arXiv:2606. 05693v1 Announce Type: new Abstract: Large language models (LLMs) have shown promise for molecular property prediction, but their ability to reason over chemical structures remains limited, as molecular representations such as SMILES differ substantially from the natural language on which LLMs are primarily trained.
By Joey Chan, Wonbin Kweon, Ashley Shin, Niharika Bhattacharjee, Pengcheng Jiang, Yue Guo, Jiawei Han
The paper introduces MolPAIR, a framework that enhances tabular foundation models (TFMs) for predicting molecular properties under structural shifts by incorporating molecule-level and molecular-pair contexts without task‑specific parameter updates. MolPAIR refines initial predictions from a global TFM by using a second frozen TFM to predict differences in prediction errors between a query molecule and labeled reference molecules. Experiments on 58 MoleculeACE and Polaris tasks show that MolPAIR improves performance on 46 tasks across multiple molecular representations and TFM backbones, demonstrating that explicit molecular comparisons strengthen tabular in‑context learning for structural generalization.
By Jinmo Lee, Dooho Lee, Minho Jeong, Jaemin Yoo
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
The paper introduces a benchmark to evaluate compositional generalisation in machine learning interatomic potentials. It comprises four tasks that test models on unseen molecules, designed so that learning underlying chemical principles should enable generalisation. Experiments show that current state‑of‑the‑art models struggle, with out‑of‑distribution errors often an order of magnitude higher than in‑distribution errors, even for foundation models pre‑trained on millions of molecules.
By Amir Masoud Nourollah, Irtaza Khalid, Stefano Leoni, Steven Schockaert
BOOM is a new benchmark for evaluating out‑of‑distribution (OOD) molecular property predictions in machine learning. It provides chemically‑informed tests across common property prediction tasks and assesses over 150 model‑task combinations. The study shows that current models, including chemical foundation models, struggle to generalize OOD, with the best model still exhibiting three times higher error than in‑distribution predictions.
By Evan R. Antoniuk, Shehtab Zaman, Tal Ben-Nun, Peggy Li, James Diffenderfer, Busra Sahin, Obadiah Smolenski, Everett Grethel, Tim Hsu, Anna M. Hiszpanski, Kenneth Chiu, Bhavya Kailkhura, Brian Van Essen
Monroe is a new molecular foundation model that improves upon existing models by pre‑training on over 81 million molecules from the PM6 quantum chemistry dataset, enhancing stereochemistry representation, and introducing novel training losses such as conformer denoising and embedding decorrelation. It also incorporates a prior‑data‑fitted model (TabPFN) for downstream in‑context prediction and demonstrates superior performance on Polaris benchmarks and activity cliff tests. Ablation studies show that the PFN‑based downstream approach can upgrade other models, producing state‑of‑the‑art variants MiniMol_PFN and CheMeleon_PFN.
By Blazej Banaszewski, Andrew W. Fitzgibbon