nanoTabPFN

Note

This is a reimplementation of nanoTabPFN in JAX, please cite their work. To avoid recompilation for different numbers of input features, a padding was added.

Train your own small TabPFN in less than 500 LOC and a few minutes.

The purpose of this repository is to be a good starting point for students and researchers that are interested in learning about how TabPFN works under the hood.

Our Code

• model.py contains the implementation of the architecture and a sklearn-like interface in less than 200 lines of code.
• train.py implements a simple training loop and prior dump data loader in under 200 lines
• experiment.ipynb will recreate the experiment from the paper

Pretrain your own nanoTabPFN

To pretrain your own nanoTabPFN, you need to first download a prior data dump from here, then run train.py.

cd nanoTabPFN

# download data dump
curl http://ml.informatik.uni-freiburg.de/research-artifacts/nanoTabPFN/300k_150x5_2.h5 --output 300k_150x5.h5

python train.py

Evaluation

We repeated training for two seeds only; the paper uses 20. To reproduce these results, run experiment.ipynb.

Step by Step explanation:

First we import our code from model.py and train.py

from model import NanoTabPFNModel
from model import NanoTabPFNClassifier
from train import PriorDumpDataLoader
from train import train

Then we instantiate our model

model = NanoTabPFNModel(
    embedding_size=96,
    num_attention_heads=4,
    mlp_hidden_size=192,
    num_layers=3,
    num_outputs=2
)

and our dataloader

prior = PriorDumpDataLoader(
    "300k_150x5_2.h5",
    num_steps=2500,
    batch_size=32,
)

Now we can train our model:

model, _ = train(
    model,
    prior,
    lr = 4e-3,
)

and finally we can instantiate our classifier:

clf = NanoTabPFNClassifier(model)

and use its .fit, .predict and .predict_proba:

from sklearn.datasets import load_breast_cancer
from sklearn.metrics import roc_auc_score, accuracy_score
from sklearn.model_selection import train_test_split

X, y = load_breast_cancer(return_X_y=True)
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.5)

clf.fit(X_train, y_train)
prob = clf.predict_proba(X_test)
pred = clf.predict(X_test)
print('ROC AUC', roc_auc_score(y_test, prob))
print('Accuracy', accuracy_score(y_test, pred))

TFM-Playground

The nanoTabPFN repository is supposed to stay ultra small and simple, but we created another repository, the TFM-Playground which we are building out to have a lot more features, like regression, multiple prior interfaces, multiple architectures, ensembling of different pre-processings and more, so check it out if you are interested!

BibTex Citation

@article{pfefferle2025nanotabpfn,
  title={nanoTabPFN: A Lightweight and Educational Reimplementation of TabPFN},
  author={Pfefferle, Alexander and Hog, Johannes and Purucker, Lennart and Hutter, Frank},
  journal={arXiv preprint arXiv:2511.03634},
  year={2025}
}