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PreTab: Tabular Preprocessing Made Simple

PreTab is a modular, scikit-learn compatible representation and preprocessing library for tabular data. A single Preprocessor detects numerical and categorical columns and turns them into model-ready features. Every strategy it uses (splines, neural basis expansions, piecewise-linear encoding, binning, kernel approximations, and language embeddings) is also available as a standalone transformer. Because it speaks the sklearn API, PreTab drops straight into Pipeline and ColumnTransformer workflows and accepts any sklearn transformer alongside its own.

Beyond the transformers themselves, every fitted representation is self-describing: it reports per-output-column lineage, guards supervised methods against leakage, serializes to a portable versioned spec, and can be extended with your own representations through a public, discoverable protocol.

Why PreTab?

• Familiar interface. A scikit-learn fit/transform/fit_transform API that drops into existing pipelines and works with both pandas.DataFrame and numpy.ndarray inputs.
• Automatic feature handling. Feature-type detection and per-feature strategies let you describe intent once instead of wiring transformers by hand.
• Beyond scaling. Spline bases, neural basis maps, piecewise-linear encoding, and kernel approximations turn raw numerical columns into expressive representations.
• Categoricals done right. Ordinal and one-hot encoding and pretrained language embeddings cover both low- and high-cardinality columns.
• Self-describing and reproducible. Fitted preprocessors expose per-column feature lineage. Supported built-in state serializes to a versioned spec with a stable fingerprint for reproduction in the same environment.
• Explicit target usage. Supervised representations declare their target usage and warn when fit outside a controlled context, with a cross-fitting wrapper for out-of-fold training features.
• Composable and extensible. Every strategy is a standalone transformer you can import, compose, or subclass; register your own representation and it behaves like a built-in.

Tip: See how this compares to scikit-learn's own preprocessing transformers for what each one adds where scope overlaps.

🏃 Quickstart

import numpy as np
import pandas as pd

from pretab import Preprocessor

df = pd.DataFrame({
    "age": np.random.randint(18, 65, size=100),
    "income": np.random.normal(60_000, 15_000, size=100).astype(int),
    "city": np.random.choice(["Berlin", "Munich", "Hamburg"], size=100),
    "experience": np.random.randint(0, 40, size=100),
})
y = np.random.randn(100)

# Global strategies: PLE for numerics, integer codes for categoricals
preprocessor = Preprocessor(numerical_method="ple", categorical_method="int")

X = preprocessor.fit_transform(df, y)   # single stacked array, one row per sample

print(X.shape)
# (100, 22)

Note: PreTab accepts a pandas.DataFrame or a numpy.ndarray and infers numerical versus categorical columns either way.

Tip: Swap the global methods for a feature_preprocessing map, for example {"age": "ple", "income": "rbf", "city": "one-hot"}, and PreTab fits each column with its own strategy in a single pass. See Usage for a full example.

Available Transformers

PreTab groups its transformers by representation taxonomy. Each one follows the standard fit / transform API and is importable from pretab.transformers (the stable, flat public import); advanced users can also reach them through the namespace shown per table (pretab.expansion.spline, pretab.expansion.functional, and so on).

Spline expansions

Functional expansions

Kernel approximation

Numerical encoding

Categorical encoding and embeddings

Warning: OneHotFromOrdinalTransformer is deprecated. Use categorical_method="one-hot" (backed by sklearn.preprocessing.OneHotEncoder) instead.

Note: Inside the Preprocessor you select these by short name, for example "ple", "rbf", "one-hot", "pretrained". See Representations for the full catalogue, including exact input/output shapes and per-parameter effects, and the comparison table to filter by capability.

📚 Documentation

Full documentation: pretab.readthedocs.io

Quick Links

• Getting Started: Installation and quickstart
• Core Concepts: Configuration, resolution, target awareness, reproducibility
• Representations: The full method catalogue and how to choose one
• Tutorials: Worked, end-to-end examples
• API Reference: The Preprocessor and every transformer
• Developer Guide: Contributing, testing, and releases

🛠️ Installation

Basic installation:

pip install pretab

With optional extras:

pip install "pretab[embeddings]"   # adds sentence-transformers, for the `pretrained` strategy
pip install "pretab[lightgbm]"     # adds lightgbm, for placement_strategy="lightgbm"
pip install "pretab[all]"          # both of the above

Note: The core install has no heavy dependencies. Each extra is opt-in and only needed if you use the corresponding strategy. PreTab requires Python 3.10 to 3.13.

From source:

git clone https://github.com/OpenTabular/PreTab
cd PreTab
poetry install

Usage

The Preprocessor

The Preprocessor is the high-level entry point. Set a global strategy per feature type, or override individual columns with feature_preprocessing.

from pretab import Preprocessor

# Per-feature configuration overrides the global defaults
preprocessor = Preprocessor(
    feature_preprocessing={
        "age": "ple",
        "income": "rbf",
        "experience": "quantile",
        "city": "one-hot",
    },
    task="regression",
)

X_array = preprocessor.fit_transform(df, y)              # single stacked ndarray
X_dict = preprocessor.transform(df, return_array=False)  # {"num_age": ..., "cat_city": ...}

preprocessor.get_feature_info(verbose=True)              # inspect resolved strategies

get_feature_info(verbose=True) prints the resolved layout so you can confirm every column at a glance:

feature     kind         pipeline                        dim   cats
-------------------------------------------------------------------
age         numerical    imputer -> minmax -> ple          7      -
income      numerical    imputer -> minmax -> rbf          7      -
experience  numerical    imputer -> minmax -> quantile     1      -
city        categorical  imputer -> onehot -> to_float     3      3

Note: transform returns a single stacked array by default, so a Preprocessor drops straight into a plain sklearn.pipeline.Pipeline. Pass output_structure="blocks" (or return_array=False for a single call) for the dict-of-feature-blocks form instead (keys prefixed num_ and cat_).

Standalone transformers

Each transformer works on its own and composes with any sklearn estimator.

import numpy as np

from pretab.transformers import PLETransformer

x = np.random.randn(100, 1)
y = np.random.randn(100, 1)

x_ple = PLETransformer(output_dim=15, task="regression").fit_transform(x, y)
assert x_ple.shape[1] == 15

Important: PLETransformer is supervised. It uses the target y during fit to place its bin edges and raises if you omit it, so always pass y when fitting it directly.

Inside an sklearn Pipeline

Because every transformer follows the sklearn API, you can drop them into a Pipeline or ColumnTransformer.

from sklearn.compose import ColumnTransformer
from sklearn.linear_model import Ridge
from sklearn.pipeline import Pipeline

from pretab.transformers import NaturalCubicSplineTransformer, RBFExpansionTransformer

features = ColumnTransformer([
    ("age", NaturalCubicSplineTransformer(output_dim=10), ["age"]),
    ("income", RBFExpansionTransformer(), ["income"]),
])

model = Pipeline([("features", features), ("ridge", Ridge())])
model.fit(df[["age", "income"]], y)

Spline penalty matrices

Spline transformers expose their penalty matrix for penalized (smoothing) models.

import numpy as np

from pretab.transformers import NaturalCubicSplineTransformer

x = np.random.randn(100, 1)

spline = NaturalCubicSplineTransformer(output_dim=10)
x_spline = spline.fit_transform(x)
penalty = spline.get_penalty_matrix()   # (output_dim, output_dim) smoothing penalty

Advanced Features

Presets

preset sets numerical_method, categorical_method, and the output width in one call, so you can start from a sensible default instead of choosing every parameter by hand.

Preprocessor(preset="standard")   # bspline (regression) / ple (classification), int codes, output_dim=7
Preprocessor(preset="expanded")   # same numerical method, one-hot codes, output_dim=10
Preprocessor(preset="adaptive")   # same numerical method, int codes, adaptive width in [7, 15]

Note: Every preset resolves numerical_method from task: "bspline" for regression, "ple" for classification. Any parameter you also pass explicitly overrides the preset's value for that parameter.

Automatic feature-type detection

By default PreTab inspects each column and classifies it as numerical or categorical. String and object columns are treated as categorical, low-cardinality integer columns are categorical, and integer columns with enough distinct values stay numerical. Tune the behavior with cat_cutoff and treat_all_integers_as_numerical.

preprocessor = Preprocessor(
    treat_all_integers_as_numerical=False,
    cat_cutoff=0.03,
)

Language embeddings for categoricals

The pretrained strategy encodes categorical values with a sentence-transformer, which helps with high-cardinality or semantically rich columns.

preprocessor = Preprocessor(
    feature_preprocessing={"job_title": "pretrained"},
)

Note: Install with pip install "pretab[embeddings]" before using the pretrained strategy.

Numeric binning

NumericBinningTransformer (selected as "custombin") discretizes a numerical column into uniformly- or quantile-spaced bins, with ordinal, onehot, or soft output encodings.

preprocessor = Preprocessor(
    numerical_method="custombin",
    output_dim=32,
)

Feature lineage and inspection

Every fitted Preprocessor can explain itself. get_feature_info summarizes the resolved per-column pipeline, and get_feature_lineage maps every output column back to its source feature, representation family, and component.

preprocessor.fit(df, y)
preprocessor.get_feature_info(verbose=True)      # resolved strategies, widths, categories
lineage = preprocessor.get_feature_lineage()     # one record per output column

Tip: Pass verbose=1 (or higher) to Preprocessor for fit-time logging through the shared "pretab" logger, including a one-line summary of the resolved method(s) per feature kind. See Outputs and inspection for the full level reference.

Leakage-safe supervised representations

Methods like PLETransformer place their bins using the target. PreTab warns when a supervised transformer is fit outside a Pipeline or cross-validation context, and ships a cross-fitting wrapper that produces out-of-fold training features.

from pretab import CrossFittedTransformer
from pretab.transformers import PLETransformer

x_train = df[["age"]].to_numpy()
y_train = y.ravel()
cf = CrossFittedTransformer(PLETransformer(), n_folds=5, random_state=0)
X_train_features = cf.fit_transform(x_train, y_train)   # out-of-fold, leakage-free

Warning: Fitting a supervised transformer on the same rows you later evaluate on leaks target information into the features. CrossFittedTransformer removes that leakage from the training features themselves; inside a Pipeline, cross-validation already keeps each fold's fit confined to its training data.

Choosing a representation with cross-validation

RepresentationSearchCV cross-validates a downstream estimator over a set of candidate numerical_method values and refits the best one on all the data, keeping every candidate's scoring honest by fitting a fresh Preprocessor per fold.

import numpy as np
import pandas as pd
from sklearn.linear_model import Ridge

from pretab import RepresentationSearchCV

rng = np.random.default_rng(0)
X = pd.DataFrame({"x": rng.uniform(-3, 3, size=300)})
y = np.sin(X["x"]) + rng.normal(0, 0.1, size=300)

search = RepresentationSearchCV(
    estimator=Ridge(),
    methods=["minmax", "ple", "bspline", "rbf"],
    cv=5,
    random_state=0,
)
search.fit(X, y)
search.best_method_
# 'bspline'

Note: This searches only the single numerical_method axis with one global method for every numerical column, not a per-column feature_preprocessing search. See Target awareness for the full explanation.

Serialization and reproducibility

A supported fitted preprocessor serializes to a versioned JSON spec and reports a stable fingerprint for tracking what was fitted. Load specs only from trusted sources and restore them with the same library versions; see the serialization contract.

preprocessor.to_spec("representation.json")
restored = Preprocessor.from_spec("representation.json")

preprocessor.fingerprint_          # stable sha256 hash of the fitted representation

Extending PreTab

Add your own representation by subclassing BaseRepresentation, then register it so it behaves like a built-in, selectable via Preprocessor(numerical_method=...).

from pretab import BaseRepresentation, register_representation

class MyRepresentation(BaseRepresentation):
    representation_name = "my_representation"
    feature_kind = "numerical"
    scope = "univariate"
    supervision = "unsupervised"
    # implement fit / transform / _output_sizes

register_representation("my_representation", MyRepresentation)

Tip: See the custom representation tutorial for a complete, runnable example.

📄 License

PreTab is licensed under the MIT License. See LICENSE for details.

🤝 Contributing

Contributions are welcome, whether you are fixing bugs, adding transformers, or improving the docs. Clone the repository and install it in editable mode as shown in the Installation section above, then see the Contributing Guide and our Code of Conduct.

📞 Support

• Issues: GitHub Issues
• Discussions: GitHub Discussions
• Security: see SECURITY.md for how to report a vulnerability privately.