MolParser: End-to-end Visual Recognition of Molecule Structures in the Wild

TL;DR

MolParser is an innovative end-to-end system that accurately recognizes complex molecular structures from real-world images, including challenging Markush structures, using a large annotated dataset and curriculum learning.

Contribution

This work introduces MolParser, the largest annotated molecular image dataset and a novel end-to-end recognition method that outperforms existing approaches in real-world scenarios.

Findings

MolParser achieves superior accuracy over classical methods.

The dataset MolParser-7M is publicly available for research.

Active learning effectively incorporates real-world data into training.

Abstract

In recent decades, chemistry publications and patents have increased rapidly. A significant portion of key information is embedded in molecular structure figures, complicating large-scale literature searches and limiting the application of large language models in fields such as biology, chemistry, and pharmaceuticals. The automatic extraction of precise chemical structures is of critical importance. However, the presence of numerous Markush structures in real-world documents, along with variations in molecular image quality, drawing styles, and noise, significantly limits the performance of existing optical chemical structure recognition (OCSR) methods. We present MolParser, a novel end-to-end OCSR method that efficiently and accurately recognizes chemical structures from real-world documents, including difficult Markush structure. We use a extended SMILES encoding rule to annotate our training dataset. Under this rule, we build MolParser-7M, the largest annotated molecular image dataset to our knowledge. While utilizing a large amount of synthetic data, we employed active learning methods to incorporate substantial in-the-wild data, specifically samples cropped from real patents and scientific literature, into the training process. We trained an end-to-end molecular image captioning model, MolParser, using a curriculum learning approach. MolParser significantly outperforms classical and learning-based methods across most scenarios, with potential for broader downstream applications. The dataset is publicly available in huggingface.