# MolGround: A Benchmark for Molecular Grounding

arXiv: https://arxiv.org/abs/2503.23668 · HTML: https://mlsanity.com/paper/2503.23668/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 12 of its 46 references that are in the map.
- First posted on arXiv 31 Mar 2025.

## Builds on (most cited first, 12 of 12)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [A Comprehensive Survey on Graph Neural Networks](https://mlsanity.com/paper/1901.00596/) (2019)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [An Introduction to Convolutional Neural Networks](https://mlsanity.com/paper/1511.08458/) (2015)
- [TransVG: End-to-End Visual Grounding with Transformers](https://mlsanity.com/paper/2104.08541/) (2021)
- [ChemRL-GEM: Geometry Enhanced Molecular Representation Learning for Property Prediction](https://mlsanity.com/paper/2106.06130/) (2021)
- [Learning to Plan Chemical Syntheses](https://mlsanity.com/paper/1708.04202/) (2017)
- [BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuning](https://mlsanity.com/paper/2402.17810/) (2024)
- [MoleculeQA: A Dataset to Evaluate Factual Accuracy in Molecular Comprehension](https://mlsanity.com/paper/2403.08192/) (2024)
- [L+M-24: Building a Dataset for Language + Molecules @ ACL 2024](https://mlsanity.com/paper/2403.00791/) (2024)
- [Referencing Where to Focus: Improving VisualGrounding with Referential Query](https://mlsanity.com/paper/2412.19155/) (2024)
- [Do Large Language Models Advocate for Inferentialism?](https://mlsanity.com/paper/2412.14501/) (2024)

## Built on by (most cited first, 1 of 1)

- [Breaking Bad Molecules: Are MLLMs Ready for Structure-Level Molecular Detoxification?](https://mlsanity.com/paper/2506.10912/) (2025)

## Abstract (arXiv)

Current molecular understanding approaches predominantly focus on the descriptive aspect of human perception, providing broad, topic-level insights. However, the referential aspect -- linking molecular concepts to specific structural components -- remains largely unexplored. To address this gap, we propose a molecular grounding benchmark designed to evaluate a model's referential abilities. We align molecular grounding with established conventions in NLP, cheminformatics, and molecular science, showcasing the potential of NLP techniques to advance molecular understanding within the AI for Science movement. Furthermore, we constructed the largest molecular understanding benchmark to date, comprising 117k QA pairs, and developed a multi-agent grounding prototype as proof of concept. This system outperforms existing models, including GPT-4o, and its grounding outputs have been integrated to enhance traditional tasks such as molecular captioning and ATC (Anatomical, Therapeutic, Chemical) classification.