2023/08/01 by Siwoo Lee, Lee, Siwoo, Stefan Heinen +5 · 1 citation
Biochemistry, Genetics and Molecular Biology · Computer Science · Materials Science · #Chemical Physics (physics.chem-ph) #Computational Drug Discovery Methods #FOS: Physical sciences #Machine Learning in Materials Science #Metabolomics and Mass Spectrometry Studies
paper · pdf · doi:10.48550/arxiv.2308.00389
openalex publication_date 2023/08/01 · openalex created_date 2023/08/18 · openalex updated_date 2026/08/03
We present an automated data-collection pipeline involving a convolutional neural network and a large language model to extract user-specified tabular data from peer-reviewed literature. The pipeline is applied to 74 reports published between 1957 and 2014 with experimentally-measured oxidation potentials for 592 organic molecules (-0.75 to 3.58 V). After data curation (solvents, reference electrodes, and missed data points), we trained multiple supervised machine learning models reaching prediction errors similar to experimental uncertainty (∼0.2 V). For experimental measurements of identical molecules reported in multiple studies, we identified the most likely value based on out-of-sample machine learning predictions. Using the trained machine learning models, we then estimated oxidation potentials of ∼132k small organic molecules from the QM9 data set, with predicted values spanning 0.21 to 3.46 V. Analysis of the QM9 predictions in terms of plausible descriptor-property trends suggests that aliphaticity increases the oxidation potential of an organic molecule on average from ∼1.5 V to ∼2 V, while an increase in number of heavy atoms lowers it systematically. The pipeline introduced offers significant reductions in human labor otherwise required for conventional manual data collection of experimental results, and exemplifies how to accelerate scientific research through automation.