RoFt-Mol: Benchmarking Robust Fine-tuning with Molecular Graph Foundation Models

In the era of foundation models, fine-tuning pre-trained models for specific downstream tasks has become crucial. This drives the need for robust fine-tuning methods to address challenges such as model overfitting and sparse labeling. Moleculargraph foundation models (MGFMs) face unique difficulties that complicate fine-tuning. These models are limited by smaller pre-training datasets and more severedata scarcity for downstream tasks, both of which require enhanced model generalization. Moreover, MGFMs must accommodate diverse objectives, including bothregression and classification tasks. To better understand and improve fine-tuningtechniques under these conditions, we classify eight fine-tuning methods into threemechanisms: weight-based, representation-based, and partial fine-tuning. Webenchmark these methods on downstream regression and classification tasks acrosssupervised and self-supervised pre-trained models in diverse labeling settings. Thisextensive evaluation provides valuable insights and informs the design of a refinedrobust fine-tuning method, ROFT-MOL. This approach combines the strengths ofsimple post-hoc weight interpolation with more complex weight ensemble fine-tuning methods, delivering improved performance across both task types whilemaintaining the ease of use inherent in post-hoc weight interpolation.