Recent advances in molecular large language models have led to strong performance on molecular understanding and generation tasks, yet these gains often come without reliable structural grounding. In particular, existing approaches conflict with the chemistry principle that structure determines function: despite their downstream success, current molecular LLMs perform poorly on basic structure recognition, suggesting that they fail to capture molecular graphs from canonical SMILES. To remedy this, we propose MolBasic, a structure-first framework that strengthens structural comprehension via SMILES-Graph translation. MolBasic is built around a multi-level structure perception benchmark, where bidirectional SMILES-Graph conversion serves as the core task to align sequential and topological representations. On top of this foundation, we employ a progressive learning scheme with a standardized Chain-of-Thought (CoT) to steer models from structure acquisition toward higher-level molecular reasoning. Experiments show that MolBasic substantially improves structural understanding and yields robust gains on downstream tasks, including property prediction and objective optimization, supporting our structure-first paradigm.
Scientific reasoning is an increasingly important capability of large language models, yet improving the robustness and efficiency of training such reasoning remains a key open challenge. We study this problem in instruction-based molecular optimization, where answer-only supervi…
Effective molecular representation learning is crucial for accurate molecular property prediction. Recently, numerous self-supervised learning (SSL) approaches leveraging 3D GNNs have been developed to capture comprehensive 3D structural information for drug discovery. However, e…
Protein language models are standard priors for biological sequence generation, but steering them toward explicit distributional design targets remains largely unexplored. We study a constrained protein generation problem in which sequences must match a desired amino-acid (AA) co…
Using molecular large language models (LLMs) as a unified framework for understanding molecular structures and functions is emerging as a new trend in tasks such as molecular design and drug discovery. However, these models struggle to fully capture the visual representation of m…
Small language models (SLMs) have shown promise for zero-shot molecular property prediction from SMILES strings, yet they often suffer from structural blindness because sequence representations under-specify key graph-topological cues. We propose a modular Context-Augmented Promp…
Accurate prediction of ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) is important for drug discovery. Most predictors use undirected molecular graphs and pairwise edges. This choice misses asymmetric interactions, nonreversible dynamics, and motif level ef…