A real-world graph has a complex topological structure, which is often formed by the interaction of different latent factors. However, most existing methods lack consideration of the intrinsic differences in relations between nodes caused by factor entanglement. In this paper, we propose an \underline{\textbf{A}}dversarial \underline{\textbf{D}}isentangled \underline{\textbf{G}}raph \underline{\textbf{C}}onvolutional \underline{\textbf{N}}etwork (ADGCN) for disentangled graph representation learning. To begin with, we point out two aspects of graph disentanglement that need to be considered, i.e., micro-disentanglement and macro-disentanglement. For them, a component-specific aggregation approach is proposed to achieve micro-disentanglement by inferring latent components that cause the links between nodes. On the basis of micro-disentanglement, we further propose a macro-disentanglement adversarial regularizer to improve the separability among component distributions, thus restricting the interdependence among components. Additionally, to reveal the topological graph structure, a diversity-preserving node sampling approach is proposed, by which the graph structure can be progressively refined in a way of local structure awareness. The experimental results on various real-world graph data verify that our ADGCN obtains more favorable performance over currently available alternatives. The source codes of ADGCN are available at \textit{\url{https://github.com/SsGood/ADGCN}}.
In general, graph representation learning methods assume that the train and test data come from the same distribution. In this work we consider an underexplored area of an otherwise rapidly developing field of graph representation learning: The task of out-of-distribution (OOD) graph classification, where train and test data have different distributions, with test data unavailable during training. Our work shows it is possible to use a causal model to learn approximately invariant representations that better extrapolate between train and test data. Finally, we conclude with synthetic and real-world dataset experiments showcasing the benefits of representations that are invariant to train/test distribution shifts.
Scene understanding is a critical problem in computer vision. In this paper, we propose a 3D point-based scene graph generation ($\mathbf{SGG_{point}}$) framework to effectively bridge perception and reasoning to achieve scene understanding via three sequential stages, namely scene graph construction, reasoning, and inference. Within the reasoning stage, an EDGE-oriented Graph Convolutional Network ($\texttt{EdgeGCN}$) is created to exploit multi-dimensional edge features for explicit relationship modeling, together with the exploration of two associated twinning interaction mechanisms between nodes and edges for the independent evolution of scene graph representations. Overall, our integrated $\mathbf{SGG_{point}}$ framework is established to seek and infer scene structures of interest from both real-world and synthetic 3D point-based scenes. Our experimental results show promising edge-oriented reasoning effects on scene graph generation studies. We also demonstrate our method advantage on several traditional graph representation learning benchmark datasets, including the node-wise classification on citation networks and whole-graph recognition problems for molecular analysis.
Graph neural networks (GNNs) have attracted tremendous attention from the graph learning community in recent years. It has been widely adopted in various real-world applications from diverse domains, such as social networks and biological graphs. The research and applications of graph deep learning present new challenges, including the sparse nature of graph data, complicated training of GNNs, and non-standard evaluation of graph tasks. To tackle the issues, we present CogDL, a comprehensive library for graph deep learning that allows researchers and practitioners to conduct experiments, compare methods, and build applications with ease and efficiency. In CogDL, we propose a unified design for the training and evaluation of GNN models for various graph tasks, making it unique among existing graph learning libraries. By utilizing this unified trainer, CogDL can optimize the GNN training loop with several training techniques, such as mixed precision training. Moreover, we develop efficient sparse operators for CogDL, enabling it to become the most competitive graph library for efficiency. Another important CogDL feature is its focus on ease of use with the aim of facilitating open and reproducible research of graph learning. We leverage CogDL to report and maintain benchmark results on fundamental graph tasks, which can be reproduced and directly used by the community.
As the representations output by Graph Neural Networks (GNNs) are increasingly employed in real-world applications, it becomes important to ensure that these representations are fair and stable. In this work, we establish a key connection between counterfactual fairness and stability and leverage it to propose a novel framework, NIFTY (uNIfying Fairness and stabiliTY), which can be used with any GNN to learn fair and stable representations. We introduce a novel objective function that simultaneously accounts for fairness and stability and develop a layer-wise weight normalization using the Lipschitz constant to enhance neural message passing in GNNs. In doing so, we enforce fairness and stability both in the objective function as well as in the GNN architecture. Further, we show theoretically that our layer-wise weight normalization promotes counterfactual fairness and stability in the resulting representations. We introduce three new graph datasets comprising of high-stakes decisions in criminal justice and financial lending domains. Extensive experimentation with the above datasets demonstrates the efficacy of our framework.
We consider two popular Graph Representation Learning (GRL) methods: message passing for node classification and network embedding for link prediction. For each, we pick a popular model that we: (i) linearize and (ii) and switch its training objective to Frobenius norm error minimization. These simplifications can cast the training into finding the optimal parameters in closed-form. We program in TensorFlow a functional form of Truncated Singular Value Decomposition (SVD), such that, we could decompose a dense matrix $\mathbf{M}$, without explicitly computing $\mathbf{M}$. We achieve competitive performance on popular GRL tasks while providing orders of magnitude speedup. We open-source our code at http://github.com/samihaija/tf-fsvd
This paper describes an end-to-end solution for the relationship prediction task in heterogeneous, multi-relational graphs. We particularly address two building blocks in the pipeline, namely heterogeneous graph representation learning and negative sampling. Existing message passing-based graph neural networks use edges either for graph traversal and/or selection of message encoding functions. Ignoring the edge semantics could have severe repercussions on the quality of embeddings, especially when dealing with two nodes having multiple relations. Furthermore, the expressivity of the learned representation depends on the quality of negative samples used during training. Although existing hard negative sampling techniques can identify challenging negative relationships for optimization, new techniques are required to control false negatives during training as false negatives could corrupt the learning process. To address these issues, first, we propose RelGNN -- a message passing-based heterogeneous graph attention model. In particular, RelGNN generates the states of different relations and leverages them along with the node states to weigh the messages. RelGNN also adopts a self-attention mechanism to balance the importance of attribute features and topological features for generating the final entity embeddings. Second, we introduce a parameter-free negative sampling technique -- adaptive self-adversarial (ASA) negative sampling. ASA reduces the false-negative rate by leveraging positive relationships to effectively guide the identification of true negative samples. Our experimental evaluation demonstrates that RelGNN optimized by ASA for relationship prediction improves state-of-the-art performance across established benchmarks as well as on a real industrial dataset.
Self-supervised learning provides a promising path towards eliminating the need for costly label information in representation learning on graphs. However, to achieve state-of-the-art performance, methods often need large numbers of negative examples and rely on complex augmentations. This can be prohibitively expensive, especially for large graphs. To address these challenges, we introduce Bootstrapped Graph Latents (BGRL) - a graph representation learning method that learns by predicting alternative augmentations of the input. BGRL uses only simple augmentations and alleviates the need for contrasting with negative examples, and is thus scalable by design. BGRL outperforms or matches prior methods on several established benchmarks, while achieving a 2-10x reduction in memory costs. Furthermore, we show that BGRL can be scaled up to extremely large graphs with hundreds of millions of nodes in the semi-supervised regime - achieving state-of-the-art performance and improving over supervised baselines where representations are shaped only through label information. In particular, our solution centered on BGRL constituted one of the winning entries to the Open Graph Benchmark - Large Scale Challenge at KDD Cup 2021, on a graph orders of magnitudes larger than all previously available benchmarks, thus demonstrating the scalability and effectiveness of our approach.
Missing node attributes is a common problem in real-world graphs. Graph neural networks have been demonstrated power in graph representation learning while their performance is affected by the completeness of graph information. Most of them are not specified for missing-attribute graphs and fail to leverage incomplete attribute information effectively. In this paper, we propose an innovative node representation learning framework, Wasserstein Graph Neural Network (WGNN), to mitigate the problem. To make the most of limited observed attribute information and capture the uncertainty caused by missing values, we express nodes as low-dimensional distributions derived from the decomposition of the attribute matrix. Furthermore, we strengthen the expressiveness of representations by developing a novel message passing schema that aggregates distributional information from neighbors in the Wasserstein space. We test WGNN in node classification tasks under two missing-attribute cases on both synthetic and real-world datasets. In addition, we find WGNN suitable to recover missing values and adapt them to tackle matrix completion problems with graphs of users and items. Experimental results on both tasks demonstrate the superiority of our method.
Graph Representation Learning (GRL) methods have impacted fields from chemistry to social science. However, their algorithmic implementations are specialized to specific use-cases e.g.message passing methods are run differently from node embedding ones. Despite their apparent differences, all these methods utilize the graph structure, and therefore, their learning can be approximated with stochastic graph traversals. We propose Graph Traversal via Tensor Functionals(GTTF), a unifying meta-algorithm framework for easing the implementation of diverse graph algorithms and enabling transparent and efficient scaling to large graphs. GTTF is founded upon a data structure (stored as a sparse tensor) and a stochastic graph traversal algorithm (described using tensor operations). The algorithm is a functional that accept two functions, and can be specialized to obtain a variety of GRL models and objectives, simply by changing those two functions. We show for a wide class of methods, our algorithm learns in an unbiased fashion and, in expectation, approximates the learning as if the specialized implementations were run directly. With these capabilities, we scale otherwise non-scalable methods to set state-of-the-art on large graph datasets while being more efficient than existing GRL libraries - with only a handful of lines of code for each method specialization. GTTF and its various GRL implementations are on: https://github.com/isi-usc-edu/gttf.
Graph contrastive learning algorithms have demonstrated remarkable success in various applications such as node classification, link prediction, and graph clustering. However, in unsupervised graph contrastive learning, some contrastive pairs may contradict the truths in downstream tasks and thus the decrease of losses on these pairs undesirably harms the performance in the downstream tasks. To assess the discrepancy between the prediction and the ground-truth in the downstream tasks for these contrastive pairs, we adapt the expected calibration error (ECE) to graph contrastive learning. The analysis of ECE motivates us to propose a novel regularization method, Contrast-Reg, to ensure that decreasing the contrastive loss leads to better performance in the downstream tasks. As a plug-in regularizer, Contrast-Reg effectively improves the performance of existing graph contrastive learning algorithms. We provide both theoretical and empirical results to demonstrate the effectiveness of Contrast-Reg in enhancing the generalizability of the Graph Neural Network(GNN) model and improving the performance of graph contrastive algorithms with different similarity definitions and encoder backbones across various downstream tasks.
Prior highly-tuned image parsing models are usually studied in a certain domain with a specific set of semantic labels and can hardly be adapted into other scenarios (e.g., sharing discrepant label granularity) without extensive re-training. Learning a single universal parsing model by unifying label annotations from different domains or at various levels of granularity is a crucial but rarely addressed topic. This poses many fundamental learning challenges, e.g., discovering underlying semantic structures among different label granularity or mining label correlation across relevant tasks. To address these challenges, we propose a graph reasoning and transfer learning framework, named "Graphonomy", which incorporates human knowledge and label taxonomy into the intermediate graph representation learning beyond local convolutions. In particular, Graphonomy learns the global and structured semantic coherency in multiple domains via semantic-aware graph reasoning and transfer, enforcing the mutual benefits of the parsing across domains (e.g., different datasets or co-related tasks). The Graphonomy includes two iterated modules: Intra-Graph Reasoning and Inter-Graph Transfer modules. The former extracts the semantic graph in each domain to improve the feature representation learning by propagating information with the graph; the latter exploits the dependencies among the graphs from different domains for bidirectional knowledge transfer. We apply Graphonomy to two relevant but different image understanding research topics: human parsing and panoptic segmentation, and show Graphonomy can handle both of them well via a standard pipeline against current state-of-the-art approaches. Moreover, some extra benefit of our framework is demonstrated, e.g., generating the human parsing at various levels of granularity by unifying annotations across different datasets.
Deep generative models, since their inception, have become increasingly more capable of generating novel and perceptually realistic signals (e.g., images and sound waves). With the emergence of deep models for graph structured data, natural interests seek extensions of these generative models for graphs. Successful extensions were seen recently in the case of learning from a collection of graphs (e.g., protein data banks), but the learning from a single graph has been largely under explored. The latter case, however, is important in practice. For example, graphs in financial and healthcare systems contain so much confidential information that their public accessibility is nearly impossible, but open science in these fields can only advance when similar data are available for benchmarking. In this work, we propose an approach to generating a doppelganger graph that resembles a given one in many graph properties but nonetheless can hardly be used to reverse engineer the original one, in the sense of a near zero edge overlap. The approach is an orchestration of graph representation learning, generative adversarial networks, and graph realization algorithms. Through comparison with several graph generative models (either parameterized by neural networks or not), we demonstrate that our result barely reproduces the given graph but closely matches its properties. We further show that downstream tasks, such as node classification, on the generated graphs reach similar performance to the use of the original ones.
Graph neural networks (GNNs) are powerful models that have been successful in various graph representation learning tasks. Whereas gradient boosted decision trees (GBDT) often outperform other machine learning methods when faced with heterogeneous tabular data. But what approach should be used for graphs with tabular node features? Previous GNN models have mostly focused on networks with homogeneous sparse features and, as we show, are suboptimal in the heterogeneous setting. In this work, we propose a novel architecture that trains GBDT and GNN jointly to get the best of both worlds: the GBDT model deals with heterogeneous features, while GNN accounts for the graph structure. Our model benefits from end-to-end optimization by allowing new trees to fit the gradient updates of GNN. With an extensive experimental comparison to the leading GBDT and GNN models, we demonstrate a significant increase in performance on a variety of graphs with tabular features. The code is available: https://github.com/nd7141/bgnn.
Graph representation learning has attracted increasing research attention. However, most existing studies fuse all structural features and node attributes to provide an overarching view of graphs, neglecting finer substructures' semantics, and suffering from interpretation enigmas. This paper presents a novel hierarchical subgraph-level selection and embedding based graph neural network for graph classification, namely SUGAR, to learn more discriminative subgraph representations and respond in an explanatory way. SUGAR reconstructs a sketched graph by extracting striking subgraphs as the representative part of the original graph to reveal subgraph-level patterns. To adaptively select striking subgraphs without prior knowledge, we develop a reinforcement pooling mechanism, which improves the generalization ability of the model. To differentiate subgraph representations among graphs, we present a self-supervised mutual information mechanism to encourage subgraph embedding to be mindful of the global graph structural properties by maximizing their mutual information. Extensive experiments on six typical bioinformatics datasets demonstrate a significant and consistent improvement in model quality with competitive performance and interpretability.
Graph representation learning has made major strides over the past decade. However, in many relational domains, the input data are not suited for simple graph representations as the relationships between entities go beyond pairwise interactions. In such cases, the relationships in the data are better represented as hyperedges (set of entities) of a non-uniform hypergraph. While there have been works on principled methods for learning representations of nodes of a hypergraph, these approaches are limited in their applicability to tasks on non-uniform hypergraphs (hyperedges with different cardinalities). In this work, we exploit the incidence structure to develop a hypergraph neural network to learn provably expressive representations of variable sized hyperedges which preserve local-isomorphism in the line graph of the hypergraph, while also being invariant to permutations of its constituent vertices. Specifically, for a given vertex set, we propose frameworks for (1) hyperedge classification and (2) variable sized expansion of partially observed hyperedges which captures the higher order interactions among vertices and hyperedges. We evaluate performance on multiple real-world hypergraph datasets and demonstrate consistent, significant improvement in accuracy, over state-of-the-art models.
Face parsing infers a pixel-wise label to each facial component, which has drawn much attention recently. Previous methods have shown their success in face parsing, which however overlook the correlation among facial components. As a matter of fact, the component-wise relationship is a critical clue in discriminating ambiguous pixels in facial area. To address this issue, we propose adaptive graph representation learning and reasoning over facial components, aiming to learn representative vertices that describe each component, exploit the component-wise relationship and thereby produce accurate parsing results against ambiguity. In particular, we devise an adaptive and differentiable graph abstraction method to represent the components on a graph via pixel-to-vertex projection under the initial condition of a predicted parsing map, where pixel features within a certain facial region are aggregated onto a vertex. Further, we explicitly incorporate the image edge as a prior in the model, which helps to discriminate edge and non-edge pixels during the projection, thus leading to refined parsing results along the edges. Then, our model learns and reasons over the relations among components by propagating information across vertices on the graph. Finally, the refined vertex features are projected back to pixel grids for the prediction of the final parsing map. To train our model, we propose a discriminative loss to penalize small distances between vertices in the feature space, which leads to distinct vertices with strong semantics. Experimental results show the superior performance of the proposed model on multiple face parsing datasets, along with the validation on the human parsing task to demonstrate the generalizability of our model.
Recent work on predicting patient outcomes in the Intensive Care Unit (ICU) has focused heavily on the physiological time series data, largely ignoring sparse data such as diagnoses and medications. When they are included, they are usually concatenated in the late stages of a model, which may struggle to learn from rarer disease patterns. Instead, we propose a strategy to exploit diagnoses as relational information by connecting similar patients in a graph. To this end, we propose LSTM-GNN for patient outcome prediction tasks: a hybrid model combining Long Short-Term Memory networks (LSTMs) for extracting temporal features and Graph Neural Networks (GNNs) for extracting the patient neighbourhood information. We demonstrate that LSTM-GNNs outperform the LSTM-only baseline on length of stay prediction tasks on the eICU database. More generally, our results indicate that exploiting information from neighbouring patient cases using graph neural networks is a promising research direction, yielding tangible returns in supervised learning performance on Electronic Health Records.
In this paper, we study the problem of mobile user profiling, which is a critical component for quantifying users' characteristics in the human mobility modeling pipeline. Human mobility is a sequential decision-making process dependent on the users' dynamic interests. With accurate user profiles, the predictive model can perfectly reproduce users' mobility trajectories. In the reverse direction, once the predictive model can imitate users' mobility patterns, the learned user profiles are also optimal. Such intuition motivates us to propose an imitation-based mobile user profiling framework by exploiting reinforcement learning, in which the agent is trained to precisely imitate users' mobility patterns for optimal user profiles. Specifically, the proposed framework includes two modules: (1) representation module, which produces state combining user profiles and spatio-temporal context in real-time; (2) imitation module, where Deep Q-network (DQN) imitates the user behavior (action) based on the state that is produced by the representation module. However, there are two challenges in running the framework effectively. First, epsilon-greedy strategy in DQN makes use of the exploration-exploitation trade-off by randomly pick actions with the epsilon probability. Such randomness feeds back to the representation module, causing the learned user profiles unstable. To solve the problem, we propose an adversarial training strategy to guarantee the robustness of the representation module. Second, the representation module updates users' profiles in an incremental manner, requiring integrating the temporal effects of user profiles. Inspired by Long-short Term Memory (LSTM), we introduce a gated mechanism to incorporate new and old user characteristics into the user profile.
Many real-world problems are naturally modeled as heterogeneous graphs, where nodes and edges represent multiple types of entities and relations. Existing learning models for heterogeneous graph representation usually depend on the computation of specific and user-defined heterogeneous paths, or in the application of large and often not scalable deep neural network architectures. We propose Het-node2vec, an extension of the node2vec algorithm, designed for embedding heterogeneous graphs. Het-node2vec addresses the challenge of capturing the topological and structural characteristics of graphs and the semantic information underlying the different types of nodes and edges of heterogeneous graphs, by introducing a simple stochastic node and edge type switching strategy in second order random walk processes. The proposed approach also introduces an ''attention mechanism'' to focus the random walks on specific node and edge types, thus allowing more accurate embeddings and more focused predictions on specific node and edge types of interest. Empirical results on benchmark datasets show that Hetnode2vec achieves comparable or superior performance with respect to state-of-the-art methods for heterogeneous graphs in node label and edge prediction tasks.