t-SMILES: A Scalable Fragment-based Molecular Representation Framework for De Novo Molecule Generation

Understand

Effective representation of molecules is a crucial factor affecting the performance of artificial intelligence models.

• This study introduces a flexible, fragment-based, multiscale molecular representation framework called t-SMILES (tree-based SMILES) with three code algorithms: TSSA, TSDY and TSID.
• It describes molecules using SMILES-type strings obtained by performing a breadth-first search on a full binary tree formed from a fragmented molecular graph.
• Systematic evaluations using JTVAE, BRICS, MMPA, and Scaffold show the feasibility of constructing a multi-code molecular description system, where various descriptions complement each other, enhancing the overall performance.