buhito

buhito is a Python library for enumerating graphlets and analyzing graphlet-based features from graphs.

Installation

git clone https://github.com/lanl/buhito.git
cd buhito
uv sync --all-extras

Quick Start

Enumerate graphlets with BFS

import networkx as nx
from buhito import generate_subgraphs_breadthwise

G = nx.petersen_graph()

nx.set_node_attributes(G, {n: "C" for n in G.nodes}, "atom_key")
nx.set_edge_attributes(G, {e: "1" for e in G.edges}, "bond_key")

fp, bitinfo = generate_subgraphs_breadthwise(
    G,
    depth=4,
    return_nodewise=False,
    full_hash=True,
    node_key="atom_key",
    edge_key="bond_key"
)

print("Graphlet fingerprint length:", len(fp))

Enumerate graphlets with DFS

from buhito import generate_subgraphs_depthwise

subsets, counts = generate_subgraphs_depthwise(G, maxlen=4)
print("Found graphlet subsets:", len(subsets))

Examples

Available example scripts:

• examples/plotting_example.py — visualize graphlets from the Petersen graph
• examples/qm9/benchmark_graphlet_featurizers_train_test.py — benchmark featurizers on QM9 chemical properties data

Run Examples

QM9

python examples/qm9/benchmark_graphlet_featurizers_train_test.py \
  --data examples/qm9/qm9data/qm9_processed.csv \
  --max-len 2 3 4 5 6 \
  --repeats 3 \
  --n-jobs -1 \
  --outdir bench_qm9

Testing

pytest tests/

Package structure

• src/buhito/ — core features
• src/buhito/converters.py — converters to NetworkX graphs
• src/buhito/plotting.py — graphlet visualization helpers

Authors

• Yulia Pimonova (LANL)
• Nicholas Lubbers (LANL)
• Nathan Lemons (LANL)
• Pieter Swart (LANL)

Citation

If you use buhito in your work, please cite this repository. A publication citation is coming.

Copyright and licensing

buhito is released under the BSD-3 License. See LICENSE.txt for the full license.

The copyright to buhito is owned by Triad National Security, LLC and is released for open source use as project number O5043.

© 2026. Triad National Security, LLC. All rights reserved. This program was produced under U.S. Government contract 89233218CNA000001 for Los Alamos National Laboratory (LANL), which is operated by Triad National Security, LLC for the U.S. Department of Energy/National Nuclear Security Administration. All rights in the program are. reserved by Triad National Security, LLC, and the U.S. Department of Energy/National Nuclear Security Administration. The Government is granted for itself and others acting on its behalf a nonexclusive, paid-up, irrevocable worldwide license in this material to reproduce, prepare. derivative works, distribute copies to the public, perform publicly and display publicly, and to permit. others to do so.