The paper reports a large-scale, compute-controlled study of Chemical Language Models (CLMs) involving over 30,000 experiments across different molecular representations, tokenizations, model sizes, datasets, and architectures. It finds clear scaling trends in pretraining loss but shows that these improvements do not translate into proportional gains in goal-directed molecular design, with chemical syntax saturating early while semantic properties develop more slowly. The authors release a new suite of models, NovoMolGen, that achieves state-of-the-art results in drug discovery tasks, highlighting a disconnect between representation learning and downstream design and calling for new pretraining paradigms that target chemical semantics.
By Roshan Balaji, Kamran Chitsaz, Quentin Fournier, Nirav Pravinbhai Bhatt, Sarath Chandar
arXiv:2607. 02212v1 Announce Type: cross Abstract: Aqueous solubility is a key property in early-stage drug discovery, but most predictive models merge physicochemical descriptors and molecular graph information into a single representation, obscuring whether a prediction is driven by global chemistry, molecular structure, or both.
By Sampreeti Bhattacharya, Arkaprava Roy
arXiv:2608. 10480v1 Announce Type: new Abstract: Large language models (LLMs) are widely applied across chemical tasks, such as molecular property prediction, which underpins drug discovery.
By Junwoo Park, Minyoung Shin, Cheol Soon Lee, Sujee Lee
arXiv:2609.37384v1 Announce Type: new
Abstract: Molecular representation learning is central to computer-aided drug discovery. Molecular graphs, SMILES strings, and 3D conformations provide complemen...
By Linqing Mo, Jiayu Zhou, Bin Chen
arXiv:2606. 11508v1 Announce Type: new Abstract: Accurate prediction of absorption, distribution, metabolism, and excretion (ADME) properties is critical to drug discovery, but remains challenging because ADME endpoints are noisy, interdependent, and often data-limited.
By Yifan Xue, Srimukh Prasad Veccham, Saee Paliwal, Tyler Shimko, Micha Livne
Large language models (LLMs) are widely applied across chemical tasks, such as molecular property prediction, which underpins drug discovery. Molecular LLMs represent a molecule through several modalities, notably a 1D SMILES sequence or a 2D molecular graph.