# Back to Basics: Improving Molecular Understanding in LLMs via SMILES-Graph Translation

arXiv: https://arxiv.org/abs/2607.03007 · HTML: https://mlsanity.com/paper/2607.03007/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 16 of its 46 references that are in the map.
- First posted on arXiv 3 Jul 2026.

## Builds on (most cited first, 16 of 16)

- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Qwen3 Technical Report](https://mlsanity.com/paper/2505.09388/) (2025)
- [DeepSeek-R1: Incentivizing Reasoning Capability in LLMs via Reinforcement Learning](https://mlsanity.com/paper/2501.12948/) (2025)
- [Qwen2.5-VL Technical Report](https://mlsanity.com/paper/2502.13923/) (2025)
- [Qwen Technical Report](https://mlsanity.com/paper/2309.16609/) (2023)
- [OpenAI o1 System Card](https://mlsanity.com/paper/2412.16720/) (2024)
- [ChatGLM: A Family of Large Language Models from GLM-130B to GLM-4 All Tools](https://mlsanity.com/paper/2406.12793/) (2024)
- [OpenAI GPT-5 System Card](https://mlsanity.com/paper/2601.03267/) (2025)
- [Translation between Molecules and Natural Language](https://mlsanity.com/paper/2204.11817/) (2022)
- [Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for Large Language Models](https://mlsanity.com/paper/2306.08018/) (2023)
- [A Molecular Multimodal Foundation Model Associating Molecule Graphs with Natural Language](https://mlsanity.com/paper/2209.05481/) (2022)
- [ChemLLM: A Chemical Large Language Model](https://mlsanity.com/paper/2402.06852/) (2024)
- [Learning Multimodal Graph-to-Graph Translation for Molecular Optimization](https://mlsanity.com/paper/1812.01070/) (2018)
- [Chemception: A Deep Neural Network with Minimal Chemistry Knowledge Matches the Performance of Expert-developed QSAR/QSPR Models](https://mlsanity.com/paper/1706.06689/) (2017)

## Abstract (arXiv)

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.