Zeoformer: Coarse-Grained Periodic Graph Transformer for OSDA-Zeolite Affinity Prediction

To date, the International Zeolite Association Structure Commission (IZA-SC) has cataloged merely 255 distinct zeolite structures, with millions of theoretically possible structures yet to be discovered. The synthesis of a specific zeolite typically necessitates the use of an organic structure-directing agent (OSDA), since the selectivity for a particular zeolite is largely determined by the affinity between the OSDA and the zeolite. Therefore, finding the best affinity OSDA-zeolite pair is the key to the synthesis of targeted zeolite. However, OSDA-zeolite pairs frequently exhibit complex geometric structures, i.e., a complex crystal structure formed by a large number of atoms. Although some existing machine learning methods can represent the periodicity of crystals, they cannot accurately represent crystal structures with local variability. To address this issue, we propose a novel approach called Zeoformer, which can effectively represent coarse-grained crystal periodicity and fine-grained local variability. Zeoformer reconstructs the unit cell centered around each atom and encodes the pairwise distances between this central atom and other atoms within the reconstructed unit cell. The introduction of pairwise distances within the reconstructed unit cell more effectively represents the overall structure of the unit cell and the differences between different unit cells, enabling the model to more accurately and efficiently predict the properties of OSDA-zeolite pairs and general crystal structures. Through comprehensive evaluation, our Zeoformer model demonstrates the best performance on OSDA-zeolite pair datasets and two types of crystal material datasets.

Clustering Bioactive Molecules in 3D Chemical Space with Unsupervised Deep Learning

Unsupervised clustering has broad applications in data stratification, pattern investigation and new discovery beyond existing knowledge. In particular, clustering of bioactive molecules facilitates chemical space mapping, structure-activity studies, and drug discovery. These tasks, conventionally conducted by similarity-based methods, are complicated by data complexity and diversity. We ex-plored the superior learning capability of deep autoencoders for unsupervised clustering of 1.39 mil-lion bioactive molecules into band-clusters in a 3-dimensional latent chemical space. These band-clusters, displayed by a space-navigation simulation software, band molecules of selected bioactivity classes into individual band-clusters possessing unique sets of common sub-structural features beyond structural similarity. These sub-structural features form the frameworks of the literature-reported pharmacophores and privileged fragments. Within each band-cluster, molecules are further banded into selected sub-regions with respect to their bioactivity target, sub-structural features and molecular scaffolds. Our method is potentially applicable for big data clustering tasks of different fields.