Abstract—Materials Genomics initiative has the goal of rapidly synthesizing materials with a given set of desired properties using data science techniques. An important step in this direction is the ability to predict the outcomes of complex chemical reactions. Some graph-based feature learning algorithms have been proposed recently. However, the comprehensive relationship between atoms or structures is not learned properly and not explainable, and multiple graphs cannot be handled. In this paper, chemical reaction processes are formulated as translation processes. Both atoms and edges are mapped to vectors represent- ing the structural information. We employ the graph convolution layers to learn meaningful information of atom graphs, and further employ its variations, message passing networks (MPNN) and edge attention graph convolution network (EAGCN) to learn edge representations. Particularly, multi-view EAGCN groups and maps edges to a set of representations for the properties of the chemical bond between atoms from multiple views. Each bond is viewed from its atom type, bond type, distance and neighbor environment. The final node and edge representations are mapped to a sequence defined by the SMILES of the molecule and then fed to a decoder model with attention. To make full usage of multi-view information, we propose multi-view attention model to handle self correlation inside each atom or edge, and mutual correlation between edges and atoms, both of which are important in chemical reaction processes. We have evaluated our method on the standard benchmark datasets (that have been used by all the prior works), and the results show that edge embedding with multi-view attention achieves superior accuracy compared to existing techniques.
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ABM: Attention-based Message Passing Network for Knowledge Graph Completion
Knowledge graph is ubiquitous and plays an important role in many real-world applications, including recommender systems, question answering, fact-checking, and so on. However, most of the knowledge graphs are incomplete which can hamper their practical usage. Fortunately, knowledge graph completion (KGC) can mitigate this problem by inferring missing edges in the knowledge graph according to the existing information. In this paper, we propose a novel KGC method named ABM (Attention-Based Message passing) which focuses on predicting the relation between any two entities in a knowledge graph. The proposed ABM consists of three integral parts, including (1) context embedding, (2) structure embedding, and (3) path embedding. In the context embedding, the proposed ABM generalizes the existing message passing neural network to update the node embedding and the edge embedding to assimilate the knowledge of nodes' neighbors, which captures the relative role information of the edge that we want to predict. In the structure embedding, the proposed method overcomes the shortcomings of the existing GNN method (i.e., most methods ignore the structural similarity between nodes.) by assigning different attention weights to different nodes while doing the aggregation. Path embedding generates paths between any two entities and treats these paths as sequences. Then, the sequence can be used as the input of the Transformer to update the embedding of the knowledge graph to gather the global role of the missing edges. By utilizing these three mutually complementary strategies, the proposed ABM is able to capture both the local and global information which in turn leads to a superb performance. Experiment results show that ABM outperforms baseline methods on a wide range of datasets.
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- NSF-PAR ID:
- 10428931
- Date Published:
- Journal Name:
- 2022 IEEE International Conference on Big Data (Big Data)
- Page Range / eLocation ID:
- 339 to 348
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Knowledge graphs are graph-based data models which can represent real-time data that is constantly growing with the addition of new information. The question-answering systems over knowledge graphs (KGQA) retrieve answers to a natural language question from the knowledge graph. Most existing KGQA systems use static knowledge bases for offline training. After deployment, they fail to learn from unseen new entities added to the graph. There is a need for dynamic algorithms which can adapt to the evolving graphs and give interpretable results. In this research work, we propose using new auction algorithms for question answering over knowledge graphs. These algorithms can adapt to changing environments in real-time, making them suitable for offline and online training. An auction algorithm computes paths connecting an origin node to one or more destination nodes in a directed graph and uses node prices to guide the search for the path. The prices are initially assigned arbitrarily and updated dynamically based on defined rules. The algorithm navigates the graph from the high-price to the low-price nodes. When new nodes and edges are dynamically added or removed in an evolving knowledge graph, the algorithm can adapt by reusing the prices of existing nodes and assigning arbitrary prices to the new nodes. For subsequent related searches, the “learned” prices provide the means to “transfer knowledge” and act as a “guide”: to steer it toward the lower-priced nodes. Our approach reduces the search computational effort by 60% in our experiments, thus making the algorithm computationally efficient. The resulting path given by the algorithm can be mapped to the attributes of entities and relations in knowledge graphs to provide an explainable answer to the query. We discuss some applications for which our method can be used.
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Message passing neural networks have shown a lot of success on graph-structured data. However, there are many instances where message passing can lead to over-smoothing or fail when neighboring nodes belong to different classes. In this work, we introduce a simple yet general framework for improving learning in message passing neural networks. Our approach essentially upsamples edges in the original graph by adding “slow nodes” at each edge that can mediate com- munication between a source and a target node. Our method only modifies the input graph, making it plug-and-play and easy to use with existing models. To understand the benefits of slowing down message passing, we provide theoretical and empirical analyses. We report results on several supervised and self-supervised benchmarks, and show improvements across the board, notably in heterophilic conditions where adjacent nodes are more likely to have different labels. Finally, we show how our approach can be used to generate augmentations for self-supervised learning, where slow nodes are randomly introduced into different edges in the graph to generate multi-scale views with variable path lengths.more » « less
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null (Ed.)Logical queries constitute an important subset of questions posed in knowledge graph question answering systems. Yet, effectively answering logical queries on large knowledge graphs remains a highly challenging problem. Traditional subgraph matching based methods might suffer from the noise and incompleteness of the underlying knowledge graph, often with a prolonged online response time. Recently, an alternative type of method has emerged whose key idea is to embed knowledge graph entities and the query in an embedding space so that the embedding of answer entities is close to that of the query. Compared with subgraph matching based methods, it can better handle the noisy or missing information in knowledge graph, with a faster online response. Promising as it might be, several fundamental limitations still exist, including the linear transformation assumption for modeling relations and the inability to answer complex queries with multiple variable nodes. In this paper, we propose an embedding based method (NewLook) to address these limitations. Our proposed method offers three major advantages. First (Applicability), it supports four types of logical operations and can answer queries with multiple variable nodes. Second (Effectiveness), the proposed NewLook goes beyond the linear transformation assumption, and thus consistently outperforms the existing methods. Third (Efficiency), compared with subgraph matching based methods, NewLook is at least 3 times faster in answering the queries; compared with the existing embed-ding based methods, NewLook bears a comparable or even faster online response and offline training time.more » « less
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Label Propagation Algorithm (LPA) and Graph Convolutional Neural Networks (GCN) are both message passing algorithms on graphs. Both solve the task of node classification, but LPA propagates node label information across the edges of the graph, while GCN propagates and transforms node feature information. However, while conceptually similar, theoretical relationship between LPA and GCN has not yet been systematically investigated. Moreover, it is unclear how LPA and GCN can be combined under a unified framework to improve the performance. Here we study the relationship between LPA and GCN in terms of feature/label influence , in which we characterize how much the initial feature/label of one node influences the final feature/label of another node in GCN/LPA. Based on our theoretical analysis, we propose an end-to-end model that combines GCN and LPA. In our unified model, edge weights are learnable, and the LPA serves as regularization to assist the GCN in learning proper edge weights that lead to improved performance. Our model can also be seen as learning the weights of edges based on node labels, which is more direct and efficient than existing feature-based attention models or topology-based diffusion models. In a number of experiments for semi-supervised node classification and knowledge-graph-aware recommendation, our model shows superiority over state-of-the-art baselines.more » « less
- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Conference Paper:
- https://doi.org/10.1109/BigData55660.2022.10021003
