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| Main Authors: | , , , , , |
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| Format: | Preprint |
| Published: |
2025
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| Subjects: | |
| Online Access: | https://arxiv.org/abs/2510.06162 |
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| _version_ | 1866910080617676800 |
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| author | Kolberg, Christopher Kreuer, Jules Huurdeman, Jonas Ouaari, Sofiane Eggensperger, Katharina Pfeifer, Nico |
| author_facet | Kolberg, Christopher Kreuer, Jules Huurdeman, Jonas Ouaari, Sofiane Eggensperger, Katharina Pfeifer, Nico |
| contents | Revealing novel insights from the relationship between molecular measurements and pathology remains a very impactful application of machine learning in biomedicine. Data in this domain typically contain only a few observations but thousands of potentially noisy features, posing challenges for conventional tabular machine learning approaches. While prior-data fitted networks emerge as foundation models for predictive tabular data tasks, they are currently not suited to handle large feature counts (>500). Although feature reduction enables their application, it hinders feature importance analysis. We propose a strategy that extends existing models through continued pre-training on synthetic data sampled from a customized prior. The resulting model, TabPFN-Wide, matches or exceeds its base model's performance, while exhibiting improved robustness to noise. It seamlessly scales beyond 30,000 categorical and continuous features, regardless of noise levels, while maintaining inherent interpretability, which is critical for biomedical applications. Our results demonstrate that prior-informed adaptation is suitable to enhance the capability of foundation models for high-dimensional data. On real-world omics datasets, we show that many of the most relevant features identified by the model overlap with previous biological findings, while others propose potential starting points for future studies. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2510_06162 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | TabPFN-Wide: Continued Pre-Training for Extreme Feature Counts Kolberg, Christopher Kreuer, Jules Huurdeman, Jonas Ouaari, Sofiane Eggensperger, Katharina Pfeifer, Nico Machine Learning Revealing novel insights from the relationship between molecular measurements and pathology remains a very impactful application of machine learning in biomedicine. Data in this domain typically contain only a few observations but thousands of potentially noisy features, posing challenges for conventional tabular machine learning approaches. While prior-data fitted networks emerge as foundation models for predictive tabular data tasks, they are currently not suited to handle large feature counts (>500). Although feature reduction enables their application, it hinders feature importance analysis. We propose a strategy that extends existing models through continued pre-training on synthetic data sampled from a customized prior. The resulting model, TabPFN-Wide, matches or exceeds its base model's performance, while exhibiting improved robustness to noise. It seamlessly scales beyond 30,000 categorical and continuous features, regardless of noise levels, while maintaining inherent interpretability, which is critical for biomedical applications. Our results demonstrate that prior-informed adaptation is suitable to enhance the capability of foundation models for high-dimensional data. On real-world omics datasets, we show that many of the most relevant features identified by the model overlap with previous biological findings, while others propose potential starting points for future studies. |
| title | TabPFN-Wide: Continued Pre-Training for Extreme Feature Counts |
| topic | Machine Learning |
| url | https://arxiv.org/abs/2510.06162 |