submine

submine is a research‑grade Python library for frequent subgraph mining that provides a unified, safe, and extensible interface over heterogeneous mining algorithms implemented in Python, C++, and Java.

The goal of submine is to let users focus on what to mine rather than how each algorithm expects its input. Users select an algorithm and parameters; submine automatically validates inputs, converts graph formats, and executes the backend in a controlled and reproducible manner.

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Key Features

• Algorithm‑centric API You specify the mining algorithm and parameters; submine handles format adaptation and execution.

• Direct format transcoding (no redundant rewrites) Input graphs are converted directly into the native format required by the selected algorithm.

• Multi‑format graph support Edge lists, gSpan datasets, single‑graph .lg files, and GEXF are supported out of the box.

• Safe and reproducible execution Parameter validation, deterministic format detection, and hardened subprocess execution are enforced by default.

• Extensible design New algorithms can be added via a clean backend interface without modifying core logic.

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Supported Algorithms

gSpan (Frequent Subgraph Mining)

• Graph type: Multiple graphs (transactional dataset)
• Typical use case: Discovering frequent substructures across many graphs
• Backend: C++

The gSpan backend in submine is a C++ implementation adapted and extended from the widely used gBoost / gSpan reference implementations, with additional input validation, format handling, and Python bindings for safe integration.

SoPaGraMi (Single‑Graph Pattern Mining)

• Graph type: Single large graph
• Typical use case: Social, biological, or information networks
• Backend: C++

SoPaGraMi is used for scalable subgraph mining on a single graph, where frequency is defined structurally rather than transactionally.

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Supported Input Formats

submine automatically detects the input format and converts it to the format required by the chosen algorithm:

• Edge lists: .txt, .edgelist
• gSpan datasets: .data, .data.x, .data.N
• SoPaGraMi graphs: .lg
• GEXF: .gexf

Format detection is deterministic and does not rely on user‑supplied flags.

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Installation

Standard installation

pip install submine

Development installation

pip install -e ".[dev]"

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Basic Usage

gSpan example

from submine.api import mine_subgraphs

results = mine_subgraphs(
    data="graphs.data",
    algorithm="gspan",
    min_support=5
)

Parameters

• data (str or path): Path to the input graph dataset
• algorithm (str): Mining algorithm ("gspan", "sopagrami", …)
• min_support (int): Minimum support threshold (algorithm‑specific semantics)

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SoPaGraMi example

results = mine_subgraphs(
    data="citeseer.lg",
    algorithm="sopagrami",
    min_support=100,
    sorted_seeds=4,
    dump_images_csv=True,
    dump_sample_embeddings=False,
    out_dir="."
)

SoPaGraMi‑specific parameters

• min_support (int): Minimum frequency threshold
• sorted_seeds (int): Seed sorting strategy (implementation‑specific)
• dump_images_csv (bool): Whether to dump pattern images as CSV metadata
• dump_sample_embeddings (bool): Whether to dump sample embeddings (experimental)
• out_dir (str or path): Output directory for results (default: ./sopagrami_result)

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Design Philosophy

• No algorithm‑specific I/O burden on the user Users never manually convert graph formats.

• Minimal assumptions about graph structure Directed/undirected and labeled/unlabeled graphs are handled at the backend level.

• Research‑grade transparency Backends are explicitly documented and citable.

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Citation

If you use gSpan, please cite:

@inproceedings{yan2002gspan,
  title={gspan: Graph-based substructure pattern mining},
  author={Yan, Xifeng and Han, Jiawei},
  booktitle={Proceedings of the IEEE International Conference on Data Mining},
  pages={721--724},
  year={2002}
}

If you use SoPaGraMi, please cite:

@article{nguyen2020fast,
  title={Fast and scalable algorithms for mining subgraphs in a single large graph},
  author={Nguyen, Lam BQ and Vo, Bay and Le, Ngoc-Thao and Snasel, Vaclav and Zelinka, Ivan},
  journal={Engineering Applications of Artificial Intelligence},
  volume={90},
  pages={103539},
  year={2020}
}

To cite this library:

@misc{amure_submine,
  title  = {submine: A Unified Subgraph Mining Library},
  author = {Amure, Ridwan},
  year   = {2025},
  url    = {https://github.com/instabaines/submine}
}