Novel machine learning insights into the QM7b and QM9 quantum mechanics datasets

• Published in: Journal of computational chemistry Vol. 45; no. 15; pp. 1193 - 1214
• Main Authors: Valdés, Julio J, Tchagang, Alain B
• Format: Journal Article
• Language: English
• Published: United States Wiley Subscription Services, Inc 05-06-2024
• Subjects: Atomic properties; Chemical composition; Chemical compounds; Chemical elements; Chemical properties; Clustering; Data analysis; Datasets; Inverse design; Machine learning; Molecular structure; Organic chemistry; Outliers (statistics); Quantum mechanics; Quantum physics; outlier analysis; feature generation; molecular composition prediction; intrinsic dimensionality; AutoML; feature selection; manifold extraction
• ISSN: 0192-8651; 1096-987X
• DOI: 10.1002/jcc.27295

This paper (i) explores the internal structure of two quantum mechanics datasets (QM7b, QM9), composed of several thousands of organic molecules and described in terms of electronic properties, and (ii) further explores an inverse design approach to molecular design consisting of using machine learning methods to approximate the atomic composition of molecules, using QM9 data. Understanding the structure and characteristics of this kind of data is important when predicting the atomic composition from physical-chemical properties in inverse molecular designs. Intrinsic dimension analysis, clustering, and outlier detection methods were used in the study. They revealed that for both datasets the intrinsic dimensionality is several times smaller than the descriptive dimensions. The QM7b data is composed of well-defined clusters related to atomic composition. The QM9 data consists of an outer region predominantly composed of outliers, and an inner, core region that concentrates clustered inliner objects. A significant relationship exists between the number of atoms in the molecule and its outlier/inliner nature. The spatial structure exhibits a relationship with molecular weight. Despite the structural differences between the two datasets, the predictability of variables of interest for inverse molecular design is high. This is exemplified by models estimating the number of atoms of the molecule from both the original properties and from lower dimensional embedding spaces. In the generative approach the input is given by a set of desired properties of the molecule and the output is an approximation of the atomic composition in terms of its constituent chemical elements. This could serve as the starting region for further search in the huge space determined by the set of possible chemical compounds. The quantum mechanic's dataset QM9 is used in the study, composed of 133,885 small organic molecules and 19 electronic properties. Different multi-target regression approaches were considered for predicting the atomic composition from the properties, including feature engineering techniques in an auto-machine learning framework. High-quality models were found that predict the atomic composition of the molecules from their electronic properties, as well as from a subset of only 52.6% size. Feature selection worked better than feature generation. The results validate the generative approach to inverse molecular design.