4 papers · 1 filter
Task- and dataset-specific information in protein language models
Roman Joeres, Ilya Senatorov, Anastasia Kolchina +2
Protein language models (PLMs) have transferred the latest advances from natural language processing to computational biology. These models, trained on large corpora of protein seq…
Probing Chemical Language Models: Effects of Pre-training and Fine-tuning
Anna Karnysheva, Dietrich Klakow, Ji-Ung Lee
Chemical language models (CLMs) are trained with linearized representations such as SMILES, yet it remains unclear which chemically meaningful substructures they encode. To foster…
Chemical Language Models for Natural Products: A State-Space Model Approach
Ho-Hsuan Wang, Afnan Sultan, Andrea Volkamer +1
Language models are widely used in chemistry for molecular property prediction and small-molecule generation, yet Natural Products (NPs) remain underexplored despite their importan…
Transformers for molecular property prediction: Domain adaptation efficiently improves performance
Afnan Sultan, Max Rausch-Dupont, Shahrukh Khan +3
Over the past six years, molecular transformer models have become key tools in drug discovery. Most existing models are pre-trained on large, unlabeled datasets such as ZINC or ChE…