neural-trees

Soft decision trees, mixture of experts, and statistical model comparison tests for Python. A scikit-learn compatible library implementing classic machine learning algorithms from research papers, with a PyTorch backend.

Decision boundary learning with Soft Decision Trees on a toy dataset.

Features

• scikit-learn compatible API (fit, predict, score, works in Pipeline)
• PyTorch backend with GPU support
• Soft Decision Trees, Hierarchical Mixture of Experts, Multivariate and Omnivariate Trees, GAL
• Combined 5x2cv F test, McNemar's test, paired t-test for classifier comparison
• Tested on standard benchmarks (Iris, Wine, Breast Cancer)

Installation

pip install neural-trees

Install from source

git clone https://github.com/cgrtml/neural-trees.git
cd neural-trees
pip install -e .

Quick Start

Train a Soft Decision Tree on the Iris dataset:

from neural_trees import SoftDecisionTree
from sklearn.datasets import load_iris
from sklearn.model_selection import train_test_split

X, y = load_iris(return_X_y=True)
X_train, X_test, y_train, y_test = train_test_split(X, y, random_state=42)

model = SoftDecisionTree(depth=4, max_epochs=40)
model.fit(X_train, y_train)
print(model.score(X_test, y_test))  # ~0.97

Use it inside a scikit-learn pipeline:

from sklearn.pipeline import Pipeline
from sklearn.preprocessing import StandardScaler

pipe = Pipeline([
    ("scaler", StandardScaler()),
    ("model", SoftDecisionTree(depth=4, max_epochs=40)),
])
pipe.fit(X_train, y_train)
pipe.score(X_test, y_test)

Interactive playground

app.py is a Streamlit dashboard for comparing the models side by side on standard and synthetic datasets, with live decision boundaries and hyperparameter controls:

pip install streamlit plotly
streamlit run app.py

Benchmark

5-fold stratified cross-validation accuracy with StandardScaler preprocessing, averaged over 5 seeds. Every number comes from benchmarks/run_benchmarks.py, so the table can be re-run and checked:

python benchmarks/run_benchmarks.py --seeds 5

Model	Iris	Wine	Breast Cancer
Soft Decision Tree (depth=4)	0.900	0.979	0.976
Multivariate Tree (depth=3)	0.973	0.989	0.952
CART (sklearn)	0.943	0.917	0.920
Random Forest	0.945	0.980	0.960
SVM (RBF)	0.959	0.984	0.978

On Wine and Breast Cancer the soft tree closes most of the gap between CART and kernel or ensemble methods while staying differentiable. On Iris it does not: 150 samples over 3 classes is too little data for a depth-4 tree with 15 gates trained for 40 epochs, and a single oblique split does better. growth="incremental" lets the tree choose its own depth against a validation split rather than being given one. That is the honest shape of the trade-off, and it is why the comparison scripts in examples/ use a hypothesis test rather than a single accuracy number.

Algorithms

These implementations start from the published algorithms below and depart from them where this library makes its own design choices. Where an implementation deviates deliberately, the module docstring says so. Treat the references as the lineage of an idea, not as a claim of exact reproduction.

Algorithm	Reference
Soft Decision Trees	İrsoy, Yıldız, Alpaydın (ICPR 2012)
Hard export of a soft tree	to_hard_tree(), this library
Multivariate Decision Trees	Alpaydın & Çetin (1995), Yıldız & Alpaydın (IEEE TNN 2001)
Omnivariate Decision Trees	Yıldız & Alpaydın (IEEE TNN 2001)
Hierarchical Mixture of Experts with subtree dropout	İrsoy & Alpaydın (Neurocomputing 2021)
GAL: Grow and Learn Networks	Alpaydın (IJPRAI 1994)
Combined 5x2cv F Test	Alpaydın (Neural Computation 1999)
McNemar's Test, Paired t-test	Standard references
Naive Bayes, Weighted KNN	Textbook chapters 3 to 8

Use Cases

Research. Reproduce or extend results from the original papers with a clean, tested codebase.

Statistical model comparison. Compare classifiers with proper hypothesis tests instead of ad hoc accuracy diffs:

from neural_trees import combined_5x2cv_f_test
from sklearn.svm import SVC
from sklearn.tree import DecisionTreeClassifier
from sklearn.datasets import load_breast_cancer

X, y = load_breast_cancer(return_X_y=True)

result = combined_5x2cv_f_test(
    DecisionTreeClassifier(),
    SVC(kernel="rbf"),
    X, y,
)

print(result)

Education. A working reference for soft splits and mixtures of experts beyond textbook diagrams.

Why Soft Decision Trees

Standard decision trees use hard splits, which makes them non-differentiable and unstable to small input changes. Soft Decision Trees replace each split with a sigmoid gate, which means:

• The tree is fully differentiable and trains with gradient descent
• Predictions are smooth, not piecewise constant
• Performance often lands between CART and ensemble methods
• The tree stays interpretable, you can still read off split decisions

Examples

Runnable scripts in examples/:

Script	What it shows
01_iris_classification.py	Minimal train/test loop on Iris
02_pipeline_with_scaler.py	StandardScaler + SoftDecisionTree in a Pipeline, 5-fold CV
03_classifier_comparison.py	Combined 5x2cv F test against CART
04_decision_boundary.py	Decision boundary plot on make_moons

python examples/01_iris_classification.py

Notebooks

• 01_soft_decision_trees.ipynb: training, decision boundary visualization, comparison with CART
• 02_classifier_comparison_tests.ipynb: when to use which statistical test
• 03_multivariate_decision_trees.ipynb: oblique splits against CART and soft trees

Citation

If you use this library in academic work, please cite the original papers:

@inproceedings{irsoy2012soft,
  title     = {Soft Decision Trees},
  author    = {\.{I}rsoy, O{\u{g}}uzhan and Y{\i}ld{\i}z, Olcay Taner and Alpayd{\i}n, Ethem},
  booktitle = {ICPR},
  year      = {2012}
}

@article{alpaydin1999combined,
  title   = {Combined 5x2cv {F} Test for Comparing Supervised Classification Learning Algorithms},
  author  = {Alpayd{\i}n, Ethem},
  journal = {Neural Computation},
  volume  = {11},
  number  = {8},
  pages   = {1885--1892},
  year    = {1999}
}

To cite this implementation:

@software{temel_neural_trees,
  author = {Temel, Cagri},
  title  = {neural-trees: scikit-learn compatible Soft Decision Trees and Mixture of Experts},
  year   = {2026},
  url    = {https://github.com/cgrtml/neural-trees}
}

Limitations

neural-trees is not the right tool for every problem:

• Very high-dimensional data. Every internal node holds a dense weight vector, so parameter count grows as 2^depth x n_features. Beyond a few thousand features, reduce dimensionality first or use a linear model.
• Streaming or online learning. Training is batch only; there is no partial_fit. Refit from scratch when new data arrives.
• Sub-millisecond inference. The PyTorch backend adds per-call overhead. SoftDecisionTree.to_hard_tree() exports the learned gates as a plain numpy model that predicts about 5x faster and prints its rules, at the cost of reading each gate as a hard decision rather than a soft one.
• Very large sample counts. Training is full-batch gradient descent over epochs, not an optimized tree-growing routine like CART. Millions of rows will be slow on CPU.
• Categorical features. There is no built-in encoding; sigmoid gates expect continuous, scaled inputs. Encode and scale in a Pipeline.

Changelog

See CHANGELOG.md. Versions 0.2.0 and 0.3.0 fixed four models that did not work in 0.1.x, so upgrade if you are on an earlier release. Every classifier passes scikit-learn's estimator checks as of 0.4.0.

Contributing

Contributions are welcome. New to open source? See CONTRIBUTING.md for a beginner-friendly walkthrough.

Every open issue states what would close it, so you can judge the size before you start.

First contribution, no deep ML background needed, tagged good first issue: write a test file for one of the pure-numpy estimators, wire ruff into CI, move packaging to pyproject.toml, add a coverage threshold, or run the notebooks in CI so their committed outputs cannot go stale.

If you know scikit-learn and PyTorch: sample_weight and class_weight support, or vectorizing the mixture-of-experts gating tree the way SoftDecisionTree already is (that one has a worked reference implementation in the repo to copy).

If you want a research problem: incremental tree growing from İrsoy, Yıldız and Alpaydın (ICPR 2012), which the fixed-depth implementation here does not do, or distilling a trained soft tree into a hard one for readable rules and fast inference.

For larger changes, open an issue first to discuss the approach. If this project is useful to you, a star helps others find it.

Contributors

Thanks to everyone who has improved this library.

Contributor	Contribution
@snoopuppy582	Symmetric McNemar disagreement test (#20), development requirements (#23), depth validation (#22), reproducibility test (#24)
@aribaskagan	Fixed the coverage target in CI, which had been measuring a module that no longer exists (#25)
@yunaremaia	Migrated packaging to pyproject.toml and wired ruff into CI (#46)

The list began with the GitHub Sprint segment of the WSU Data and Analytics Breakout (May 15, 2026) and stays open to anyone. Full history: the contributors graph.

License

MIT. See LICENSE.