tabpfnwide 0.1.0

TabPFN-Wide: Extension of the TabPFN-2 foundation model, specifically designed for wide datasets (many features, few samples).

TabPFN-Wide

[!NOTE] DOI: XXX Author: Christopher Kolberg, Jules Kreuer, Jonas Huurdeman, Sofiane Ouaari, Katharina Eggensperger, Nico Pfeifer

TabPFN-Wide is an extension of the TabPFN-2 foundation model, specifically designed for wide datasets (many features, few samples), such as multi-omics data. It allows for training and evaluating large-scale tabular models that can handle thousands of features.

This repository provides a release (v0.1.0) of the tabpfnwide package along with a suite of scripts for training, feature-smearing analysis, and biological interpretation used in the TabPFN-Wide paper.

Latter releases will include bug fixes and new features.

Publication

The TabPFN-Wide preprint is available at arXiv.

License

The model weights and code of the tabpfnwide project are licensed under the Prior Labs License Version 1.1.

[!IMPORTANT] The license includes an attribution requirement. If you use this work to improve an AI model, you must include "TabPFN" in the model name and display "Built with PriorLabs-TabPFN". See LICENSE for details.

Quick Start

Installation

Using pip:

pip install tabpfnwide

From Source:

pip install "tabpfnwide @ git+https://github.com/not-a-feature/TabPFN-Wide.git"

Model Weights

Model weights are automatically downloaded from GitHub Releases upon first use and cached in ~/.tabpfnwide/models/. If you are running in an offline environment, you can manually download the .pt files from the Releases page and place them in that directory.

Basic Usage

TabPFN-Wide works just like a scikit-learn classifier.

from tabpfnwide.classifier import TabPFNWideClassifier
from sklearn.datasets import load_breast_cancer
from sklearn.model_selection import train_test_split

# Load a 'wide' dataset (or any tabular data)
X, y = load_breast_cancer(return_X_y=True)
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.2, random_state=42)

# Initialize the classifier with a wide model (e.g., handles up to 5k features)
clf = TabPFNWideClassifier(model_name="wide-v2-5k", device="cpu")

# Fit and predict
clf.fit(X_train, y_train)
predictions = clf.predict(X_test)

See demo_run_prediction.py for more details

Interpreting the Model

TabPFN-Wide provides built-in tools to extract attention-based feature importance.

import numpy as np

# Note: Attention maps require n_estimators=1 and features_per_group=1
clf = TabPFNWideClassifier(
    model_name="wide-v2-5k", 
    save_attention_maps=True,
    n_estimators=1,
    features_per_group=1
)
clf.fit(X_train, y_train)

# 1. Get raw feature-to-feature attention maps (list of maps per layer)
attn_per_layer = clf.get_attention_maps()
avg_attn_matrix = np.mean(attn_per_layer, axis=0)

# 2. Get direct feature importance based on label-to-feature attention
# This represents how much the model's prediction 'attends' to each input feature
importances = clf.get_attention_to_label()

See demo_attention_maps.py for more details.

Continued Pretraining

[!NOTE] Training scripts require the dev dependencies.

The training logic is contained in the training/ directory. You can run training jobs using the provided python script or shell wrapper.

Using the Python script:

python training/train.py \
    --prior_type mlp_scm \
    --prior_max_features 100 \
    --batch_size 8

Using the shell script:

bash training/train.sh

Evaluation & Analysis

bash analysis/run_analysis.sh "$CHECKPOINT_PATH" "$OUTPUT_DIR"

See analysis/analysis.sbatch for more details.

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Citation

If you use this code or model in your research, please cite:

TODO

For the original TabPFN work, please cite:

@article{hollmann2025tabpfn,
 title={Accurate predictions on small data with a tabular foundation model},
 author={Hollmann, Noah and M{\"u}ller, Samuel and Purucker, Lennart and
         Krishnakumar, Arjun and K{\"o}rfer, Max and Hoo, Shi Bin and
         Schirrmeister, Robin Tibor and Hutter, Frank},
 journal={Nature},
 year={2025},
 month={01},
 day={09},
 doi={10.1038/s41586-024-08328-6},
 publisher={Springer Nature},
 url={https://www.nature.com/articles/s41586-024-08328-6},
}

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