DPG 0.3.4__tar.gz → 0.3.6__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- dpg-0.3.6/PKG-INFO +190 -0
- dpg-0.3.6/README.md +137 -0
- {dpg-0.3.4 → dpg-0.3.6}/pyproject.toml +1 -1
- dpg-0.3.4/PKG-INFO +0 -433
- dpg-0.3.4/README.md +0 -380
- {dpg-0.3.4 → dpg-0.3.6}/LICENSE +0 -0
- {dpg-0.3.4 → dpg-0.3.6}/dpg/__init__.py +0 -0
- {dpg-0.3.4 → dpg-0.3.6}/dpg/cli.py +0 -0
- {dpg-0.3.4 → dpg-0.3.6}/dpg/context_order.py +0 -0
- {dpg-0.3.4 → dpg-0.3.6}/dpg/core.py +0 -0
- {dpg-0.3.4 → dpg-0.3.6}/dpg/explainer.py +0 -0
- {dpg-0.3.4 → dpg-0.3.6}/dpg/py.typed +0 -0
- {dpg-0.3.4 → dpg-0.3.6}/dpg/sklearn_dpg.py +0 -0
- {dpg-0.3.4 → dpg-0.3.6}/dpg/sklearn_normalizer.py +0 -0
- {dpg-0.3.4 → dpg-0.3.6}/dpg/themes.py +0 -0
- {dpg-0.3.4 → dpg-0.3.6}/dpg/utils.py +0 -0
- {dpg-0.3.4 → dpg-0.3.6}/dpg/visualizer.py +0 -0
- {dpg-0.3.4 → dpg-0.3.6}/metrics/__init__.py +0 -0
- {dpg-0.3.4 → dpg-0.3.6}/metrics/edges.py +0 -0
- {dpg-0.3.4 → dpg-0.3.6}/metrics/graph.py +0 -0
- {dpg-0.3.4 → dpg-0.3.6}/metrics/nodes.py +0 -0
- {dpg-0.3.4 → dpg-0.3.6}/metrics/py.typed +0 -0
dpg-0.3.6/PKG-INFO
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Metadata-Version: 2.4
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Name: dpg
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Version: 0.3.6
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Summary: A Python library for extracting Decision Predicate Graphs and global explanations from ensemble models.
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License: MIT
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License-File: LICENSE
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Keywords: decision graph,ensemble learning,explainable ai,explainability,global explanations
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Author: Sylvio Barbon Junior
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Author-email: sylvio.barbonjunior@units.it
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Requires-Python: >=3.10
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Classifier: License :: OSI Approved :: MIT License
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Classifier: Programming Language :: Python :: 3
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Classifier: Programming Language :: Python :: 3.10
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Classifier: Programming Language :: Python :: 3.11
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Classifier: Programming Language :: Python :: 3.12
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Classifier: Programming Language :: Python :: 3.13
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Classifier: Programming Language :: Python :: 3.14
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Provides-Extra: dev
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Provides-Extra: docs
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Requires-Dist: contourpy (>=1.2)
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Requires-Dist: cycler (>=0.12)
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Requires-Dist: fonttools (>=4.53)
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Requires-Dist: graphviz (>=0.20)
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Requires-Dist: joblib (>=1.4)
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Requires-Dist: kiwisolver (>=1.4)
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Requires-Dist: matplotlib (>=3.9.1)
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Requires-Dist: myst-nb (>=1.1) ; extra == "docs"
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Requires-Dist: myst-parser (>=3.0) ; extra == "docs"
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Requires-Dist: networkx (>=3.3)
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Requires-Dist: numpy (>=2.0.0)
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Requires-Dist: packaging (>=24.1)
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Requires-Dist: pandas (>=2.2)
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Requires-Dist: pillow (>=10.4)
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Requires-Dist: pydata-sphinx-theme (>=0.15) ; extra == "docs"
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Requires-Dist: pyparsing (>=3.1)
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Requires-Dist: python-dateutil (>=2.9)
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Requires-Dist: pytz (>=2024.1)
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Requires-Dist: pyyaml (>=6.0.2)
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Requires-Dist: scikit-learn (>=1.5)
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Requires-Dist: scipy (>=1.14)
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Requires-Dist: six (>=1.16)
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Requires-Dist: sphinx (>=7.3) ; extra == "docs"
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Requires-Dist: sphinx-autoapi (>=3.1) ; extra == "docs"
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Requires-Dist: sphinx-copybutton (>=0.5) ; extra == "docs"
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Requires-Dist: sphinx-design (>=0.6) ; extra == "docs"
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Requires-Dist: threadpoolctl (>=3.5)
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Requires-Dist: tqdm (>=4.67)
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Requires-Dist: tzdata (>=2024.1)
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Project-URL: Homepage, https://github.com/Meta-Group/DPG
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Project-URL: Repository, https://github.com/Meta-Group/DPG
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Description-Content-Type: text/markdown
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# Decision Predicate Graph (DPG)
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[](LICENSE)
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[](https://pypi.org/project/dpg/)
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[](pyproject.toml)
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[](https://github.com/Meta-Group/DPG/actions/workflows/tests.yml)
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[](https://github.com/Meta-Group/DPG/actions/workflows/release.yml)
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[](https://dpg.readthedocs.io/en/latest/)
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[](https://machinelearning.inginf.units.it/DPG_web/#how)
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<p align="center">
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<img src="https://raw.githubusercontent.com/Meta-Group/DPG/main/DPG.png" alt="DPG logo" width="300">
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</p>
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DPG is a model-agnostic framework for explaining tree ensembles. It converts
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their decision logic into a graph, making predicates, transitions, predictions,
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and structural diagnostics available in one representation.
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## Highlights
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- Global and local explanations through `DPGExplainer`
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- Graph metrics, including constraints, betweenness centrality, local reaching
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centrality, and communities
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- Local-path inspection, local-on-global plots, and faithfulness diagnostics
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- Support for common scikit-learn tree ensembles
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## Install
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```bash
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pip install dpg
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```
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DPG requires Python 3.10 or later. To render graphs, also install the Graphviz
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system package so that `dot` is on your `PATH`.
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For development and documentation builds, see [docs/README.md](docs/README.md).
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## Quick start
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```python
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import numpy as np
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from sklearn.datasets import load_iris
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from sklearn.ensemble import RandomForestClassifier
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from dpg import DPGExplainer
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X, y = load_iris(return_X_y=True, as_frame=True)
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model = RandomForestClassifier(n_estimators=5, random_state=42).fit(X, y)
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explainer = DPGExplainer(
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model=model,
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feature_names=X.columns.tolist(),
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target_names=np.unique(y).astype(str).tolist(),
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)
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explanation = explainer.explain_global(X.values, communities=True)
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explainer.plot("iris_dpg", explanation, save_dir="results")
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```
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## How DPG works
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The concept behind DPG is to convert a generic tree-based ensemble model for classification into a graph, where:
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- Nodes represent predicates, i.e., the feature-value associations present in each node of every tree;
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- Edges denote the frequency with which these predicates are satisfied during the model training phase by the samples of the dataset.
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<p align="center">
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<img src="https://raw.githubusercontent.com/Meta-Group/DPG/main/dpg_image_examples/example.png" width="600" />
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</p>
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## Metrics
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The graph-based nature of DPG provides significant enhancements in the direction of a complete mapping of the ensemble structure.
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| Property | Definition | Utility |
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|--------------|------------|---------|
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| _Constraints_ | The intervals of values for each feature obtained from all predicates connected by a path that culminates in a given class. | Calculate the classification boundary values of each feature associated with each class. |
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| _Betweenness centrality_ | Quantifies the fraction of all the shortest paths between every pair of nodes of the graph passing through the considered node. | Identify potential bottleneck nodes that correspond to crucial decisions. |
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| _Local reaching centrality_ | Quantifies the proportion of other nodes reachable from the local node through its outgoing edges. | Assess the importance of nodes similarly to feature importance, but enrich the information by encompassing the values associated with features across all decisions. |
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| _Community_ | A subset of nodes of the DPG which is characterised by dense interconnections between its elements and sparse connections with the other nodes of the DPG that do not belong to the community. | Understanding the characteristics of nodes to be assigned to a particular community class, identifying predominant predicates, and those that play a marginal role in the classification process. |
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|Constraints | Betweenness centrality | Local reaching centrality | Community|
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|------------|------------|--------------|--------------------|
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| Constraints(Class 1) = val3 < F1 ≤ val1, F2 ≤ val2 | BC(F2 ≤ val2) = 4/24 | LRC(F1 ≤ val1) = 6 / 7 | Community(Class 1) = F1 ≤ val1, F2 ≤ val2 |
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## Local explanations and faithfulness
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Fit the explainer once, then inspect an individual prediction or compare local
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explanations with the fitted model:
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```python
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explainer.fit(X.values)
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local = explainer.explain_local(X.iloc[0].values, sample_id=0)
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details = explainer.evaluate_faithfulness(X.values, return_details=True)
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print(local.majority_vote)
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print(details["faithfulness_score"])
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```
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`evaluate_faithfulness` reports model agreement, trace coverage,
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recombination, evidence margin, and a composite heuristic score. It is an
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explanation-fidelity measure, not a probability of ground-truth correctness.
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## Documentation and examples
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- [Full documentation](https://dpg.readthedocs.io/en/latest/)
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- [Quickstart](https://dpg.readthedocs.io/en/latest/quickstart.html)
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- [Supported models](https://dpg.readthedocs.io/en/latest/supported_models.html)
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- [Visualizations](https://dpg.readthedocs.io/en/latest/visualization.html)
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- [Examples](examples), including [local explanations](examples/local_explanation_iris.py)
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- [Parameter-sensitivity benchmark](tutorials/parameter_sensitivity_benchmark/README.md)
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- [Interactive DPG sandbox](https://machinelearning.inginf.units.it/DPG_web/#how) — explore how DPG turns an ensemble into a graph in the browser.
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<p align="center">
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<a href="https://machinelearning.inginf.units.it/DPG_web/#how">
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<img src="docs/_static/DPG.png" alt="Open the interactive DPG sandbox" width="180">
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</a>
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</p>
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The packaged CLI mirrors `examples/run_dpg_standard.py`. Run `dpg --help` for
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its current options and use `examples/run_dpg_custom.py` for a dataset with a
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specified target column.
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## Citation
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If you use DPG in research, please cite:
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```bibtex
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@inproceedings{arrighi2024dpg,
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title={Decision Predicate Graphs: Enhancing Interpretability in Tree Ensembles},
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author={Arrighi, Leonardo and Pennella, Luca and Marques Tavares, Gabriel and Barbon Junior, Sylvio},
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booktitle={World Conference on Explainable Artificial Intelligence},
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pages={311--332},
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year={2024},
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isbn={978-3-031-63797-1},
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doi={10.1007/978-3-031-63797-1_16},
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publisher={Springer Nature Switzerland},
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}
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```
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dpg-0.3.6/README.md
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# Decision Predicate Graph (DPG)
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[](LICENSE)
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[](https://pypi.org/project/dpg/)
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[](pyproject.toml)
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[](https://github.com/Meta-Group/DPG/actions/workflows/tests.yml)
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[](https://github.com/Meta-Group/DPG/actions/workflows/release.yml)
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[](https://dpg.readthedocs.io/en/latest/)
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[](https://machinelearning.inginf.units.it/DPG_web/#how)
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<p align="center">
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<img src="https://raw.githubusercontent.com/Meta-Group/DPG/main/DPG.png" alt="DPG logo" width="300">
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</p>
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DPG is a model-agnostic framework for explaining tree ensembles. It converts
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their decision logic into a graph, making predicates, transitions, predictions,
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and structural diagnostics available in one representation.
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## Highlights
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- Global and local explanations through `DPGExplainer`
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- Graph metrics, including constraints, betweenness centrality, local reaching
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centrality, and communities
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- Local-path inspection, local-on-global plots, and faithfulness diagnostics
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- Support for common scikit-learn tree ensembles
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## Install
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```bash
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pip install dpg
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```
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DPG requires Python 3.10 or later. To render graphs, also install the Graphviz
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system package so that `dot` is on your `PATH`.
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For development and documentation builds, see [docs/README.md](docs/README.md).
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## Quick start
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```python
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import numpy as np
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from sklearn.datasets import load_iris
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from sklearn.ensemble import RandomForestClassifier
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from dpg import DPGExplainer
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X, y = load_iris(return_X_y=True, as_frame=True)
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model = RandomForestClassifier(n_estimators=5, random_state=42).fit(X, y)
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explainer = DPGExplainer(
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model=model,
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feature_names=X.columns.tolist(),
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target_names=np.unique(y).astype(str).tolist(),
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)
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explanation = explainer.explain_global(X.values, communities=True)
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explainer.plot("iris_dpg", explanation, save_dir="results")
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```
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## How DPG works
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The concept behind DPG is to convert a generic tree-based ensemble model for classification into a graph, where:
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- Nodes represent predicates, i.e., the feature-value associations present in each node of every tree;
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- Edges denote the frequency with which these predicates are satisfied during the model training phase by the samples of the dataset.
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<p align="center">
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<img src="https://raw.githubusercontent.com/Meta-Group/DPG/main/dpg_image_examples/example.png" width="600" />
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</p>
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## Metrics
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The graph-based nature of DPG provides significant enhancements in the direction of a complete mapping of the ensemble structure.
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| Property | Definition | Utility |
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|--------------|------------|---------|
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| _Constraints_ | The intervals of values for each feature obtained from all predicates connected by a path that culminates in a given class. | Calculate the classification boundary values of each feature associated with each class. |
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| _Betweenness centrality_ | Quantifies the fraction of all the shortest paths between every pair of nodes of the graph passing through the considered node. | Identify potential bottleneck nodes that correspond to crucial decisions. |
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| _Local reaching centrality_ | Quantifies the proportion of other nodes reachable from the local node through its outgoing edges. | Assess the importance of nodes similarly to feature importance, but enrich the information by encompassing the values associated with features across all decisions. |
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| _Community_ | A subset of nodes of the DPG which is characterised by dense interconnections between its elements and sparse connections with the other nodes of the DPG that do not belong to the community. | Understanding the characteristics of nodes to be assigned to a particular community class, identifying predominant predicates, and those that play a marginal role in the classification process. |
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|Constraints | Betweenness centrality | Local reaching centrality | Community|
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|------------|------------|--------------|--------------------|
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|  |  |  |  |
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| Constraints(Class 1) = val3 < F1 ≤ val1, F2 ≤ val2 | BC(F2 ≤ val2) = 4/24 | LRC(F1 ≤ val1) = 6 / 7 | Community(Class 1) = F1 ≤ val1, F2 ≤ val2 |
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## Local explanations and faithfulness
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explanations with the fitted model:
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```python
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explainer.fit(X.values)
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local = explainer.explain_local(X.iloc[0].values, sample_id=0)
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```
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## Documentation and examples
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- [Examples](examples), including [local explanations](examples/local_explanation_iris.py)
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- [Interactive DPG sandbox](https://machinelearning.inginf.units.it/DPG_web/#how) — explore how DPG turns an ensemble into a graph in the browser.
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<a href="https://machinelearning.inginf.units.it/DPG_web/#how">
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<img src="docs/_static/DPG.png" alt="Open the interactive DPG sandbox" width="180">
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```bibtex
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@inproceedings{arrighi2024dpg,
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title={Decision Predicate Graphs: Enhancing Interpretability in Tree Ensembles},
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author={Arrighi, Leonardo and Pennella, Luca and Marques Tavares, Gabriel and Barbon Junior, Sylvio},
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doi={10.1007/978-3-031-63797-1_16},
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# Decision Predicate Graph (DPG)
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[](LICENSE)
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[](pyproject.toml)
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[](https://github.com/Meta-Group/DPG/actions/workflows/tests.yml)
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[](https://github.com/Meta-Group/DPG/actions/workflows/release.yml)
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[](https://dpg.readthedocs.io/en/latest/)
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</p>
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DPG is a model-agnostic framework for global and local explanation of tree-based ensemble models.
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It turns ensemble decision logic into a graph so users can inspect predicates, transitions, predictions,
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and structural explanation diagnostics in a single representation.
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DPG is a graph structure that captures the tree-based ensemble model and learned dataset details,
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preserving the relations among features, logical decisions, and predictions towards emphasising
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insightful points. DPG enables graph-based evaluations and the identification of model decisions
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towards facilitating comparisons between features and their associated values while offering insights
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into the entire model. DPG provides descriptive metrics that enhance the understanding of the
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decisions inherent in the model, offering valuable insights.
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---
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## At a glance
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- High-level API for global and local explanation with `DPGExplainer`
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- Local path inspection, local-on-global visualization, and faithfulness diagnostics
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## Quick links
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- Faithfulness evaluation: [Faithfulness evaluation](#faithfulness-evaluation)
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- Visualizations: [https://dpg.readthedocs.io/en/latest/visualization.html](https://dpg.readthedocs.io/en/latest/visualization.html)
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- CLI usage and gallery examples: [CLI scripts](#cli-scripts)
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- Full docs: [https://dpg.readthedocs.io/](https://dpg.readthedocs.io/)
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## How DPG works
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The concept behind DPG is to convert a generic tree-based ensemble model for classification into a graph, where:
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- Nodes represent predicates, i.e., the feature-value associations present in each node of every tree;
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</p>
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## Metrics
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The graph-based nature of DPG provides significant enhancements in the direction of a complete mapping of the ensemble structure.
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| Property | Definition | Utility |
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|--------------|------------|---------|
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| _Constraints_ | The intervals of values for each feature obtained from all predicates connected by a path that culminates in a given class. | Calculate the classification boundary values of each feature associated with each class. |
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| _Betweenness centrality_ | Quantifies the fraction of all the shortest paths between every pair of nodes of the graph passing through the considered node. | Identify potential bottleneck nodes that correspond to crucial decisions. |
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| _Local reaching centrality_ | Quantifies the proportion of other nodes reachable from the local node through its outgoing edges. | Assess the importance of nodes similarly to feature importance, but enrich the information by encompassing the values associated with features across all decisions. |
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| _Community_ | A subset of nodes of the DPG which is characterised by dense interconnections between its elements and sparse connections with the other nodes of the DPG that do not belong to the community. | Understanding the characteristics of nodes to be assigned to a particular community class, identifying predominant predicates, and those that play a marginal role in the classification process. |
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|Constraints | Betweenness centrality | Local reaching centrality | Community|
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|------------|------------|--------------|--------------------|
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 |  |  |  |
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|Constraints(Class 1) = val3 < F1 ≤ val1, F2 ≤ val2 | BC(F2 ≤ val2) = 4/24 | LRC(F1 ≤ val1) = 6 / 7 | Community(Class 1) = F1 ≤ val1, F2 ≤ val2 |
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## Installation
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Install the package from PyPI:
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`dot` executable is available on your `PATH`:
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For local development installs, editable mode, and documentation builds, see
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[docs/README.md](docs/README.md).
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---
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## Documentation
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## High-level usage
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import pandas as pd
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import numpy as np
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from sklearn.ensemble import RandomForestClassifier, GradientBoostingClassifier
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df = pd.read_csv("datasets/custom.csv", index_col=0)
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# Train a classifier (supports RandomForest, GradientBoosting, AdaBoost, ExtraTree, and more)
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model.fit(X, y)
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)
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explanation = explainer.explain_global(X.values, communities=True)
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# Render the graph to disk
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explainer.plot("dpg_output", explanation, save_dir="datasets", export_pdf=True)
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explainer.plot_communities("dpg_output", explanation, save_dir="datasets", export_pdf=True)
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```
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### Common workflows
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The high-level API is designed to return structured outputs so downstream tools can use them directly.
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- `DPGExplainer.explain_local(sample, sample_id=0, X=None, validate_graph=True)`: returns a `DPGLocalExplanation`
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- `DPGExplainer.local_path_dataframe(local_explanation)`: flattens local paths into a tabular view
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- `DPGExplainer.plot_communities(...)`: renders a community-colored DPG
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- `DPGExplainer.plot_local_on_dpg(...)`: overlays one sample's local paths on the fitted DPG
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`DPGExplanation` includes `dot`, `graph`, `nodes`, `node_metrics`, `edge_metrics`, `class_boundaries`, and optional `communities`.
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### Local explanations
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DPG also supports sample-level explanations on top of the fitted global graph.
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#### Graph construction modes
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```python
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explainer = DPGExplainer(
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model=model,
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feature_names=X.columns.tolist(),
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dpg_config={
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"dpg": {
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"default": {
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"perc_var": 1e-9,
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"graph_construction": {
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```
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- `"aggregated_transitions"`: current default behavior; filters path variants first, then discovers the DPG.
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`context_order` controls predicate identity in `execution_trace` mode. `1`
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preserves the legacy graph exactly; an order greater than one uses the last k
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executed predicates as context and keeps one sink per class. `"auto"` resolves
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the smallest order for which every pooled graph path is supported by an
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observed execution trace, including recombinations that only appear after
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multiple hops. Orders greater than one require `mode: "execution_trace"`.
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`context_order="auto"` also requires `execution_trace`; in
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`aggregated_transitions` mode context resolution is not applied.
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A phantom path is a multi-hop path assembled by pooling edges from different
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tree executions even though no single execution produced it. DPG-k removes
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these recombinations at the resolved context order while retaining one graph.
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The effective order and each node's context are available through
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`get_context_order()` and `get_node_context(node)`.
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**Regression scope (0.3.0):** `context_order` builds without raising for
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regressors (regression leaves, labeled `"Pred <value>"`, are treated as
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terminal sinks just like class leaves), but "one sink per output" is not a
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defined guarantee for regression the way it is for classification: two
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leaves collapse into the same sink only when their rounded values coincide,
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which is an artifact of label rounding, not a modeled invariant. A
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principled regression sink policy is deferred past 0.3.0. `class_boundaries`
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and `communities` remain classifier-only; calling `explain_global`
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with `communities=True` on a regressor raises a clear `ValueError`.
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#### Minimal local workflow
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```python
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from sklearn.datasets import load_iris
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from sklearn.ensemble import RandomForestClassifier
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from dpg import DPGExplainer
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import numpy as np
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X, y = load_iris(return_X_y=True, as_frame=True)
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model = RandomForestClassifier(n_estimators=5, random_state=42).fit(X, y)
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explainer = DPGExplainer(
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model=model,
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feature_names=X.columns.tolist(),
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target_names=np.unique(y).astype(str).tolist(),
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)
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explainer.fit(X.values)
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local = explainer.explain_local(sample=X.iloc[0].values, sample_id=0)
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print(local.majority_vote)
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print(local.class_votes)
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print(local.sample_confidence)
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df_local = explainer.local_path_dataframe(local)
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print(df_local.head())
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```
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`local.tree_paths[*].labels` stay in DPG label format such as `"sepal width (cm) <= 3.0"` and `"Class 0"`.
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For easier aggregation, `local.class_votes` and `local.majority_vote` use normalized class names such as `"0"` instead of `"Class 0"`.
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#### Local plotting
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```python
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explainer.plot_local_on_dpg(
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"iris_local_sample0",
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local_explanation=local,
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true_class_label=str(y.iloc[0]),
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save_dir="results/",
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theme="dpg",
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palette="olive",
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layout_template="vertical",
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show=False,
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)
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```
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A runnable example is available at [examples/local_explanation_iris.py](examples/local_explanation_iris.py).
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#### Faithfulness evaluation
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You can also evaluate local explanations against the fitted black-box model:
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```python
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details = explainer.evaluate_faithfulness(
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X_test,
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y_true=y_test,
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return_details=True,
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)
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print(details["faithfulness_score"])
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print(details["output_fidelity"])
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print(details["mean_trace_coverage_score"])
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print(details["mean_recombination_rate"])
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```
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This reports:
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- `output_fidelity`: agreement between the local explanation and the black-box model
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- structural metrics such as trace coverage and recombination
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- semantic metrics such as evidence margin
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- a composite `faithfulness_score`
|
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|
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Important:
|
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- the composite score is a heuristic summary, not a calibrated probability
|
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- `output_fidelity` is model agreement, not ground-truth correctness
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|
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- `local_accuracy` is only reported when `y_true` is provided
|
|
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|
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- structural faithfulness here means recovering the executed decision traces used by the model
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|
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|
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|
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|
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### Runnable examples
|
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|
-
|
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|
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- [examples/quickstart_iris.py](examples/quickstart_iris.py)
|
|
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|
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- [examples/local_explanation_iris.py](examples/local_explanation_iris.py)
|
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- [examples](examples)
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## CLI scripts
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The library contains two different scripts to apply DPG:
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- `examples/run_dpg_standard.py`: with this script it is possible to test DPG on a standard classification dataset provided by `sklearn` such as `iris`, `digits`, `wine`, `breast cancer`, and `diabetes`.
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- `examples/run_dpg_custom.py`: with this script it is possible to apply DPG to your classification dataset, specifying the target class.
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### Implementation notes
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The library also contains two other essential scripts:
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- `core.py` contains all the functions used to calculate and create the DPG and the metrics.
|
|
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|
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- `visualizer.py` contains the functions used to manage the visualization of DPG.
|
|
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|
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|
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### Output
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The DPG output, through `examples/run_dpg_standard.py` or `examples/run_dpg_custom.py`, produces several files:
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- the visualization of DPG in a dedicated environment, which can be zoomed and saved;
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- a `.txt` file containing the DPG metrics;
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- a `.csv` file containing the information about all the nodes of the DPG and their associated metrics;
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- a `.txt` file containing the Random Forest statistics (accuracy, confusion matrix, classification report)
|
|
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|
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|
|
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|
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### CLI parameter reference
|
|
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Usage: `dpg --dataset <dataset_name> --n_learners <integer_number> --pv <threshold_value> --t <integer_number> --model_name <str_model_name> --dir <save_dir_path> --plot --save_plot_dir <save_plot_dir_path> --attribute <attribute> --communities --clusters --threshold_clusters <float> --class_flag --seed <int>`
|
|
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|
-
|
|
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|
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After installing DPG, the `dpg` command is the packaged equivalent of
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`python examples/run_dpg_standard.py`.
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Where:
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- `dataset` is the name of the standard classification `sklearn` dataset to be analyzed;
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- `n_learners` is the number of base learners for the ensemble model;
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- `pv` is the threshold value indicating the desire to retain only those paths that occur with a frequency exceeding a specified proportion across the trees;
|
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- `t` is the decimal precision of each feature;
|
|
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|
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- `model_name` is the name of the `sklearn` model chosen to perform classification. Supported models include:
|
|
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|
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- `RandomForestClassifier` (default)
|
|
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|
-
- `GradientBoostingClassifier` (new!)
|
|
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|
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- `RandomForestRegressor`
|
|
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|
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- `GradientBoostingRegressor`
|
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|
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- `ExtraTreesClassifier`
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- `AdaBoostClassifier`
|
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|
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- `AdaBoostRegressor`
|
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|
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- `BaggingClassifier`
|
|
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|
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- `dir` is the path of the directory to save the files;
|
|
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|
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- `plot` is a store_true variable which can be added to plot the DPG;
|
|
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|
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- `save_plot_dir` is the path of the directory to save the plot image;
|
|
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|
-
- `attribute` is the specific node metric which can be visualized on the DPG;
|
|
386
|
-
- `communities` is a store_true variable which can be added to visualize communities on the DPG;
|
|
387
|
-
- `clusters` is a store_true variable which can be added to visualize clusters on the DPG;
|
|
388
|
-
- `threshold_clusters` is the threshold used to detect ambiguous nodes in clusters;
|
|
389
|
-
- `class_flag` is a store_true variable which can be added to highlight class nodes;
|
|
390
|
-
- `seed` controls the random split.
|
|
391
|
-
|
|
392
|
-
Disclaimer: `attribute`, `communities`, and `clusters` are mutually exclusive: DPG supports just one visualization mode at a time.
|
|
393
|
-
|
|
394
|
-
The usage of `examples/run_dpg_custom.py` is similar, but it requires another parameter:
|
|
395
|
-
- `target_column`, which is the name of the column to be used as the target variable;
|
|
396
|
-
- while `ds` is the path of the directory where the dataset is.
|
|
397
|
-
|
|
398
|
-
### Example `examples/run_dpg_standard.py`
|
|
399
|
-
Some examples can be appreciated in the `examples` folder: https://github.com/Meta-Group/DPG/tree/main/examples
|
|
400
|
-
|
|
401
|
-
In particular, the following DPG is obtained by transforming a Random Forest with 5 base learners, trained on Iris dataset.
|
|
402
|
-
The used command is `dpg --dataset iris --n_learners 5 --pv 0.001 --t 2 --dir examples --plot --save_plot_dir examples`.
|
|
403
|
-
<p align="center">
|
|
404
|
-
<img src="https://raw.githubusercontent.com/Meta-Group/DPG/main/dpg_image_examples/iris_bl5_perc0.001_dec2.png" width="800" />
|
|
405
|
-
</p>
|
|
406
|
-
|
|
407
|
-
The following visualizations are obtained using the same parameters as the previous example, but they show two different metrics: _Community_ and _Betweenness centrality_.
|
|
408
|
-
The used command for showing communities is `dpg --dataset iris --n_learners 5 --pv 0.001 --t 2 --dir examples --plot --save_plot_dir examples --communities`.
|
|
409
|
-
<p align="center">
|
|
410
|
-
<img src="https://raw.githubusercontent.com/Meta-Group/DPG/main/dpg_image_examples/iris_bl5_perc0.001_dec2_communities.png" width="800" />
|
|
411
|
-
</p>
|
|
412
|
-
|
|
413
|
-
The used command for showing a specific property is `dpg --dataset iris --n_learners 5 --pv 0.001 --t 2 --dir examples --plot --save_plot_dir examples --attribute "Betweenness centrality" --class_flag`.
|
|
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|
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<p align="center">
|
|
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|
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<img src="https://raw.githubusercontent.com/Meta-Group/DPG/main/dpg_image_examples/iris_bl5_perc0.001_dec2_Betweennesscentrality.png" width="800" />
|
|
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|
-
</p>
|
|
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|
-
|
|
418
|
-
***
|
|
419
|
-
## Citation
|
|
420
|
-
If you use this for research, please cite. Here is an example BibTeX entry:
|
|
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|
-
|
|
422
|
-
```bibtex
|
|
423
|
-
@inproceedings{arrighi2024dpg,
|
|
424
|
-
title={Decision Predicate Graphs: Enhancing Interpretability in Tree Ensembles},
|
|
425
|
-
author={Arrighi, Leonardo and Pennella, Luca and Marques Tavares, Gabriel and Barbon Junior, Sylvio},
|
|
426
|
-
booktitle={World Conference on Explainable Artificial Intelligence},
|
|
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|
-
pages={311--332},
|
|
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|
-
year={2024},
|
|
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|
-
isbn = {978-3-031-63797-1},
|
|
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|
-
doi = {10.1007/978-3-031-63797-1_16},
|
|
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|
-
publisher = {Springer Nature Switzerland},
|
|
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|
-
}
|
|
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|
dpg-0.3.4/README.md
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# Decision Predicate Graph (DPG)
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[](LICENSE)
|
|
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[](pyproject.toml)
|
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|
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[](https://github.com/Meta-Group/DPG/actions/workflows/tests.yml)
|
|
6
|
-
[](https://github.com/Meta-Group/DPG/actions/workflows/release.yml)
|
|
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|
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[](https://dpg.readthedocs.io/en/latest/)
|
|
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|
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|
|
9
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<p align="center">
|
|
10
|
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<img src="https://raw.githubusercontent.com/Meta-Group/DPG/main/DPG.png" alt="DPG logo" width="300">
|
|
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</p>
|
|
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|
-
|
|
13
|
-
|
|
14
|
-
DPG is a model-agnostic framework for global and local explanation of tree-based ensemble models.
|
|
15
|
-
It turns ensemble decision logic into a graph so users can inspect predicates, transitions, predictions,
|
|
16
|
-
and structural explanation diagnostics in a single representation.
|
|
17
|
-
|
|
18
|
-
DPG is a graph structure that captures the tree-based ensemble model and learned dataset details,
|
|
19
|
-
preserving the relations among features, logical decisions, and predictions towards emphasising
|
|
20
|
-
insightful points. DPG enables graph-based evaluations and the identification of model decisions
|
|
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|
-
towards facilitating comparisons between features and their associated values while offering insights
|
|
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|
-
into the entire model. DPG provides descriptive metrics that enhance the understanding of the
|
|
23
|
-
decisions inherent in the model, offering valuable insights.
|
|
24
|
-
<p align="center">
|
|
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|
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<img src="https://raw.githubusercontent.com/Meta-Group/DPG/main/image.png" width="600" />
|
|
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|
-
</p>
|
|
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|
-
|
|
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|
-
---
|
|
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|
-
|
|
30
|
-
## At a glance
|
|
31
|
-
|
|
32
|
-
- High-level API for global and local explanation with `DPGExplainer`
|
|
33
|
-
- Graph-based metrics such as constraints, betweenness centrality, and local reaching centrality
|
|
34
|
-
- Local path inspection, local-on-global visualization, and faithfulness diagnostics
|
|
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|
-
- Lightweight experiment runners and analysis utilities for sklearn datasets
|
|
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|
-
|
|
37
|
-
## Quick links
|
|
38
|
-
|
|
39
|
-
- Installation: [Installation](#installation)
|
|
40
|
-
- High-level usage: [High-level usage](#high-level-usage)
|
|
41
|
-
- Local explanations: [Local explanations](#local-explanations)
|
|
42
|
-
- Faithfulness evaluation: [Faithfulness evaluation](#faithfulness-evaluation)
|
|
43
|
-
- Visualizations: [https://dpg.readthedocs.io/en/latest/visualization.html](https://dpg.readthedocs.io/en/latest/visualization.html)
|
|
44
|
-
- CLI usage and gallery examples: [CLI scripts](#cli-scripts)
|
|
45
|
-
- Full docs: [https://dpg.readthedocs.io/](https://dpg.readthedocs.io/)
|
|
46
|
-
|
|
47
|
-
## How DPG works
|
|
48
|
-
The concept behind DPG is to convert a generic tree-based ensemble model for classification into a graph, where:
|
|
49
|
-
- Nodes represent predicates, i.e., the feature-value associations present in each node of every tree;
|
|
50
|
-
- Edges denote the frequency with which these predicates are satisfied during the model training phase by the samples of the dataset.
|
|
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|
-
|
|
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|
-
<p align="center">
|
|
53
|
-
<img src="https://raw.githubusercontent.com/Meta-Group/DPG/main/dpg_image_examples/example.png" width="600" />
|
|
54
|
-
</p>
|
|
55
|
-
|
|
56
|
-
## Metrics
|
|
57
|
-
The graph-based nature of DPG provides significant enhancements in the direction of a complete mapping of the ensemble structure.
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| Property | Definition | Utility |
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|--------------|------------|---------|
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| _Constraints_ | The intervals of values for each feature obtained from all predicates connected by a path that culminates in a given class. | Calculate the classification boundary values of each feature associated with each class. |
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| _Betweenness centrality_ | Quantifies the fraction of all the shortest paths between every pair of nodes of the graph passing through the considered node. | Identify potential bottleneck nodes that correspond to crucial decisions. |
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| _Local reaching centrality_ | Quantifies the proportion of other nodes reachable from the local node through its outgoing edges. | Assess the importance of nodes similarly to feature importance, but enrich the information by encompassing the values associated with features across all decisions. |
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| _Community_ | A subset of nodes of the DPG which is characterised by dense interconnections between its elements and sparse connections with the other nodes of the DPG that do not belong to the community. | Understanding the characteristics of nodes to be assigned to a particular community class, identifying predominant predicates, and those that play a marginal role in the classification process. |
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|Constraints | Betweenness centrality | Local reaching centrality | Community|
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|------------|------------|--------------|--------------------|
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|Constraints(Class 1) = val3 < F1 ≤ val1, F2 ≤ val2 | BC(F2 ≤ val2) = 4/24 | LRC(F1 ≤ val1) = 6 / 7 | Community(Class 1) = F1 ≤ val1, F2 ≤ val2 |
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---
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## Installation
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Install the package from PyPI:
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```bash
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pip install dpg
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```
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DPG requires Python 3.10+.
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If you want graph rendering, install the system Graphviz package as well so the
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`dot` executable is available on your `PATH`:
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- macOS (Homebrew): `brew install graphviz`
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- Ubuntu/Debian: `sudo apt-get install graphviz`
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- Windows (winget): `winget install Graphviz.Graphviz`
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For local development installs, editable mode, and documentation builds, see
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[docs/README.md](docs/README.md).
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---
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## Documentation
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For full documentation, visit [https://dpg.readthedocs.io/](https://dpg.readthedocs.io/).
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To build and serve documentation locally, see [docs/README.md](docs/README.md).
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Practitioner-focused benchmark material for `perc_var` and `decimal_threshold` is available in
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[tutorials/parameter_sensitivity_benchmark/README.md](tutorials/parameter_sensitivity_benchmark/README.md).
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---
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## High-level usage
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Here is a minimal high-level example:
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```python
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import pandas as pd
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import numpy as np
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from sklearn.ensemble import RandomForestClassifier, GradientBoostingClassifier
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from dpg import DPGExplainer
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# Load dataset (last column assumed to be target)
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df = pd.read_csv("datasets/custom.csv", index_col=0)
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X = df.iloc[:, :-1]
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y = df.iloc[:, -1]
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# Train a classifier (supports RandomForest, GradientBoosting, AdaBoost, ExtraTree, and more)
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model = RandomForestClassifier(n_estimators=10, random_state=27)
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# or: model = GradientBoostingClassifier(n_estimators=10, random_state=27)
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model.fit(X, y)
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# Build the DPG and extract global explanations
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explainer = DPGExplainer(
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model=model,
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feature_names=X.columns,
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target_names=np.unique(y).astype(str).tolist(),
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)
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explanation = explainer.explain_global(X.values, communities=True)
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# Render the graph to disk
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explainer.plot("dpg_output", explanation, save_dir="datasets", export_pdf=True)
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explainer.plot_communities("dpg_output", explanation, save_dir="datasets", export_pdf=True)
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```
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### Common workflows
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The high-level API is designed to return structured outputs so downstream tools can use them directly.
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- `DPGExplainer.fit(X)`: builds the DPG structure
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- `DPGExplainer.explain_global(X=None, communities=False, community_threshold=0.2)`: returns a `DPGExplanation`
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- `DPGExplainer.explain_local(sample, sample_id=0, X=None, validate_graph=True)`: returns a `DPGLocalExplanation`
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- `DPGExplainer.local_path_dataframe(local_explanation)`: flattens local paths into a tabular view
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- `DPGExplainer.plot(...)`: renders the standard DPG
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- `DPGExplainer.plot_communities(...)`: renders a community-colored DPG
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- `DPGExplainer.plot_local_on_dpg(...)`: overlays one sample's local paths on the fitted DPG
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- `DPGExplainer.evaluate_faithfulness(...)`: summarizes local explanation fidelity and structural faithfulness over a dataset
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`DPGExplanation` includes `dot`, `graph`, `nodes`, `node_metrics`, `edge_metrics`, `class_boundaries`, and optional `communities`.
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### Local explanations
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DPG also supports sample-level explanations on top of the fitted global graph.
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#### Graph construction modes
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You can control how the graph is built through `dpg.graph_construction.mode`:
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```python
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from dpg import DPGExplainer
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explainer = DPGExplainer(
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model=model,
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feature_names=X.columns.tolist(),
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target_names=class_names,
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dpg_config={
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"dpg": {
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"default": {
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"perc_var": 1e-9,
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"decimal_threshold": 6,
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"n_jobs": -1,
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},
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"graph_construction": {
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"mode": "execution_trace", # or "aggregated_transitions"
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"context_order": 1, # 1, an integer > 1, or "auto"
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},
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}
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},
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)
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```
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- `"aggregated_transitions"`: current default behavior; filters path variants first, then discovers the DPG.
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- `"execution_trace"`: builds directly from raw traces and filters edges instead of whole-path variants when `perc_var > 0`.
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`context_order` controls predicate identity in `execution_trace` mode. `1`
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preserves the legacy graph exactly; an order greater than one uses the last k
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executed predicates as context and keeps one sink per class. `"auto"` resolves
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the smallest order for which every pooled graph path is supported by an
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observed execution trace, including recombinations that only appear after
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multiple hops. Orders greater than one require `mode: "execution_trace"`.
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`context_order="auto"` also requires `execution_trace`; in
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`aggregated_transitions` mode context resolution is not applied.
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A phantom path is a multi-hop path assembled by pooling edges from different
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tree executions even though no single execution produced it. DPG-k removes
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these recombinations at the resolved context order while retaining one graph.
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The effective order and each node's context are available through
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`get_context_order()` and `get_node_context(node)`.
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**Regression scope (0.3.0):** `context_order` builds without raising for
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regressors (regression leaves, labeled `"Pred <value>"`, are treated as
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terminal sinks just like class leaves), but "one sink per output" is not a
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defined guarantee for regression the way it is for classification: two
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leaves collapse into the same sink only when their rounded values coincide,
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which is an artifact of label rounding, not a modeled invariant. A
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principled regression sink policy is deferred past 0.3.0. `class_boundaries`
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and `communities` remain classifier-only; calling `explain_global`
|
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|
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with `communities=True` on a regressor raises a clear `ValueError`.
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#### Minimal local workflow
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```python
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from sklearn.datasets import load_iris
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from sklearn.ensemble import RandomForestClassifier
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from dpg import DPGExplainer
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|
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import numpy as np
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X, y = load_iris(return_X_y=True, as_frame=True)
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model = RandomForestClassifier(n_estimators=5, random_state=42).fit(X, y)
|
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|
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explainer = DPGExplainer(
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model=model,
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feature_names=X.columns.tolist(),
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|
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target_names=np.unique(y).astype(str).tolist(),
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)
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explainer.fit(X.values)
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local = explainer.explain_local(sample=X.iloc[0].values, sample_id=0)
|
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|
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print(local.majority_vote)
|
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print(local.class_votes)
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|
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print(local.sample_confidence)
|
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|
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|
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df_local = explainer.local_path_dataframe(local)
|
|
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|
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print(df_local.head())
|
|
237
|
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```
|
|
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|
-
|
|
239
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`local.tree_paths[*].labels` stay in DPG label format such as `"sepal width (cm) <= 3.0"` and `"Class 0"`.
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|
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For easier aggregation, `local.class_votes` and `local.majority_vote` use normalized class names such as `"0"` instead of `"Class 0"`.
|
|
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|
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|
|
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#### Local plotting
|
|
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|
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|
|
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```python
|
|
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explainer.plot_local_on_dpg(
|
|
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|
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"iris_local_sample0",
|
|
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|
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local_explanation=local,
|
|
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true_class_label=str(y.iloc[0]),
|
|
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save_dir="results/",
|
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theme="dpg",
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palette="olive",
|
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layout_template="vertical",
|
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show=False,
|
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|
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)
|
|
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|
-
```
|
|
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|
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|
|
257
|
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A runnable example is available at [examples/local_explanation_iris.py](examples/local_explanation_iris.py).
|
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|
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|
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#### Faithfulness evaluation
|
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You can also evaluate local explanations against the fitted black-box model:
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|
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```python
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details = explainer.evaluate_faithfulness(
|
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X_test,
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y_true=y_test,
|
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return_details=True,
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)
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|
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|
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|
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print(details["faithfulness_score"])
|
|
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print(details["output_fidelity"])
|
|
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|
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print(details["mean_trace_coverage_score"])
|
|
273
|
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print(details["mean_recombination_rate"])
|
|
274
|
-
```
|
|
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|
|
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This reports:
|
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- `output_fidelity`: agreement between the local explanation and the black-box model
|
|
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- structural metrics such as trace coverage and recombination
|
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- semantic metrics such as evidence margin
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- a composite `faithfulness_score`
|
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|
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Important:
|
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- the composite score is a heuristic summary, not a calibrated probability
|
|
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- `output_fidelity` is model agreement, not ground-truth correctness
|
|
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- `local_accuracy` is only reported when `y_true` is provided
|
|
286
|
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- structural faithfulness here means recovering the executed decision traces used by the model
|
|
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|
-
|
|
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### Runnable examples
|
|
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|
-
|
|
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- [examples/quickstart_iris.py](examples/quickstart_iris.py)
|
|
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- [examples/local_explanation_iris.py](examples/local_explanation_iris.py)
|
|
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|
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- [examples](examples)
|
|
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|
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|
|
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## CLI scripts
|
|
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The library contains two different scripts to apply DPG:
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- `examples/run_dpg_standard.py`: with this script it is possible to test DPG on a standard classification dataset provided by `sklearn` such as `iris`, `digits`, `wine`, `breast cancer`, and `diabetes`.
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|
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- `examples/run_dpg_custom.py`: with this script it is possible to apply DPG to your classification dataset, specifying the target class.
|
|
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|
-
|
|
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|
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### Implementation notes
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|
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The library also contains two other essential scripts:
|
|
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|
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- `core.py` contains all the functions used to calculate and create the DPG and the metrics.
|
|
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|
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- `visualizer.py` contains the functions used to manage the visualization of DPG.
|
|
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|
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|
|
304
|
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### Output
|
|
305
|
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The DPG output, through `examples/run_dpg_standard.py` or `examples/run_dpg_custom.py`, produces several files:
|
|
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|
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- the visualization of DPG in a dedicated environment, which can be zoomed and saved;
|
|
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|
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- a `.txt` file containing the DPG metrics;
|
|
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|
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- a `.csv` file containing the information about all the nodes of the DPG and their associated metrics;
|
|
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|
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- a `.txt` file containing the Random Forest statistics (accuracy, confusion matrix, classification report)
|
|
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|
-
|
|
311
|
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### CLI parameter reference
|
|
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Usage: `dpg --dataset <dataset_name> --n_learners <integer_number> --pv <threshold_value> --t <integer_number> --model_name <str_model_name> --dir <save_dir_path> --plot --save_plot_dir <save_plot_dir_path> --attribute <attribute> --communities --clusters --threshold_clusters <float> --class_flag --seed <int>`
|
|
313
|
-
|
|
314
|
-
After installing DPG, the `dpg` command is the packaged equivalent of
|
|
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|
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`python examples/run_dpg_standard.py`.
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|
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|
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Where:
|
|
317
|
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- `dataset` is the name of the standard classification `sklearn` dataset to be analyzed;
|
|
318
|
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- `n_learners` is the number of base learners for the ensemble model;
|
|
319
|
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- `pv` is the threshold value indicating the desire to retain only those paths that occur with a frequency exceeding a specified proportion across the trees;
|
|
320
|
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- `t` is the decimal precision of each feature;
|
|
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|
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- `model_name` is the name of the `sklearn` model chosen to perform classification. Supported models include:
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|
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|
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- `RandomForestClassifier` (default)
|
|
323
|
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- `GradientBoostingClassifier` (new!)
|
|
324
|
-
- `RandomForestRegressor`
|
|
325
|
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- `GradientBoostingRegressor`
|
|
326
|
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- `ExtraTreesClassifier`
|
|
327
|
-
- `AdaBoostClassifier`
|
|
328
|
-
- `AdaBoostRegressor`
|
|
329
|
-
- `BaggingClassifier`
|
|
330
|
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- `dir` is the path of the directory to save the files;
|
|
331
|
-
- `plot` is a store_true variable which can be added to plot the DPG;
|
|
332
|
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- `save_plot_dir` is the path of the directory to save the plot image;
|
|
333
|
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- `attribute` is the specific node metric which can be visualized on the DPG;
|
|
334
|
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- `communities` is a store_true variable which can be added to visualize communities on the DPG;
|
|
335
|
-
- `clusters` is a store_true variable which can be added to visualize clusters on the DPG;
|
|
336
|
-
- `threshold_clusters` is the threshold used to detect ambiguous nodes in clusters;
|
|
337
|
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- `class_flag` is a store_true variable which can be added to highlight class nodes;
|
|
338
|
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- `seed` controls the random split.
|
|
339
|
-
|
|
340
|
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Disclaimer: `attribute`, `communities`, and `clusters` are mutually exclusive: DPG supports just one visualization mode at a time.
|
|
341
|
-
|
|
342
|
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The usage of `examples/run_dpg_custom.py` is similar, but it requires another parameter:
|
|
343
|
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- `target_column`, which is the name of the column to be used as the target variable;
|
|
344
|
-
- while `ds` is the path of the directory where the dataset is.
|
|
345
|
-
|
|
346
|
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### Example `examples/run_dpg_standard.py`
|
|
347
|
-
Some examples can be appreciated in the `examples` folder: https://github.com/Meta-Group/DPG/tree/main/examples
|
|
348
|
-
|
|
349
|
-
In particular, the following DPG is obtained by transforming a Random Forest with 5 base learners, trained on Iris dataset.
|
|
350
|
-
The used command is `dpg --dataset iris --n_learners 5 --pv 0.001 --t 2 --dir examples --plot --save_plot_dir examples`.
|
|
351
|
-
<p align="center">
|
|
352
|
-
<img src="https://raw.githubusercontent.com/Meta-Group/DPG/main/dpg_image_examples/iris_bl5_perc0.001_dec2.png" width="800" />
|
|
353
|
-
</p>
|
|
354
|
-
|
|
355
|
-
The following visualizations are obtained using the same parameters as the previous example, but they show two different metrics: _Community_ and _Betweenness centrality_.
|
|
356
|
-
The used command for showing communities is `dpg --dataset iris --n_learners 5 --pv 0.001 --t 2 --dir examples --plot --save_plot_dir examples --communities`.
|
|
357
|
-
<p align="center">
|
|
358
|
-
<img src="https://raw.githubusercontent.com/Meta-Group/DPG/main/dpg_image_examples/iris_bl5_perc0.001_dec2_communities.png" width="800" />
|
|
359
|
-
</p>
|
|
360
|
-
|
|
361
|
-
The used command for showing a specific property is `dpg --dataset iris --n_learners 5 --pv 0.001 --t 2 --dir examples --plot --save_plot_dir examples --attribute "Betweenness centrality" --class_flag`.
|
|
362
|
-
<p align="center">
|
|
363
|
-
<img src="https://raw.githubusercontent.com/Meta-Group/DPG/main/dpg_image_examples/iris_bl5_perc0.001_dec2_Betweennesscentrality.png" width="800" />
|
|
364
|
-
</p>
|
|
365
|
-
|
|
366
|
-
***
|
|
367
|
-
## Citation
|
|
368
|
-
If you use this for research, please cite. Here is an example BibTeX entry:
|
|
369
|
-
|
|
370
|
-
```bibtex
|
|
371
|
-
@inproceedings{arrighi2024dpg,
|
|
372
|
-
title={Decision Predicate Graphs: Enhancing Interpretability in Tree Ensembles},
|
|
373
|
-
author={Arrighi, Leonardo and Pennella, Luca and Marques Tavares, Gabriel and Barbon Junior, Sylvio},
|
|
374
|
-
booktitle={World Conference on Explainable Artificial Intelligence},
|
|
375
|
-
pages={311--332},
|
|
376
|
-
year={2024},
|
|
377
|
-
isbn = {978-3-031-63797-1},
|
|
378
|
-
doi = {10.1007/978-3-031-63797-1_16},
|
|
379
|
-
publisher = {Springer Nature Switzerland},
|
|
380
|
-
}
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