Tianhao Peng

Tianhao Peng, Xuhong Li, Haitao Yuan et al.

Graph contrastive learning has emerged as a powerful technique for learning graph representations that are robust and discriminative. However, traditional approaches often neglect the critical role of subgraph structures, particularly the intra-subgraph characteristics and inter-subgraph relationships, which are crucial for generating informative and diverse contrastive pairs. These subgraph features are crucial as they vary significantly across different graph types, such as social networks where they represent communities, and biochemical networks where they symbolize molecular interactions. To address this issue, our work proposes a novel subgraph-oriented learnable augmentation method for graph contrastive learning, termed SOLA-GCL, that centers around subgraphs, taking full advantage of the subgraph information for data augmentation. Specifically, SOLA-GCL initially partitions a graph into multiple densely connected subgraphs based on their intrinsic properties. To preserve and enhance the unique characteristics inherent to subgraphs, a graph view generator optimizes augmentation strategies for each subgraph, thereby generating tailored views for graph contrastive learning. This generator uses a combination of intra-subgraph and inter-subgraph augmentation strategies, including node dropping, feature masking, intra-edge perturbation, inter-edge perturbation, and subgraph swapping. Extensive experiments have been conducted on various graph learning applications, ranging from social networks to molecules, under semi-supervised learning, unsupervised learning, and transfer learning settings to demonstrate the superiority of our proposed approach over the state-of-the-art in GCL.

Tianhao Peng, Yuchen Li, Xuhong Li et al.

Recent advancements in computational chemistry have leveraged the power of trans-former-based language models, such as MoLFormer, pre-trained using a vast amount of simplified molecular-input line-entry system (SMILES) sequences, to understand and predict molecular properties and activities, a critical step in fields like drug discovery and materials science. To further improve performance, researchers have introduced graph neural networks with graph-based molecular representations, such as GEM, incorporating the topology, geometry, 2D or even 3D structures of molecules into pre-training. While most of molecular graphs in existing studies were automatically converted from SMILES sequences, it is to assume that transformer-based language models might be able to implicitly learn structure-aware representations from SMILES sequences. In this paper, we propose \ours{} -- a SMILES-based \underline{\em M}olecular \underline{\em L}anguage \underline{\em M}odel, which randomly masking SMILES subsequences corresponding to specific molecular \underline{\em F}unctional \underline{\em G}roups to incorporate structure information of atoms during the pre-training phase. This technique aims to compel the model to better infer molecular structures and properties, thus enhancing its predictive capabilities. Extensive experimental evaluations across 11 benchmark classification and regression tasks in the chemical domain demonstrate the robustness and superiority of \ours{}. Our findings reveal that \ours{} outperforms existing pre-training models, either based on SMILES or graphs, in 9 out of the 11 downstream tasks, ranking as a close second in the remaining ones.