https://github.com/thinklab-sjtu/pygmtools
A Python Graph Matching Toolkit.
https://github.com/thinklab-sjtu/pygmtools
combinatorial-optimization deep-learning graph-matching python-library
Last synced: 9 months ago
JSON representation
A Python Graph Matching Toolkit.
- Host: GitHub
- URL: https://github.com/thinklab-sjtu/pygmtools
- Owner: Thinklab-SJTU
- License: other
- Created: 2021-10-18T16:33:24.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2024-10-21T16:00:08.000Z (over 1 year ago)
- Last Synced: 2025-05-15T06:49:51.997Z (9 months ago)
- Topics: combinatorial-optimization, deep-learning, graph-matching, python-library
- Language: Python
- Homepage: https://pygmtools.readthedocs.io/
- Size: 128 MB
- Stars: 332
- Watchers: 4
- Forks: 19
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
- Citation: CITATION.cff
Awesome Lists containing this project
README
[](https://pypi.org/pypi/pygmtools/)
[](https://pypi.python.org/pypi/pygmtools/)
[](https://pepy.tech/project/pygmtools)
[](https://pygmtools.readthedocs.io/en/latest/?badge=latest)
[](https://codecov.io/gh/Thinklab-SJTU/pygmtools)
[](https://discord.gg/8m6n7rRz9T)
[](https://qm.qq.com/cgi-bin/qm/qr?k=QolXYJn_M5ilDEM9e2jEjlPnJ02Ktabd&jump_from=webapi&authKey=6zG6D/Js4YF5h5zj778aO5MDKOXBwPFi8gQ4LsXJN8Hn1V8uCVGV81iT4J/FjPGT)
[](https://GitHub.com/Thinklab-SJTU/pygmtools/stargazers/)
-----------------------------------------
``pygmtools`` is published in JMLR! Please [cite our paper](#citing-pygmtools)
if our tools are useful in your research!
-----------------------------------------
``pygmtools`` (Python Graph Matching Tools) provides graph matching solvers in Python and is easily accessible via:
```bash
$ pip install pygmtools
```
Official documentation: https://pygmtools.readthedocs.io
Source code: https://github.com/Thinklab-SJTU/pygmtools
Graph matching is a fundamental yet challenging problem in pattern recognition, data mining, and others.
Graph matching aims to find node-to-node correspondence among multiple graphs, by solving an NP-hard combinatorial
optimization problem.
Doing graph matching in Python used to be difficult, and this library wants to make researchers' lives easier.
To highlight, ``pygmtools`` has the following features:
* *Support various solvers*, including traditional combinatorial solvers (including linear, quadratic, and multi-graph)
and novel deep learning-based solvers;
* *Support various backends*, including ``numpy`` which is universally accessible, and some state-of-the-art deep
learning architectures with GPU support:
``pytorch``, ``paddle``, ``jittor``, ``tensorflow``, ``mindspore``;
* *Deep learning friendly*, the operations are designed to best preserve the gradient during computation and batched
operations support for the best performance.
## Installation
You can install the stable release on PyPI:
```bash
$ pip install pygmtools
```
or get the latest version by running:
```bash
$ pip install -U https://github.com/Thinklab-SJTU/pygmtools/archive/master.zip # with --user for user install (no root)
```
Now the pygmtools is available with the ``numpy`` backend.
The following packages are required, and shall be automatically installed by ``pip``:
```
Python >= 3.8
requests >= 2.25.1
scipy >= 1.4.1
Pillow >= 7.2.0
numpy >= 1.18.5
easydict >= 1.7
appdirs >= 1.4.4
tqdm >= 4.64.1
networkx >= 2.8.8
aiohttp
async-timeout
```
## Available Graph Matching Solvers
This library offers user-friendly API for the following solvers:
* [Two-Graph Matching Solvers](https://pygmtools.readthedocs.io/en/latest/api/_autosummary/pygmtools.classic_solvers.html)
* Linear assignment solvers including the differentiable soft
[Sinkhorn algorithm](https://pygmtools.readthedocs.io/en/latest/api/_autosummary/pygmtools.linear_solvers.sinkhorn.html) [1],
and the exact solver [Hungarian](https://pygmtools.readthedocs.io/en/latest/api/_autosummary/pygmtools.linear_solvers.hungarian.html) [2].
* Soft and differentiable quadratic assignment solvers, including [spectral graph matching](https://pygmtools.readthedocs.io/en/latest/api/_autosummary/pygmtools.classic_solvers.sm.html) [3]
and [random-walk-based graph matching](https://pygmtools.readthedocs.io/en/latest/api/_autosummary/pygmtools.classic_solvers.rrwm.html) [4].
* Discrete (non-differentiable) quadratic assignment solver
[integer projected fixed point method](https://pygmtools.readthedocs.io/en/latest/api/_autosummary/pygmtools.classic_solvers.ipfp.html) [5].
* [Multi-Graph Matching Solvers](https://pygmtools.readthedocs.io/en/latest/api/_autosummary/pygmtools.multi_graph_solvers.html)
* [Composition based Affinity Optimization (CAO) solver](https://pygmtools.readthedocs.io/en/latest/api/_autosummary/pygmtools.multi_graph_solvers.cao.html) [6]
by optimizing the affinity score, meanwhile gradually infusing the consistency.
* Multi-Graph Matching based on
[Floyd shortest path algorithm](https://pygmtools.readthedocs.io/en/latest/api/_autosummary/pygmtools.multi_graph_solvers.mgm_floyd.html) [7].
* [Graduated-assignment based multi-graph matching solver](https://pygmtools.readthedocs.io/en/latest/api/_autosummary/pygmtools.multi_graph_solvers.gamgm.html) [8][9]
by graduated annealing of Sinkhorn’s temperature.
* [Neural Graph Matching Solvers](https://pygmtools.readthedocs.io/en/latest/api/_autosummary/pygmtools.neural_solvers.html)
* Intra-graph and cross-graph embedding based neural graph matching solvers
[PCA-GM](https://pygmtools.readthedocs.io/en/latest/api/_autosummary/pygmtools.neural_solvers.pca_gm.html)
and [IPCA-GM](https://pygmtools.readthedocs.io/en/latest/api/_autosummary/pygmtools.neural_solvers.ipca_gm.html) [10]
for matching individual graphs.
* [Channel independent embedding (CIE)](https://pygmtools.readthedocs.io/en/latest/api/_autosummary/pygmtools.neural_solvers.cie.html) [11]
based neural graph matching solver for matching individual graphs.
* [Neural graph matching solver (NGM)](https://pygmtools.readthedocs.io/en/latest/api/_autosummary/pygmtools.neural_solvers.ngm.html) [12]
for the general quadratic assignment formulation.
* [Graph edit neural network A-star (GENN-A*)](https://pygmtools.readthedocs.io/en/latest/api/_autosummary/pygmtools.neural_solvers.genn_astar.html) [13]
for the graph edit distance problem.
## Available Backends
This library is designed to support multiple backends with the same set of API.
Please follow the official instructions to install your backend.
The following backends are available:
* [Numpy](https://numpy.org/) (**default** backend, CPU only)
* [PyTorch](https://pytorch.org/) (GPU friendly, deep learning friendly)
* [Jittor](https://github.com/Jittor/Jittor) (GPU friendly, JIT support, deep learning friendly)
* [PaddlePaddle](https://www.paddlepaddle.org.cn/en) (GPU friendly, deep learning friendly)
* [Tensorflow](https://tensorflow.google.cn/) (GPU friendly, deep learning friendly)
### Development status
| | Numpy | PyTorch | Jittor | PaddlePaddle | Tensorflow | MindSpore |
| ------------------- | ----- | ------- | ------ | ------------ | ---------- | --------- |
| Linear Solvers | ✔ | ✔ | ✔ | ✔ | ✔ | ✔ |
| Classic Solvers | ✔ | ✔ | ✔ | ✔ | ✔ | ✔ |
| Multi-Graph Solvers | ✔ | ✔ | ✔ | ✔ | 📆 | 📆 |
| Neural Solvers | ✔ | ✔ | ✔ | ✔ | 📆 | 📆 |
| Examples Gallery | ✔ | ✔ | ✔ | ✔ | 📆 | 📆 |
✔: Supported; 📆: Planned for future versions (contributions welcomed!).
For more details, please [read the documentation](https://pygmtools.readthedocs.io/en/latest/guide/get_started.html#install-other-backends).
## Pretrained Models
The library includes several neural network solvers. The pretrained models shall be automatically downloaded upon
needed from Google Drive. If you are experiencing issues accessing Google Drive, please download the pretrained models
manually and put them at ``~/.cache/pygmtools`` (for Linux).
Available at:
[[google drive]](https://drive.google.com/drive/folders/1O7vkIW8QXBJsNsHUIRiSw91HJ_0FAzu_?usp=sharing)
[[baidu drive]](https://pan.baidu.com/s/1MvzfM52NJeLWx2JXbbc6HA?pwd=x8bv)
## The Deep Graph Matching Benchmark
``pygmtools`` is also featured with a standard data interface of several graph matching benchmarks. Please read
[the corresponding documentation](https://pygmtools.readthedocs.io/en/latest/guide/benchmark.html) for details.
We also maintain a repository containing non-trivial implementation of deep graph matching models, please check out
[ThinkMatch](https://thinkmatch.readthedocs.io/) if you are interested!
## Chat with the Community
If you have any questions, or if you are experiencing any issues, feel free to [raise an issue](https://github.com/Thinklab-SJTU/pygmtools/issues/new) on GitHub.
We also offer the following chat rooms if you are more comfortable with them:
* Discord (for English speakers):
[](https://discord.gg/8m6n7rRz9T)
* QQ Group (for Chinese speakers)/QQ群(中文用户): 696401889
[](https://qm.qq.com/cgi-bin/qm/qr?k=NlPuwwvaFaHzEWD8w7jSOTzoqSLIM80V&jump_from=webapi&authKey=chI2htrWDujQed6VtVid3V1NXEoJvwz3MVwruax6x5lQIvLsC8BmpmzBJOCzhtQd)
## Contributing
Any contributions/ideas/suggestions from the community is welcomed! Before starting your contribution, please read the
[Contributing Guide](https://github.com/Thinklab-SJTU/pygmtools/blob/main/CONTRIBUTING.md).
## Developers and Maintainers
``pygmtools`` is developed and maintained by members from [ThinkLab](http://thinklab.sjtu.edu.cn) at
Shanghai Jiao Tong University.
## Citing Pygmtools
``pygmtools`` is published on Journal of Machine Learning Research (JMLR). If you find our toolkit helpful in your
research, please cite:
```
Runzhong Wang, Ziao Guo, Wenzheng Pan, Jiale Ma, Yikai Zhang, Nan Yang, Qi Liu, Longxuan Wei, Hanxue Zhang, Chang Liu, Zetian Jiang, Xiaokang Yang, and Junchi Yan.
Pygmtools: A Python Graph Matching Toolkit.
Journal of Machine Learning Research, 25(33):1−7, 2024.
```
In Bibtex format:
```
@article{wang2024pygm,
author = {Runzhong Wang and Ziao Guo and Wenzheng Pan and Jiale Ma and Yikai Zhang and Nan Yang and Qi Liu and Longxuan Wei and Hanxue Zhang and Chang Liu and Zetian Jiang and Xiaokang Yang and Junchi Yan},
title = {Pygmtools: A Python Graph Matching Toolkit},
journal = {Journal of Machine Learning Research},
year = {2024},
volume = {25},
number = {33},
pages = {1-7},
url = {https://jmlr.org/papers/v25/23-0572.html},
}
```
## References
[1] Sinkhorn, Richard, and Paul Knopp. "Concerning nonnegative matrices and doubly stochastic matrices." _Pacific Journal of Mathematics_ 21.2 (1967): 343-348.
[2] Munkres, James. "Algorithms for the assignment and transportation problems." _Journal of the Society for Industrial and Applied Mathematics_ 5.1 (1957): 32-38.
[3] Leordeanu, Marius, and Martial Hebert. "A spectral technique for correspondence problems using pairwise constraints." _International Conference on Computer Vision_ (2005).
[4] Cho, Minsu, Jungmin Lee, and Kyoung Mu Lee. "Reweighted random walks for graph matching." _European conference on Computer Vision_ (2010).
[5] Leordeanu, Marius, Martial Hebert, and Rahul Sukthankar. "An integer projected fixed point method for graph matching and map inference." _Advances in Neural Information Processing Systems_ 22 (2009).
[6] Yan, Junchi, et al. "Multi-graph matching via affinity optimization with graduated consistency regularization." _IEEE Transactions on Pattern Analysis and Machine Intelligence_ 38.6 (2015): 1228-1242.
[7] Jiang, Zetian, Tianzhe Wang, and Junchi Yan. "Unifying offline and online multi-graph matching via finding shortest paths on supergraph." _IEEE Transactions on Pattern Analysis and Machine Intelligence_ 43.10 (2020): 3648-3663.
[8] Solé-Ribalta, Albert, and Francesc Serratosa. "Graduated assignment algorithm for multiple graph matching based on a common labeling." _International Journal of Pattern Recognition and Artificial Intelligence_ 27.01 (2013): 1350001.
[9] Wang, Runzhong, Junchi Yan, and Xiaokang Yang. "Unsupervised Learning of Graph Matching with Mixture of Modes via Discrepancy Minimization." _IEEE Transactions on Pattern Analysis and Machine Intelligence_ 45.8 (2023): 10500-10518.
[10] Wang, Runzhong, Junchi Yan, and Xiaokang Yang. "Combinatorial learning of robust deep graph matching: an embedding based approach." _IEEE Transactions on Pattern Analysis and Machine Intelligence_ 45.6 (2023): 6984-7000.
[11] Yu, Tianshu, et al. "Learning deep graph matching with channel-independent embedding and hungarian attention." _International Conference on Learning Representations_. 2019.
[12] Wang, Runzhong, Junchi Yan, and Xiaokang Yang. "Neural graph matching network: Learning lawler’s quadratic assignment problem with extension to hypergraph and multiple-graph matching." _IEEE Transactions on Pattern Analysis and Machine Intelligence_ 44.9 (2022): 5261-5279.
[13] Wang, Runzhong, Junchi Yan, and Xiaokang Yang. "Combinatorial Learning of Graph Edit Distance via Dynamic Embedding." _IEEE/CVF Conference on Computer Vision and Pattern Recognition_ (2021): 5241-5250.