Optimizing SMILES token sequences via trie-based refinement and transition graph filtering.

Tokenization plays a critical role in preparing SMILES strings for molecular foundation models. Poor token units can fragment chemically meaningful substructures, inflate sequence length, and hinder model learning and interpretability. Existing approaches such as SMILES Pair Encoding (SPE) and Atom Pair Encoding (APE) compress token sequences but often ignore domain-specific chemistry or fail to generalize to larger or more diverse molecules. We propose a domain-aware method for SMILES compression that combines frequency-guided substring mining using a prefix trie with an optional entropy-based refinement step using a token transition graph (TTG). On a corpus of 100,000 PubChem molecules, the Trie+TTG method reduces token sequences by more than 50% compared to APE while preserving chemically coherent substructures. The method generalizes effectively to large, out-of-distribution molecules, achieving compression rates of up to 90% with minimal sensitivity to molecule size. To assess downstream utility, we evaluate latent-space structure using unsupervised clustering and perform QSAR regression on ESOL. Trie+TTG produces more separable molecular representations and stronger predictive performance than Trie-only and APE. In addition, on peptide corpora, our method substantially outperforms SPE and the PeptideCLM tokenizer in compression and entropy metrics. These results show that combining trie-based mining with TTG refinement yields compact, stable, and chemically meaningful tokenizations suitable for modern molecular representation learning.Scientific contributions: We present a trie-based framework that compresses SMILES sequences into shorter, chemically coherent units while guaranteeing lossless reconstruction. By incorporating a token transition graph for entropy-guided refinement, our method selects contextually stable merges that improve both compression efficiency and generalization. Unlike prior approaches such as APE and SPE, our tokenizer combines frequency and context awareness, yielding more compact, interpretable, and transferable molecular representations.