Property prediction on molecular graphs is an important application of Graph Neural Networks (GNNs).

Property prediction on molecular graphs is an important application of Graph Neural Networks (GNNs). Recently, unlabeled molecular data has become abundant, which facilitates the rapid development of self-supervised learning for GNNs in the chemical domain. In this work, we propose pretraining GNNs at the fragment level, a promising middle ground to overcome the limitations of node-level and graph-level pretraining. Borrowing techniques from recent work on principal subgraph mining, we obtain a compact vocabulary of prevalent fragments from a large pretraining dataset. From the extracted vocabulary, we introduce several fragment-based contrastive and predictive pretraining tasks.

Property prediction on molecular graphs is an important application of Graph Neural Networks (GNNs).

Property prediction on molecular graphs is an important application of Graph Neural Networks (GNNs). Recently, unlabeled molecular data has become abundant, which facilitates the rapid development of self-supervised learning for GNNs in the chemical domain. In this work, we propose pretraining GNNs at the fragment level, a promising middle ground to overcome the limitations of node-level and graph-level pretraining. Borrowing techniques from recent work on principal subgraph mining, we obtain a compact vocabulary of prevalent fragments from a large pretraining dataset. From the extracted vocabulary, we introduce several fragment-based contrastive and predictive pretraining tasks.

Property prediction on molecular graphs is an important application of Graph Neural Networks. Recently, unlabeled molecular data has become abundant, which facilitates the rapid development of self-supervised learning for GNNs in the chemical domain. In this work, we propose pretraining GNNs at the fragment level, a promising middle ground to overcome the limitations of node-level and graph-level pretraining. Borrowing techniques from recent work on principal subgraph mining, we obtain a compact vocabulary of prevalent fragments from a large pretraining dataset. From the extracted vocabulary, we introduce several fragment-based contrastive and predictive pretraining tasks. The contrastive learning task jointly pretrains two different GNNs: one on molecular graphs and the other on fragment graphs, which represents higher-order connectivity within molecules. By enforcing consistency between the fragment embedding and the aggregated embedding of the corresponding atoms from the molecular graphs, we ensure that the embeddings capture structural information at multiple resolutions. The structural information of fragment graphs is further exploited to extract auxiliary labels for graph-level predictive pretraining. We employ both the pretrained molecular-based and fragment-based GNNs for downstream prediction, thus utilizing the fragment information during finetuning. Our graph fragment-based pretraining (GraphFP) advances the performances on 5 out of 8 common molecular benchmarks and improves the performances on long-range biological benchmarks by at least 11.5%. Code is available at: https://github.com/lvkd84/GraphFP.

Graph Neural Networks have emerged as an effective machine learning tool for multi-disciplinary tasks such as pharmaceutical molecule classification and chemical reaction prediction, because they can model non-euclidean relationships between different entities. Particle crushing, as a significant field of civil engineering, describes the breakage of granular materials caused by the breakage of particle fragment bonds under the modeling of numerical simulations, which motivates us to characterize the mechanical behaviors of particle crushing through the connectivity of particle fragments with Graph Neural Networks (GNNs). However, there lacks an open-source large-scale particle crushing dataset for research due to the expensive costs of laboratory tests or numerical simulations. Therefore, we firstly generate a dataset with 45,000 numerical simulations and 900 particle types to facilitate the research progress of machine learning for particle crushing. Secondly, we devise a hybrid framework based on GNNs to predict particle crushing strength in a particle fragment view with the advances of state of the art GNNs. Finally, we compare our hybrid framework against traditional machine learning methods and the plain MLP to verify its effectiveness. The usefulness of different features is further discussed through the gradient attribution explanation w.r.t the predictions. Our data and code are released at https://github.com/doujiang-zheng/GNN-For-Particle-Crushing.