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1. Stochastic Iterative Graph Matching

   Liu, Linfeng ; Hughs, Mike ; Hassoun, Soha ; Liu, Li-Ping ( July 2021 , International Conference on Machine Learning)

   null (Ed.)

   Recent works apply Graph Neural Networks (GNNs) to graph matching tasks and show promising results. Considering that model outputs are complex matchings, we devise several techniques to improve the learning of GNNs and obtain a new model, Stochastic Iterative Graph MAtching (SIGMA). Our model predicts a distribution of matchings, instead of a single matching, for a graph pair so the model can explore several probable matchings. We further introduce a novel multi-step matching procedure, which learns how to refine a graph pair’s matching results incrementally. The model also includes dummy nodes so that the model does not have to find matchings for nodes without correspondence. We fit this model to data via scalable stochastic optimization. We conduct extensive experiments across synthetic graph datasets as well as biochemistry and computer vision applications. Across all tasks, our results show that SIGMA can produce significantly improved graph matching results compared to state-of-the-art models. Ablation studies verify that each of our components (stochastic training, iterative matching, and dummy nodes) offers noticeable improvement. 

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2. (Optimal) Online Bipartite Matching with Degree Information

   Aamand, Anders ; Chen, Justin Y ; Indyk, Piotr ( January 2022 , Conference on Neural Information Processing Systems)

   We propose a model for online graph problems where algorithms are given access to an oracle that predicts (e.g., based on modeling assumptions or on past data) the degrees of nodes in the graph. Within this model, we study the classic problem of online bipartite matching, and a natural greedy matching algorithm called MinPredictedDegree, which uses predictions of the degrees of offline nodes. For the bipartite version of a stochastic graph model due to Chung, Lu, and Vu where the expected values of the offline degrees are known and used as predictions, we show that MinPredictedDegree stochastically dominates any other online algorithm, i.e., it is optimal for graphs drawn from this model. Since the “symmetric” version of the model, where all online nodes are identical, is a special case of the well-studied “known i.i.d. model”, it follows that the competitive ratio of MinPredictedDegree on such inputs is at least 0.7299. For the special case of graphs with power law degree distributions, we show that MinPredictedDegree frequently produces matchings almost as large as the true maximum matching on such graphs. We complement these results with an extensive empirical evaluation showing that MinPredictedDegree compares favorably to state-of-the-art online algorithms for online matching. 

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3. Strategies For Pre-training Graph Neural Networks

   Hu, W. ; Liu, B. ; Gomes, J. ; Zitnik, M. ; Liang, P. ; Pande, V. ; Leskovec, J. ( April 2020 , International Conference on Learning Representations (ICLR))

   Many applications of machine learning require a model to make accurate predictions on test examples that are distributionally different from training ones, while task-specific labels are scarce during training. An effective approach to this challenge is to pre-train a model on related tasks where data is abundant, and then fine-tune it on a downstream task of interest. While pre-training has been effective in many language and vision domains, it remains an open question how to effectively use pre-training on graph datasets. In this paper, we develop a new strategy and self-supervised methods for pre-training Graph Neural Networks (GNNs). The key to the success of our strategy is to pre-train an expressive GNN at the level of individual nodes as well as entire graphs so that the GNN can learn useful local and global representations simultaneously. We systematically study pre-training on multiple graph classification datasets. We find that naïve strategies, which pre-train GNNs at the level of either entire graphs or individual nodes, give limited improvement and can even lead to negative transfer on many downstream tasks. In contrast, our strategy avoids negative transfer and improves generalization significantly across downstream tasks, leading up to 9.4% absolute improvements in ROC-AUC over non-pre-trained models and achieving state-of-the-art performance for molecular property prediction and protein function prediction. 

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4. Distance Encoding: Design Provably More Powerful Neural Networks for Graph Representation Learning

   Li, Pan ; Wang, Yanbang ; Wang, Hongwei ; Leskovec, Jure. ( January 2020 , Neural Information Processing Systems (NeurIPS))

   Learning representations of sets of nodes in a graph is crucial for applications ranging from node-role discovery to link prediction and molecule classification. Graph Neural Networks (GNNs) have achieved great success in graph representation learning. However, expressive power of GNNs is limited by the 1-Weisfeiler-Lehman (WL) test and thus GNNs generate identical representations for graph substructures that may in fact be very different. More powerful GNNs, proposed recently by mimicking higher-order-WL tests, only focus on representing entire graphs and they are computationally inefficient as they cannot utilize sparsity of the underlying graph. Here we propose and mathematically analyze a general class of structure related features, termed Distance Encoding (DE). DE assists GNNs in representing any set of nodes, while providing strictly more expressive power than the 1-WL test. DE captures the distance between the node set whose representation is to be learned and each node in the graph. To capture the distance DE can apply various graph-distance measures such as shortest path distance or generalized PageRank scores. We propose two ways for GNNs to use DEs (1) as extra node features, and (2) as controllers of message aggregation in GNNs. Both approaches can utilize the sparse structure of the underlying graph, which leads to computational efficiency and scalability. We also prove that DE can distinguish node sets embedded in almost all regular graphs where traditional GNNs always fail. We evaluate DE on three tasks over six real networks: structural role prediction, link prediction, and triangle prediction. Results show that our models outperform GNNs without DE by up-to 15% in accuracy and AUROC. Furthermore, our models also significantly outperform other state-of-the-art methods especially designed for the above tasks. 

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5. Graph mixup with soft alignments

   Hongyi Ling, Zhimeng Jiang ( July 2023 , ICML2023)

   We study graph data augmentation by mixup, which has been used successfully on images. A key operation of mixup is to compute a convex combination of a pair of inputs. This operation is straightforward for grid-like data, such as images, but challenging for graph data. The key difficulty lies in the fact that different graphs typically have different numbers of nodes, and thus there lacks a node-level correspondence between graphs. In this work, we propose S-Mixup, a simple yet effective mixup method for graph classification by soft alignments. Specifically, given a pair of graphs, we explicitly obtain node-level correspondence via computing a soft assignment matrix to match the nodes between two graphs. Based on the soft assignments, we transform the adjacency and node feature matrices of one graph, so that the transformed graph is aligned with the other graph. In this way, any pair of graphs can be mixed directly to generate an augmented graph. We conduct systematic experiments to show that S-Mixup can improve the performance and generalization of graph neural networks (GNNs) on various graph classification tasks. In addition, we show that S-Mixup can increase the robustness of GNNs against noisy labels. Our code is publicly available as part of the DIG package (https://github.com/divelab/DIG). 

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