# MarkushGlyph and OCSRGlyph: Improved Chemical Structure Recognition

arXiv: https://arxiv.org/abs/2607.28532 · HTML: https://mlsanity.com/paper/2607.28532/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 7 of its 34 references that are in the map.
- First posted on arXiv 30 Jul 2026.

## Builds on (most cited first, 7 of 7)

- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [MolScribe: Robust Molecular Structure Recognition with Image-To-Graph Generation](https://mlsanity.com/paper/2205.14311/) (2022)
- [MolGrapher: Graph-based Visual Recognition of Chemical Structures](https://mlsanity.com/paper/2308.12234/) (2023)
- [MolParser: End-to-end Visual Recognition of Molecule Structures in the Wild](https://mlsanity.com/paper/2411.11098/) (2024)
- [MolNexTR: A Generalized Deep Learning Model for Molecular Image Recognition](https://mlsanity.com/paper/2403.03691/) (2024)
- [MolSight: Optical Chemical Structure Recognition with SMILES Pretraining, Multi-Granularity Learning and Reinforcement Learning](https://mlsanity.com/paper/2511.17300/) (2025)
- [MarkushGrapher-2: End-to-end Multimodal Recognition of Chemical Structures](https://mlsanity.com/paper/2603.28550/) (2026)

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

- [A Pathway to General-Purpose Scientific AI: Multimodal Comprehension of Scientific Images](https://mlsanity.com/paper/2608.14075/) (2026)

## Abstract (arXiv)

Chemical structures appear in patents and the scientific literature as images. For programmatic usage, such as indexing in databases or constructing machine learning model training sets, they must be transformed into line notations. The two common forms of this task are translating an image of a single molecule (optical chemical structure recognition - OCSR) and translating a Markush structure that represents a family of molecules. While prior work in the former case is quite mature, Markush structure parsing remains a challenging task. In this work, we treat both tasks as an image-to-text translation problem. We then propose OCSRGlyph, a state-of-the-art OCSR model, improving performance over prior methods by carefully considering stereochemistry. For the Markush task, we introduce MarkushGlyph, a vision-language model that reads the entire Markush structure as an image. This contrasts with prior systems, which often use multiple stages to separately process visual and text input content. Finally, we introduce a new metric for determining the accuracy of Markush structure translations, handling failure modes present in prior metrics.