The paper introduces MECo, a framework that translates molecular editing intentions into executable code, bridging the gap between reasoning and execution in drug discovery. MECo generates human‑interpretable editing intentions from a molecule and design objective, then converts those intentions into precise structural edits. The method achieves over 98% accuracy on realistic edits and improves downstream benchmark consistency by 38–86 percentage points, outperforming SMILES‑based baselines while maintaining structural similarity.
arXiv:2610.18438v1 Announce Type: cross Abstract: Molecular fragments provide chemically meaningful units, but existing molecular languages rarely make their locations and connections explicit for ed...
arXiv:2606. 03057v1 Announce Type: cross Abstract: Large language models (LLMs) are increasingly used for molecular tasks, but it remains unclear which molecular representation to use.
R-GroundBench is a new diagnostic benchmark for evaluating AI models on R‑group grounding in Markush molecular editing, derived from real pharmaceutical patents. It includes a Multiple‑Choice VQA track with varying difficulty and modality splits, as well as an open‑ended Generation track. Experiments show a large performance gap: models score over 90% on easy VQA but drop to 56–66% on hard VQA, and generation exact match stays below 20% (and under 8% with visual input).
arXiv:2506. 10912v4 Announce Type: replace Abstract: Toxicity remains a leading cause of early-stage drug development failure.
arXiv:2610.20459v1 Announce Type: new Abstract: Chemical chain-of-thought can contain hallucinated structural and property claims. We thereby introduce MolLean, a process-verifiable language that gro...
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.
The study evaluates four pretrained molecular language models on six virtual libraries covering drug discovery, organic materials, and catalysis. It finds that native embeddings vary widely in performance, while molecular fingerprints remain consistently strong. Fine‑tuning the models on library‑specific data markedly improves sample efficiency, with several adapted encoders outperforming others across all tasks.
M3OS is a multi‑agent large‑language‑model system that separates molecular‑design reasoning from optimization‑state management using a Monte Carlo graph search. The system maintains a persistent graph of evaluated candidates, transformations, and evidence, while LLM agents use role‑specific contexts to generate and edit molecules with tool‑driven and knowledge‑guided approaches. Across three benchmarks, M3OS outperforms baselines, demonstrating the benefit of persistent search state, specialized agents, and controlled execution for multi‑constraint molecular optimization.
arXiv:2606. 03660v1 Announce Type: new Abstract: Large language models are increasingly used as chemistry assistants, yet most chemistry benchmarks still score only final answers.
arXiv:2602.00663v3 Announce Type: replace Abstract: Optimizing molecules to achieve desired properties is a central bottleneck across the chemical sciences, particularly in the pharmaceutical industr...
MolSC is a new dataset of 181,000 substituent-level examples that captures how attaching specific substituents to molecular scaffolds changes properties such as bioactivity and physicochemical descriptors. The authors also provide MolSC-Bench, a held‑out benchmark of 1,541 examples that are disjoint from MolSC at scaffold, substituent, and molecule levels. Experiments show that training molecular large language models on MolSC markedly improves their ability to predict substituent contributions, outperforming existing models on a range of downstream chemistry tasks.
arXiv:2602. 02320v4 Announce Type: replace-cross Abstract: Molecular function is largely determined by structure.