Tabular foundation models for in-context prediction of molecular properties

TL;DR

Tabular foundation models enable accurate, cost-effective molecular property prediction through in-context learning, outperforming classical methods without task-specific fine-tuning in low- to medium-data regimes.

Contribution

This work demonstrates the effectiveness of tabular foundation models for molecular property prediction, highlighting their advantages over traditional fine-tuning approaches and classical descriptors.

Findings

TFMs achieve up to 100% win rates on MoleculeACE tasks.

Combining TFMs with CheMeleon embeddings improves predictive performance.

Molecular representation choice significantly impacts TFM effectiveness.

Abstract

Accurate molecular property prediction is central to drug discovery, catalysis, and process design, yet real-world applications are often limited by small datasets. Molecular foundation models provide a promising direction by learning transferable molecular representations; however, they typically involve task-specific fine-tuning, require machine learning expertise, and often fail to outperform classical baselines. Tabular foundation models (TFMs) offer a fundamentally different paradigm: they perform predictions through in-context learning, enabling inference without task-specific training. Here, we evaluate TFMs in the low- to medium-data regime across both standardized pharmaceutical benchmarks and chemical engineering datasets. We evaluate both frozen molecular foundation model representations, as well as classical descriptors and fingerprints. Across the benchmarks, the approach shows excellent predictive performance while reducing computational cost, compared to fine-tuning, with these advantages also transferring to practical engineering data settings. In particular, combining TFMs with CheMeleon embeddings yields up to 100\% win rates on 30 MoleculeACE tasks, while compact RDKit2d and Mordred descriptors provide strong descriptor-based alternatives. Molecular representation emerges as a key determinant in TFM performance, with molecular foundation model embeddings and 2D descriptor sets both providing substantial gains over classic molecular fingerprints on many tasks. These results suggest that in-context learning with TFMs provides a highly accurate and cost-efficient alternative for property prediction in practical applications.