2025/04/12 by Zhe Wang, Fangcheng Fu, Wang, Zhe +19
Biochemistry, Genetics and Molecular Biology · Computer Science · #Biomedical Text Mining and Ontologies #Cell Image Analysis Techniques #Computation and Language (cs.CL) #Computational Drug Discovery Methods #FOS: Biological sciences #FOS: Computer and information sciences #Information Retrieval (cs.IR) #Quantitative Methods (q-bio.QM)
paper · pdf · doi:10.48550/arxiv.2504.10525
openalex publication_date 2025/04/12 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/31
The automated extraction of chemical structures and their corresponding bioactivity data is essential for accelerating drug discovery and enabling data-driven research. Current optical chemical structure recognition tools lack the capability to autonomously link molecular structures with their bioactivity profiles, posing a significant bottleneck in structure-activity relationship analysis. To address this, we present BioChemInsight, an open-source pipeline that integrates DECIMER Segmentation with MolNexTR for chemical structure recognition, GLM-4.5V for compound identifier association, and PaddleOCR combined with GLM-4.6 for bioactivity extraction and unit normalization. We evaluated BioChemInsight on 181 patents covering 15 therapeutic targets. The system achieved an average extraction accuracy of above 90% across three key tasks: chemical structure recognition, bioactivity data extraction, and compound identifier association. Our analysis indicates that the chemical space covered by patents is largely complementary to that contained in established public database ChEMBL. Consequently, by enabling systematic patent mining, BioChemInsight provides access to chemical information underrepresented in ChEMBL. This capability expands the landscape of explorable compound-target interactions, enriches the data foundation for quantitative structure-activity relationship modeling and targeted screening, and reduces data preprocessing time from weeks to hours. BioChemInsight is available at https://github.com/dahuilangda/BioChemInsight.