Clemence Corminboeuf

Puck van Gerwen, Ksenia R. Briling, Charlotte Bunne et al.

Geometric deep learning models, which incorporate the relevant molecular symmetries within the neural network architecture, have considerably improved the accuracy and data efficiency of predictions of molecular properties. Building on this success, we introduce 3DReact, a geometric deep learning model to predict reaction properties from three-dimensional structures of reactants and products. We demonstrate that the invariant version of the model is sufficient for existing reaction datasets. We illustrate its competitive performance on the prediction of activation barriers on the GDB7-22-TS, Cyclo-23-TS and Proparg-21-TS datasets in different atom-mapping regimes. We show that, compared to existing models for reaction property prediction, 3DReact offers a flexible framework that exploits atom-mapping information, if available, as well as geometries of reactants and products (in an invariant or equivariant fashion). Accordingly, it performs systematically well across different datasets, atom-mapping regimes, as well as both interpolation and extrapolation tasks.

Matthieu Haeberle, Puck van Gerwen, Ruben Laplaza et al.

Integer linear programming (ILP) is an elegant approach to solve linear optimization problems, naturally described using integer decision variables. Within the context of physics-inspired machine learning applied to chemistry, we demonstrate the relevance of an ILP formulation to select molecular training sets for predictions of size-extensive properties. We show that our algorithm outperforms existing unsupervised training set selection approaches, especially when predicting properties of molecules larger than those present in the training set. We argue that the reason for the improved performance is due to the selection that is based on the notion of local similarity (i.e., per-atom) and a unique ILP approach that finds optimal solutions efficiently. Altogether, this work provides a practical algorithm to improve the performance of physics-inspired machine learning models and offers insights into the conceptual differences with existing training set selection approaches.