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Register a new userMolCLR: Molecular Contrastive Learning of Representations via Graph Neural Networks
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Molecular machine learning bears promise for efficient molecule property prediction and drug discovery. However, due to the limited labeled data and the giant chemical space, machine learning models trained via supervised learning perform poorly in generalization. This greatly limits the applications of machine learning methods for molecular design and discovery. In this work, we present MolCLR: Molecular Contrastive Learning of Representations via Graph Neural Networks (GNNs), a self-supervised learning framework for large unlabeled molecule datasets. Specifically, we first build a molecular graph, where each node represents an atom and each edge represents a chemical bond. A GNN is then used to encode the molecule graph. We propose three novel molecule graph augmentations: atom masking, bond deletion, and subgraph removal. A contrastive estimator is utilized to maximize the agreement of different graph augmentations from the same molecule. Experiments show that molecule representations learned by MolCLR can be transferred to multiple downstream molecular property prediction tasks. Our method thus achieves state-of-the-art performance on many challenging datasets. We also prove the efficiency of our proposed molecule graph augmentations on supervised molecular classification tasks.
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Pre-training Graph Neural Networks (GNN) via self-supervised contrastive learning has recently drawn lots of attention. However, most existing works focus on node-level contrastive learning, which cannot capture global graph structure. The key challenge to conducting subgraph-level contrastive learning is to sample informative subgraphs that are semantically meaningful. To solve it, we propose to learn graph motifs, which are frequently-occurring subgraph patterns (e.g. functional groups of molecules), for better subgraph sampling. Our framework MotIf-driven Contrastive leaRning Of Graph representations (MICRO-Graph) can: 1) use GNNs to extract motifs from large graph datasets; 2) leverage learned motifs to sample informative subgraphs for contrastive learning of GNN. We formulate motif learning as a differentiable clustering problem, and adopt EM-clustering to group similar and significant subgraphs into several motifs. Guided by these learned motifs, a sampler is trained to generate more informative subgraphs, and these subgraphs are used to train GNNs through graph-to-subgraph contrastive learning. By pre-training on the ogbg-molhiv dataset with MICRO-Graph, the pre-trained GNN achieves 2.04% ROC-AUC average performance enhancement on various downstream benchmark datasets, which is significantly higher than other state-of-the-art self-supervised learning baselines.
Leveraging domain knowledge including fingerprints and functional groups in molecular representation learning is crucial for chemical property prediction and drug discovery. When modeling the relation between graph structure and molecular properties implicitly, existing works can hardly capture structural or property changes and complex structure, with much smaller atom vocabulary and highly frequent atoms. In this paper, we propose the Contrastive Knowledge-aware GNN (CKGNN) for self-supervised molecular representation learning to fuse domain knowledge into molecular graph representation. We explicitly encode domain knowledge via knowledge-aware molecular encoder under the contrastive learning framework, ensuring that the generated molecular embeddings equipped with chemical domain knowledge to distinguish molecules with similar chemical formula but dissimilar functions. Extensive experiments on 8 public datasets demonstrate the effectiveness of our model with a 6% absolute improvement on average against strong competitors. Ablation study and further investigation also verify the best of both worlds: incorporation of chemical domain knowledge into self-supervised learning.
We apply a temporal edge prediction model for weighted dynamic graphs to predict time-dependent changes in molecular structure. Each molecule is represented as a complete graph in which each atom is a vertex and all vertex pairs are connected by an edge weighted by the Euclidean distance between atom pairs. We ingest a sequence of complete molecular graphs into a dynamic graph neural network (GNN) to predict the graph at the next time step. Our dynamic GNN predicts atom-to-atom distances with a mean absolute error of 0.017 r{A}, which is considered ``chemically accurate for molecular simulations. We also explored the transferability of a trained network to new molecular systems and found that finetuning with less than 10% of the total trajectory provides a mean absolute error of the same order of magnitude as that when training from scratch on the full molecular trajectory.
In recent years, graph neural networks (GNNs) have been widely adopted in the representation learning of graph-structured data and provided state-of-the-art performance in various applications such as link prediction, node classification, and recommendation. Motivated by recent advances of self-supervision for representation learning in natural language processing and computer vision, self-supervised learning has been recently studied to leverage unlabeled graph-structured data. However, employing self-supervision tasks as auxiliary tasks to assist a primary task has been less explored in the literature on graphs. In this paper, we propose a novel self-supervised auxiliary learning framework to effectively learn graph neural networks. Moreover, this work is the first study showing that a meta-path prediction is beneficial as a self-supervised auxiliary task for heterogeneous graphs. Our method is learning to learn a primary task with various auxiliary tasks to improve generalization performance. The proposed method identifies an effective combination of auxiliary tasks and automatically balances them to improve the primary task. Our methods can be applied to any graph neural network in a plug-in manner without manual labeling or additional data. Also, it can be extended to any other auxiliary tasks. Our experiments demonstrate that the proposed method consistently improves the performance of node classification and link prediction.
Graph Neural Networks (GNNs) for prediction tasks like node classification or edge prediction have received increasing attention in recent machine learning from graphically structured data. However, a large quantity of labeled graphs is difficult to obtain, which significantly limits the true success of GNNs. Although active learning has been widely studied for addressing label-sparse issues with other data types like text, images, etc., how to make it effective over graphs is an open question for research. In this paper, we present an investigation on active learning with GNNs for node classification tasks. Specifically, we propose a new method, which uses node feature propagation followed by K-Medoids clustering of the nodes for instance selection in active learning. With a theoretical bound analysis we justify the design choice of our approach. In our experiments on four benchmark datasets, the proposed method outperforms other representative baseline methods consistently and significantly.
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