Does Pretraining Teach Chemical Language Models Chemistry?

Chemical language models (CLMs) are trained with linearized representations such as SMILES, yet it remains unclear which chemically meaningful substructures they encode. To foster a better understanding of CLMs, we conduct a systematic study and probe for 78 molecular substructures across eight pre-trained and six randomly initialized models. We furthermore study how fine-tuning on chemical downstream tasks affects the learned representations of molecular substructures. Our results show that pre-training generally improves molecular structure awareness of CLMs, particularly in the upper layers. Moreover, randomly initialized models already encode ring structures well in the first layer. Our analysis on two chemical downstream tasks further reveals that, interestingly, fine-tuning affects task-relevant molecular substructures more than others, indicating that the changes in the representations follow chemical theory.

Chemical Language Models (CLMs) are increasingly used in de novo drug design, driven by recent growth in model scale, compute, and dataset size. However, the relationship between design choices, training dynamics, and downstream generation quality remains poorly understood. We present a compute-controlled scaling study of CLMs comprising more than 30,000 experiments across molecular representations (SMILES, SELFIES, SAFE), tokenizations (atom-level and byte-pair encoding), model scales (0.5M-1B parameters), leakage-controlled datasets (MOSES, ChEMBL, PubChem, ZINC-22), and architectures (decoder-only and encoder-decoder). By fitting IsoFLOP profiles, we establish clear scaling trends in pretraining loss, but find that these improvements do not translate into comparable gains in goal-directed molecular design. Layer-wise probing and sparse autoencoder analysis reveal continued development of chemical representations: chemical syntax saturates early, while semantic properties emerge more slowly and become increasingly accessible with further training and model scale. These representational gains coexist with diminishing improvements in goal-directed generation under the evaluated protocols and oracle budgets. Our resulting suite of models, NovoMolGen, achieves state-of-the-art results, outperforming prior CLMs and specialized generative models in goal-directed molecular generation across drug discovery tasks. These findings expose a disconnect between chemical representation learning and downstream molecular design, motivating the development of pretraining paradigms that more directly learn chemical semantics.

Chemical language models (CLMs) have emerged as promising competitors to popular classical machine learning models for molecular property prediction (MPP) tasks. However, an increasing number of studies have reported inconsistent and contradictory results for the performance of CLMs across various MPP benchmark tasks. In this study, we conduct and analyze hundreds of meticulously controlled experiments to systematically investigate the effects of various factors, such as dataset size, model size, and standardization, on the pre-training and fine-tuning performance of CLMs for MPP. In the absence of well-established scaling laws for encoder-only masked language models, our aim is to provide comprehensive numerical evidence and a deeper understanding of the underlying mechanisms affecting the performance of CLMs for MPP tasks, some of which appear to be entirely overlooked in the literature.