MoleculeMiner: Extracting and Linking Molecule Figures with Tabular Metadata

Dey, Abhisek; Stanley, Nathaniel H.

doi:10.24963/ijcai.2025/1257

MoleculeMiner: Extracting and Linking Molecule Figures with Tabular Metadata

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Proceedings of the Thirty-Fourth International Joint Conference on Artificial Intelligence. Demo Track. Pages 11034-11038.

https://doi.org/10.24963/ijcai.2025/1257

Keywords

Computer Vision: CV: Recognition (object detection, categorization)
Knowledge Representation and Reasoning: KRR: Applications
Multidisciplinary Topics and Applications: MTA: Bioinformatics
Computer Vision: CV: Structural and model-based approaches, knowledge representation and reasoning

Abstract

Despite an ongoing shift in automated chemical literature search methods, many are fairly limited in ability to find very specific relevant information about a drawn molecule and its associated property data. We aim to tackle the challenge of converting drawn molecules to a machine readable representation and co-reference any associated molecule data. MoleculeMiner is a system where a user can feed in their own patent or paper to obtain each drawn molecule along with any specific metadata (chemical name, chemical reactivity, yield, purity etc.) provided anywhere in the PDF in a tabular format, using an interactive user-friendly environment. We also present MolScribeV2, a molecular image parser which improved upon the original MolScribe by introducing pixel-based self attention positional embedding technique. Along with other changes, MolScribeV2 is robust to varied styles of compound drawings commonly found in patents and papers--scanned or born digital. Our extraction and user interactive system can be found at https://github.com/insitro/MoleculeMiner.

Abhisek Dey, and Nathaniel H. Stanley. 2025. MoleculeMiner: Extracting and Linking Molecule Figures with Tabular Metadata. In Proceedings of the Thirty-Fourth International Joint Conference on Artificial Intelligence, IJCAI-25. IJCAI, 11034–11038. https://doi.org/10.24963/ijcai.2025/1257

@inproceedings{ijcai2025p1257,
  title     = {MoleculeMiner: Extracting and Linking Molecule Figures with Tabular Metadata},
  author    = {Dey, Abhisek and Stanley, Nathaniel H.},
  booktitle = {Proceedings of the Thirty-Fourth International Joint Conference on
               Artificial Intelligence, {IJCAI-25}},
  publisher = {International Joint Conferences on Artificial Intelligence Organization},
  editor    = {James Kwok},
  pages     = {11034--11038},
  year      = {2025},
  month     = {8},
  note      = {Demo Track},
  doi       = {10.24963/ijcai.2025/1257},
  url       = {https://doi.org/10.24963/ijcai.2025/1257},
}

TY  - CPAPER
TI  - MoleculeMiner: Extracting and Linking Molecule Figures with Tabular Metadata
AU  - Dey, Abhisek
AU  - Stanley, Nathaniel H.
T2  - Proceedings of the Thirty-Fourth International Joint Conference on Artificial Intelligence, IJCAI-25
PB  - International Joint Conferences on Artificial Intelligence Organization
PY  - 2025
SP  - 11034
EP  - 11038
DO  - 10.24963/ijcai.2025/1257
UR  - https://doi.org/10.24963/ijcai.2025/1257
ER  -