Installation
pip install directedstructure
Or build locally by cloning this repository and running
pip install .
in the base directory (requires a C++ compiler).
Usage
The public API has three objects: Config, fit, and Result.
Load a network
import directedstructure as ds
import networkx as nx
G = nx.read_gml("examples/data/networks/friends.gml")
Edges may carry a type attribute ('dominant' or 'neutral') to distinguish directed pairwise comparisons from symmetric ties. If no type information is provided all edges are treated as dominant.
Configure the model
config = ds.Config(
groups_model="general_canonical", # community structure preset
hierarchy_model="bradley_terry_ties", # auto-selected if omitted
interaction="coupled", # coupling between communities and hierarchy
)
Config is a frozen dataclass — see the API docs for the full list of parameters (mixing variation, degree correction, individual/group depth, etc.).
Run inference
result = ds.fit(
config, G,
num_samples=1000, # posterior samples to collect
sweeps_per_sample=10, # MCMC sweeps between samples
timeout=60.0, # wall-clock limit in seconds
seed=42,
)
Inspect results
# A concise summary is printed by the result itself
print(result)
# directedstructure.Result(n=62, samples=1000, mean_groups=3.2, mdl=412.100)
# Network-level posterior summary: columns parameter, mean, std, hdi_lo, hdi_hi
# Includes ICC (intraclass correlation) and sigma_T.
# Computed in C++ without materialising the full samples DataFrame.
npdf = result.network_properties_df() # default 90% HDI
npdf90 = result.network_properties_df(prob=0.90)
icc_row = npdf[npdf["parameter"] == "ICC"].iloc[0]
print(f"ICC = {icc_row['mean']:.3f} 90% HDI [{icc_row['hdi_lo']:.3f}, {icc_row['hdi_hi']:.3f}]")
# Per-node posterior summary: columns node, score_mean, score_std, group, group_score_mean
# For n ≤ 3000 uses the consensus partition (posterior summary);
# for larger networks falls back to the MDL partition with a warning.
node_df = result.node_properties_df() # auto
node_df = result.node_properties_df(partition="consensus") # always consensus
node_df = result.node_properties_df(partition="mdl") # always MDL (free)
print(node_df.sort_values("score_mean", ascending=False).head())
# Minimum description length value (model comparison)
print(result.mdl_value)
# n×n co-assignment frequency matrix (posterior)
comatrix = result.coincidence_matrix()
# Full posterior samples DataFrame (all parameters + per-node groups/scores)
samples_df = result.samples_df()
# Posterior-predictive probability of each directed outcome between two nodes.
# Returns {"a_to_b": ..., "tie": ..., "b_to_a": ...}, values sum to 1.
p = result.direction_probabilities("Spain", "Morocco")
# Set ties_allowed=False for standard Bradley-Terry (no tie term).
p = result.direction_probabilities("Spain", "Morocco", ties_allowed=False)
# {"a_to_b": ..., "b_to_a": ...}
Visualization
import matplotlib.pyplot as plt
# Node scores ranked within each inferred community (±1 std error bars,
# group mean line, communities labeled G1/G2/…)
fig, ax = ds.plot_node_properties(result)
plt.savefig("node_scores.png")
# Adjacency matrix of G reordered by inferred community, with colored
# community strips on the top and left edges.
# G can be any graph — it does not have to be the graph used in fit().
fig, ax = ds.plot_adjacency_matrix(result, G, cmap="Greens", title="Network")
plt.savefig("adjacency.png")
# Compose both panels side by side
fig, axes = plt.subplots(1, 2, figsize=(12, 5))
ds.plot_node_properties(result, ax=axes[0])
ds.plot_adjacency_matrix(result, G, ax=axes[1])
fig.tight_layout()
plt.savefig("combined.png")
fig, ax = ds.plot_MCMC_entropy(result) # convergence diagnostic
Export the graph with inferred attributes for use in Gephi or other tools:
ds.write_gml_with_inferences(G, "output.gml", result)
Fixing model components
Pass fixed values in Config to test submodels. For example, to fix group structure from node attributes and infer hierarchy only:
config = ds.Config(group_attribute="department", interaction="independent")
result = ds.fit(config, G)
Or fix the number of groups:
config = ds.Config(num_groups=4)
result = ds.fit(config, G)
Parallel tempering
For complex posteriors, enable parallel tempering:
result = ds.fit(config, G, num_tempering_chains=4, beta=1.0)
Further usage examples can be found in the examples/python/ directory of the
repository and the package documentation.
1 maintainer
Metadata
1 maintainer
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