Existing Graph Neural Networks (GNNs) follow the message-passing mechanism that conducts information interaction among nodes iteratively. While considerable progress has been made, such node interaction paradigms still have the following limitation. First, the scalability limitation precludes the broad application of GNNs in large-scale industrial settings since the node interaction among rapidly expanding neighbors incurs high computation and memory costs. Second, the over-smoothing problem restricts the discrimination ability of nodes, i.e., node representations of different classes will converge to indistinguishable after repeated node interactions. In this work, we propose a novel hop interaction paradigm to address these limitations simultaneously. The core idea is to convert the interaction target among nodes to pre-processed multi-hop features inside each node. We design a simple yet effective HopGNN framework that can easily utilize existing GNNs to achieve hop interaction. Furthermore, we propose a multi-task learning strategy with a self-supervised learning objective to enhance HopGNN. We conduct extensive experiments on 12 benchmark datasets in a wide range of domains, scales, and smoothness of graphs. Experimental results show that our methods achieve superior performance while maintaining high scalability and efficiency. The code is at https://github.com/JC-202/HopGNN.
Analogical reasoning is the process of discovering and mapping correspondences from a target subject to a base subject. As the most well-known computational method of analogical reasoning, Structure-Mapping Theory (SMT) abstracts both target and base subjects into relational graphs and forms the cognitive process of analogical reasoning by finding a corresponding subgraph (i.e., correspondence) in the target graph that is aligned with the base graph. However, incorporating deep learning for SMT is still under-explored due to several obstacles: 1) the combinatorial complexity of searching for the correspondence in the target graph; 2) the correspondence mining is restricted by various cognitive theory-driven constraints. To address both challenges, we propose a novel framework for Analogical Reasoning (DeepGAR) that identifies the correspondence between source and target domains by assuring cognitive theory-driven constraints. Specifically, we design a geometric constraint embedding space to induce subgraph relation from node embeddings for efficient subgraph search. Furthermore, we develop novel learning and optimization strategies that could end-to-end identify correspondences that are strictly consistent with constraints driven by the cognitive theory. Extensive experiments are conducted on synthetic and real-world datasets to demonstrate the effectiveness of the proposed DeepGAR over existing methods.
We introduce a new benchmark dataset, Placenta, for node classification in an underexplored domain: predicting microanatomical tissue structures from cell graphs in placenta histology whole slide images. This problem is uniquely challenging for graph learning for a few reasons. Cell graphs are large (>1 million nodes per image), node features are varied (64-dimensions of 11 types of cells), class labels are imbalanced (9 classes ranging from 0.21% of the data to 40.0%), and cellular communities cluster into heterogeneously distributed tissues of widely varying sizes (from 11 nodes to 44,671 nodes for a single structure). Here, we release a dataset consisting of two cell graphs from two placenta histology images totalling 2,395,747 nodes, 799,745 of which have ground truth labels. We present inductive benchmark results for 7 scalable models and show how the unique qualities of cell graphs can help drive the development of novel graph neural network architectures.
We introduce pyGSL, a Python library that provides efficient implementations of state-of-the-art graph structure learning models along with diverse datasets to evaluate them on. The implementations are written in GPU-friendly ways, allowing one to scale to much larger network tasks. A common interface is introduced for algorithm unrolling methods, unifying implementations of recent state-of-the-art techniques and allowing new methods to be quickly developed by avoiding the need to rebuild the underlying unrolling infrastructure. Implementations of differentiable graph structure learning models are written in PyTorch, allowing us to leverage the rich software ecosystem that exists e.g., around logging, hyperparameter search, and GPU-communication. This also makes it easy to incorporate these models as components in larger gradient based learning systems where differentiable estimates of graph structure may be useful, e.g. in latent graph learning. Diverse datasets and performance metrics allow consistent comparisons across models in this fast growing field. The full code repository can be found on https://github.com/maxwass/pyGSL.
How can we augment a dynamic graph for improving the performance of dynamic graph neural networks? Graph augmentation has been widely utilized to boost the learning performance of GNN-based models. However, most existing approaches only enhance spatial structure within an input static graph by transforming the graph, and do not consider dynamics caused by time such as temporal locality, i.e., recent edges are more influential than earlier ones, which remains challenging for dynamic graph augmentation. In this work, we propose TiaRa (Time-aware Random Walk Diffusion), a novel diffusion-based method for augmenting a dynamic graph represented as a discrete-time sequence of graph snapshots. For this purpose, we first design a time-aware random walk proximity so that a surfer can walk along the time dimension as well as edges, resulting in spatially and temporally localized scores. We then derive our diffusion matrices based on the time-aware random walk, and show they become enhanced adjacency matrices that both spatial and temporal localities are augmented. Throughout extensive experiments, we demonstrate that TiaRa effectively augments a given dynamic graph, and leads to significant improvements in dynamic GNN models for various graph datasets and tasks.
Heterogeneous trajectory forecasting is critical for intelligent transportation systems, but it is challenging because of the difficulty of modeling the complex interaction relations among the heterogeneous road agents as well as their agent-environment constraints. In this work, we propose a risk and scene graph learning method for trajectory forecasting of heterogeneous road agents, which consists of a Heterogeneous Risk Graph (HRG) and a Hierarchical Scene Graph (HSG) from the aspects of agent category and their movable semantic regions. HRG groups each kind of road agent and calculates their interaction adjacency matrix based on an effective collision risk metric. HSG of the driving scene is modeled by inferring the relationship between road agents and road semantic layout aligned by the road scene grammar. Based on this formulation, we can obtain effective trajectory forecasting in driving situations, and superior performance to other state-of-the-art approaches is demonstrated by exhaustive experiments on the nuScenes, ApolloScape, and Argoverse datasets.
Heterogeneous graph neural network has unleashed great potential on graph representation learning and shown superior performance on downstream tasks such as node classification and clustering. Existing heterogeneous graph learning networks are primarily designed to either rely on pre-defined meta-paths or use attention mechanisms for type-specific attentive message propagation on different nodes/edges, incurring many customization efforts and computational costs. To this end, we design a relation-centered Pooling and Convolution for Heterogeneous Graph learning Network, namely PC-HGN, to enable relation-specific sampling and cross-relation convolutions, from which the structural heterogeneity of the graph can be better encoded into the embedding space through the adaptive training process. We evaluate the performance of the proposed model by comparing with state-of-the-art graph learning models on three different real-world datasets, and the results show that PC-HGN consistently outperforms all the baseline and improves the performance maximumly up by 17.8%.
This paper introduces a novel Framelet Graph approach based on p-Laplacian GNN. The proposed two models, named p-Laplacian undecimated framelet graph convolution (pL-UFG) and generalized p-Laplacian undecimated framelet graph convolution (pL-fUFG) inherit the nature of p-Laplacian with the expressive power of multi-resolution decomposition of graph signals. The empirical study highlights the excellent performance of the pL-UFG and pL-fUFG in different graph learning tasks including node classification and signal denoising.
Graph few-shot learning is of great importance among various graph learning tasks. Under the few-shot scenario, models are often required to conduct classification given limited labeled samples. Existing graph few-shot learning methods typically leverage Graph Neural Networks (GNNs) and perform classification across a series of meta-tasks. Nevertheless, these methods generally rely on the original graph (i.e., the graph that the meta-task is sampled from) to learn node representations. Consequently, the graph structure used in each meta-task is identical. Since the class sets are different across meta-tasks, node representations should be learned in a task-specific manner to promote classification performance. Therefore, to adaptively learn node representations across meta-tasks, we propose a novel framework that learns a task-specific structure for each meta-task. To handle the variety of nodes across meta-tasks, we extract relevant nodes and learn task-specific structures based on node influence and mutual information. In this way, we can learn node representations with the task-specific structure tailored for each meta-task. We further conduct extensive experiments on five node classification datasets under both single- and multiple-graph settings to validate the superiority of our framework over the state-of-the-art baselines. Our code is provided at https://github.com/SongW-SW/GLITTER.
Graphical models and factor analysis are well-established tools in multivariate statistics. While these models can be both linked to structures exhibited by covariance and precision matrices, they are generally not jointly leveraged within graph learning processes. This paper therefore addresses this issue by proposing a flexible algorithmic framework for graph learning under low-rank structural constraints on the covariance matrix. The problem is expressed as penalized maximum likelihood estimation of an elliptical distribution (a generalization of Gaussian graphical models to possibly heavy-tailed distributions), where the covariance matrix is optionally constrained to be structured as low-rank plus diagonal (low-rank factor model). The resolution of this class of problems is then tackled with Riemannian optimization, where we leverage geometries of positive definite matrices and positive semi-definite matrices of fixed rank that are well suited to elliptical models. Numerical experiments on real-world data sets illustrate the effectiveness of the proposed approach.
Graph Neural Networks (GNNs) perform well in community detection and molecule classification. Counterfactual Explanations (CE) provide counter-examples to overcome the transparency limitations of black-box models. Due to the growing attention in graph learning, we focus on the concepts of CE for GNNs. We analysed the SoA to provide a taxonomy, a uniform notation, and the benchmarking datasets and evaluation metrics. We discuss fourteen methods, their evaluation protocols, twenty-two datasets, and nineteen metrics. We integrated the majority of methods into the GRETEL library to conduct an empirical evaluation to understand their strengths and pitfalls. We highlight open challenges and future work.
Message passing neural networks (MPNNs) have become a dominant flavor of graph neural networks (GNNs) in recent years. Yet, MPNNs come with notable limitations; namely, they are at most as powerful as the 1-dimensional Weisfeiler-Leman (1-WL) test in distinguishing graphs in a graph isomorphism testing frame-work. To this end, researchers have drawn inspiration from the k-WL hierarchy to develop more expressive GNNs. However, current k-WL-equivalent GNNs are not practical for even small values of k, as k-WL becomes combinatorially more complex as k grows. At the same time, several works have found great empirical success in graph learning tasks without highly expressive models, implying that chasing expressiveness with a coarse-grained ruler of expressivity like k-WL is often unneeded in practical tasks. To truly understand the expressiveness-complexity tradeoff, one desires a more fine-grained ruler, which can more gradually increase expressiveness. Our work puts forth such a proposal: Namely, we first propose the (k, c)(<=)-SETWL hierarchy with greatly reduced complexity from k-WL, achieved by moving from k-tuples of nodes to sets with <=k nodes defined over <=c connected components in the induced original graph. We show favorable theoretical results for this model in relation to k-WL, and concretize it via (k, c)(<=)-SETGNN, which is as expressive as (k, c)(<=)-SETWL. Our model is practical and progressively-expressive, increasing in power with k and c. We demonstrate effectiveness on several benchmark datasets, achieving several state-of-the-art results with runtime and memory usage applicable to practical graphs. We open source our implementation at https://github.com/LingxiaoShawn/KCSetGNN.
The concept of dimension is essential to grasp the complexity of data. A naive approach to determine the dimension of a dataset is based on the number of attributes. More sophisticated methods derive a notion of intrinsic dimension (ID) that employs more complex feature functions, e.g., distances between data points. Yet, many of these approaches are based on empirical observations, cannot cope with the geometric character of contemporary datasets, and do lack an axiomatic foundation. A different approach was proposed by V. Pestov, who links the intrinsic dimension axiomatically to the mathematical concentration of measure phenomenon. First methods to compute this and related notions for ID were computationally intractable for large-scale real-world datasets. In the present work, we derive a computationally feasible method for determining said axiomatic ID functions. Moreover, we demonstrate how the geometric properties of complex data are accounted for in our modeling. In particular, we propose a principle way to incorporate neighborhood information, as in graph data, into the ID. This allows for new insights into common graph learning procedures, which we illustrate by experiments on the Open Graph Benchmark.
In recent years, graph representation learning has gained significant popularity, which aims to generate node embeddings that capture features of graphs. One of the methods to achieve this is employing a technique called random walks that captures node sequences in a graph and then learns embeddings for each node using a natural language processing technique called Word2Vec. These embeddings are then used for deep learning on graph data for classification tasks, such as link prediction or node classification. Prior work operates on pre-collected temporal graph data and is not designed to handle updates on a graph in real-time. Real world graphs change dynamically and their entire temporal updates are not available upfront. In this paper, we propose an end-to-end graph learning pipeline that performs temporal graph construction, creates low-dimensional node embeddings, and trains multi-layer neural network models in an online setting. The training of the neural network models is identified as the main performance bottleneck as it performs repeated matrix operations on many sequentially connected low-dimensional kernels. We propose to unlock fine-grain parallelism in these low-dimensional kernels to boost performance of model training.
In this paper, we focus on multi-task classification, where related classification tasks share the same label space and are learned simultaneously. In particular, we tackle a new setting, which is more realistic than currently addressed in the literature, where categories shift from training to test data. Hence, individual tasks do not contain complete training data for the categories in the test set. To generalize to such test data, it is crucial for individual tasks to leverage knowledge from related tasks. To this end, we propose learning an association graph to transfer knowledge among tasks for missing classes. We construct the association graph with nodes representing tasks, classes and instances, and encode the relationships among the nodes in the edges to guide their mutual knowledge transfer. By message passing on the association graph, our model enhances the categorical information of each instance, making it more discriminative. To avoid spurious correlations between task and class nodes in the graph, we introduce an assignment entropy maximization that encourages each class node to balance its edge weights. This enables all tasks to fully utilize the categorical information from related tasks. An extensive evaluation on three general benchmarks and a medical dataset for skin lesion classification reveals that our method consistently performs better than representative baselines.
Graph neural network (GNN)-based graph learning has been popular in natural language and programming language processing, particularly in text and source code classification. Typically, GNNs are constructed by incorporating alternating layers which learn transformations of graph node features, along with graph pooling layers that use graph pooling operators (e.g., Max-pooling) to effectively reduce the number of nodes while preserving the semantic information of the graph. Recently, to enhance GNNs in graph learning tasks, Manifold-Mixup, a data augmentation technique that produces synthetic graph data by linearly mixing a pair of graph data and their labels, has been widely adopted. However, the performance of Manifold-Mixup can be highly affected by graph pooling operators, and there have not been many studies that are dedicated to uncovering such affection. To bridge this gap, we take an early step to explore how graph pooling operators affect the performance of Mixup-based graph learning. To that end, we conduct a comprehensive empirical study by applying Manifold-Mixup to a formal characterization of graph pooling based on 11 graph pooling operations (9 hybrid pooling operators, 2 non-hybrid pooling operators). The experimental results on both natural language datasets (Gossipcop, Politifact) and programming language datasets (JAVA250, Python800) demonstrate that hybrid pooling operators are more effective for Manifold-Mixup than the standard Max-pooling and the state-of-the-art graph multiset transformer (GMT) pooling, in terms of producing more accurate and robust GNN models.
Graph Neural Networks (GNNs) have recently been applied to graph learning tasks and achieved state-of-the-art (SOTA) results. However, many competitive methods run GNNs multiple times with subgraph extraction and customized labeling to capture information that is hard for normal GNNs to learn. Such operations are time-consuming and do not scale to large graphs. In this paper, we propose an efficient GNN framework called Geodesic GNN (GDGNN) that requires only one GNN run and injects conditional relationships between nodes into the model without labeling. This strategy effectively reduces the runtime of subgraph methods. Specifically, we view the shortest paths between two nodes as the spatial graph context of the neighborhood around them. The GNN embeddings of nodes on the shortest paths are used to generate geodesic representations. Conditioned on the geodesic representations, GDGNN can generate node, link, and graph representations that carry much richer structural information than plain GNNs. We theoretically prove that GDGNN is more powerful than plain GNNs. We present experimental results to show that GDGNN achieves highly competitive performance with SOTA GNN models on various graph learning tasks while taking significantly less time.
Leveraging artificial intelligence for automatic retrosynthesis speeds up organic pathway planning in digital laboratories. However, existing deep learning approaches are unexplainable, like "black box" with few insights, notably limiting their applications in real retrosynthesis scenarios. Here, we propose MechRetro, a chemical-mechanism-driven graph learning framework for interpretable retrosynthetic prediction and pathway planning, which learns several retrosynthetic actions to simulate a reverse reaction via elaborate self-adaptive joint learning. By integrating chemical knowledge as prior information, we design a novel Graph Transformer architecture to adaptively learn discriminative and chemically meaningful molecule representations, highlighting the strong capacity in molecule feature representation learning. We demonstrate that MechRetro outperforms the state-of-the-art approaches for retrosynthetic prediction with a large margin on large-scale benchmark datasets. Extending MechRetro to the multi-step retrosynthesis analysis, we identify efficient synthetic routes via an interpretable reasoning mechanism, leading to a better understanding in the realm of knowledgeable synthetic chemists. We also showcase that MechRetro discovers a novel pathway for protokylol, along with energy scores for uncertainty assessment, broadening the applicability for practical scenarios. Overall, we expect MechRetro to provide meaningful insights for high-throughput automated organic synthesis in drug discovery.
Recently there has been increasing interest in developing and deploying deep graph learning algorithms for many tasks, such as fraud detection and recommender systems. Albeit, there is a limited number of publicly available graph-structured datasets, most of which are tiny compared to production-sized applications or are limited in their application domain. This work tackles this shortcoming by proposing a scalable synthetic graph generation tool to scale the datasets to production-size graphs with trillions of edges and billions of nodes. The tool learns a series of parametric models from proprietary datasets that can be released to researchers to study various graph methods on the synthetic data increasing prototype development and novel applications. We demonstrate the generalizability of the framework across a series of datasets, mimicking structural and feature distributions as well as the ability to scale them across varying sizes demonstrating their usefulness for benchmarking and model development. Code can be found on https://github.com/NVIDIA/DeepLearningExamples/tree/master/Tools/DGLPyTorch/SyntheticGraphGeneration.
We present Gradient Gating (G$^2$), a novel framework for improving the performance of Graph Neural Networks (GNNs). Our framework is based on gating the output of GNN layers with a mechanism for multi-rate flow of message passing information across nodes of the underlying graph. Local gradients are harnessed to further modulate message passing updates. Our framework flexibly allows one to use any basic GNN layer as a wrapper around which the multi-rate gradient gating mechanism is built. We rigorously prove that G$^2$ alleviates the oversmoothing problem and allows the design of deep GNNs. Empirical results are presented to demonstrate that the proposed framework achieves state-of-the-art performance on a variety of graph learning tasks, including on large-scale heterophilic graphs.