Introduces SMILES Pair Encoding (SPE), a data-driven tokenization algorithm that learns high-frequency SMILES substrings from ChEMBL to produce shorter, chemically interpretable token sequences for deep learning.
SPMM pre-trains a dual-stream transformer on SMILES and 53 molecular property vectors using contrastive learning and cross-attention, enabling bidirectional structure-property generation, property prediction, and reaction prediction through a single model.
Jiang et al. survey 12 families of transformer architectures in molecular science, covering GPT, BERT, BART, graph transformers, Transformer-XL, T5, ViT, DETR, Conformer, CLIP, sparse transformers, and mobile/efficient variants, with detailed algorithmic descriptions and molecular applications.
PRISMA-based systematic review of 72 papers on chemical language models for molecular generation, comparing architectures and biased methods using MOSES metrics.
t-SMILES represents molecules by fragmenting them into substructures, building full binary trees, and traversing them breadth-first to produce SMILES-type strings that reduce nesting depth and outperform SMILES, DeepSMILES, and SELFIES on generation benchmarks.
A comprehensive review of transformer-based chemical language models operating on SMILES, categorizing encoder-only (BERT variants), decoder-only (GPT variants), and encoder-decoder models with analysis of tokenization strategies, pre-training approaches, and future directions.
This paper applies a Transformer sequence-to-sequence model to predict SMILES strings from chemical compound names (Synonyms). Two enhancements, an atom-count constraint loss and SMILES/InChI multi-task learning, improve F-measure over rule-based and vanilla Transformer baselines.
X-MOL applies large-scale Transformer pre-training on 1.1 billion molecules with a generative SMILES-to-SMILES strategy, then fine-tunes for five molecular analysis tasks including property prediction, reaction analysis, and de novo generation.
Introduces AMORE, an embedding-based retrieval framework that evaluates whether chemical language models can recognize the same molecule across different SMILES representations. Results show current models are not robust to identity-preserving augmentations.
A comprehensive survey classifying molecular representation learning foundation models by input modality (sequence, graph, 3D, image, multimodal) and analyzing four pretraining paradigms for drug discovery tasks.
Frey et al. discover empirical power-law scaling relations for both chemical language models (ChemGPT, up to 1B parameters) and equivariant GNN interatomic potentials, finding that neither domain has saturated with respect to model size, data, or compute.
BARTSmiles pre-trains a BART-large model on 1.7 billion SMILES strings from ZINC20 and achieves the best reported results on 11 classification, regression, and generation benchmarks.