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When Does TabPFN Fail? – An Empirical Study

Motivation

Tabular data remains one of the most widely used data modalities in real-world machine learning applications. Recently, TabPFN (Tabular Prior-Data Fitted Network) has emerged as a foundation model for tabular data, showing strong performance particularly in low-data regimes.

This project aims to empirically investigate the behavior of TabPFN and answer the following questions:

  • When does TabPFN outperform traditional machine learning models?
  • How does TabPFN behave under challenging conditions such as limited data and label noise?
  • What are the limitations of TabPFN compared to established methods?

Experiments

1. Small Data Regime

We evaluate model performance across varying training dataset sizes:

  • Sample sizes: 50, 100, 200, 500, 1000
  • Models compared:
    • TabPFN
    • XGBoost
    • Logistic Regression

The goal is to understand how models behave when training data is scarce.


2. Label Noise Robustness

We introduce synthetic label noise into the training data:

  • Noise levels: 0%, 10%, 20%, 30%, 40%
  • Models compared:
    • TabPFN
    • XGBoost
    • Logistic Regression

This experiment evaluates robustness to corrupted supervision, which is common in real-world datasets.


Results

Small Data Performance

Small Data Results

Noise Robustness

Noise Results


Key Findings

  • TabPFN performs strongly in low-data regimes, often outperforming traditional models when the number of training samples is limited.
  • TabPFN demonstrates stable performance under increasing label noise, particularly in high-noise settings (30–40%).
  • XGBoost shows significant degradation under high label noise, indicating sensitivity to corrupted labels.
  • Logistic Regression degrades steadily as noise increases, highlighting the limitations of linear models under noisy supervision.
  • In clean data settings, traditional models can be competitive or slightly outperform TabPFN.

Conclusion

The results suggest that TabPFN provides a robust alternative to traditional tabular learning methods, particularly in challenging scenarios such as limited data availability and noisy labels. Its prior-based learning approach appears to contribute to improved generalization under such conditions.

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