TSIS: A Supplementary Algorithm to t-SMILES for Fragment-based Molecular Representation
String-based molecular representations, such as SMILES, are a de facto standard for linearly representing molecular information. However, the must be paired symbols and the parsing algorithm result in long grammatical dependencies, making it difficult for even state-of-the-art deep learning models to accurately comprehend the syntax and semantics. Although DeepSMILES and SELFIES have addressed certain limitations, they still struggle with advanced grammar, which makes some strings difficult to read. This study introduces a supplementary algorithm, TSIS (TSID Simplified), to t-SMILES family. Comparative experiments between TSIS and another fragment-based linear solution, SAFE, indicate that SAFE presents challenges in managing long-term dependencies in grammar. TSIS continues to use the tree defined in t-SMILES as its foundational data structure, which sets it apart from the SAFE model. The performance of TSIS models surpasses that of SAFE models, indicating that the tree structure of the t-SMILES family provides certain advantages.
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