NeurIPS 2024 Papers

Graph-structured data is integral to many applications, prompting the development of various graph representation methods. Graph autoencoders (GAEs), in particular, reconstruct graph structures from node embeddings. Current GAE models primarily utilize self-correlation to represent graph structures and focus on node-level tasks, often overlooking multi-graph scenarios. Our theoretical analysis indicates that self-correlation generally falls short in accurately representing specific graph features such as islands, symmetrical structures, and directional edges, particularly in smaller or multiple graph contexts.To address these limitations, we introduce a cross-correlation mechanism that significantly enhances the GAE representational capabilities. Additionally, we propose the GraphCroc, a new GAE that supports flexible encoder architectures tailored for various downstream tasks and ensures robust structural reconstruction, through a mirrored encoding-decoding process. This model also tackles the challenge of representation bias during optimization by implementing a loss-balancing strategy. Both theoretical analysis and numerical evaluations demonstrate that our methodology significantly outperforms existing self-correlation-based GAEs in graph structure reconstruction.

Adversarial attacks against graph neural networks (GNNs) through perturbations of the graph structure are increasingly common in social network tasks like rumor detection. Social media platforms capture diverse attack sequence samples through both machine and manual screening processes. Investigating effective ways to leverage these adversarial samples to enhance robustness is imperative. We improve the maximum entropy inverse reinforcement learning (IRL) method with the mixture-of-experts approach to address multi-source graph adversarial attacks. This method reconstructs the attack policy, integrating various attack models and providing feature-level explanations, subsequently generating additional adversarial samples to fortify the robustness of detection models. We develop precise sample guidance and a bidirectional update mechanism to reduce the deviation caused by imprecise feature representation and negative sampling within the large action space of social graphs, while also accelerating policy learning. We take rumor detector as an example targeted GNN model on real-world rumor datasets. By utilizing a small subset of samples generated by various graph adversarial attack methods, we reconstruct the attack policy, closely approximating the performance of the original attack method. We validate that samples generated by the learned policy enhance model robustness through adversarial training and data augmentation.

In this paper, we approach an overlooked yet critical task Graph2Image: generating images from multimodal attributed graphs (MMAGs). This task poses significant challenges due to the explosion in graph size, dependencies among graph entities, and the need for controllability in graph conditions. To address these challenges, we propose a graph context-conditioned diffusion model called InstructG2I. InstructG2I first exploits the graph structure and multimodal information to conduct informative neighbor sampling by combining personalized page rank and re-ranking based on vision-language features. Then, a graph QFormer encoder adaptively encodes the graph nodes into an auxiliary set of graph prompts to guide the denoising process of diffusion. Finally, we propose graph classifier-free guidance, enabling controllable generation by varying the strength of graph guidance and multiple connected edges to a node. Extensive experiments conducted on three datasets from different domains demonstrate the effectiveness and controllability of our approach. The code is available at https://github.com/PeterGriffinJin/InstructG2I.

We consider a clustering problem where a learner seeks to partition a finite set by querying a faulty oracle. This models applications where learners crowdsource information from non-expert human workers or conduct noisy experiments to determine group structure. The learner aims to exactly recover a partition by submitting queries of the form ``are $u$ and $v$ in the same group?'' for any pair of elements $u$ and $v$ in the set. Moreover, because the learner only has access to faulty sources of information, they require an error-tolerant algorithm for this task: i.e. they must fully recover the correct partition, even if up to $\ell$ answers are incorrect, for some error-tolerance parameter $\ell$. We study the question: for any given error-tolerance $\ell$, what is the minimum number of queries needed to learn a finite set partition of $n$ elements into $k$ groups? We design algorithms for this task and prove that they achieve optimal query complexity. To analyze our algorithms, we first highlight a connection between this task and correlation clustering. We then use this connection to build a Rényi-Ulam style analytical framework for this problem, which yields matching lower bounds. Our analysis also reveals an inherent asymmetry between the query complexity necessary to be robust against false negative errors as opposed to false positive errors.

Equivariant machine learning is an approach for designing deep learning models that respect the symmetries of the problem, with the aim of reducing model complexity and improving generalization. In this paper, we focus on an extension of shift equivariance, which is the basis of convolution networks on images, to general graphs. Unlike images, graphs do not have a natural notion of domain translation. Therefore, we consider the graph functional shifts as the symmetry group: the unitary operators that commute with the graph shift operator. Notably, such symmetries operate in the signal space rather than directly in the spatial space. We remark that each linear filter layer of a standard spectral graph neural network (GNN) commutes with graph functional shifts, but the activation function breaks this symmetry. Instead, we propose nonlinear spectral filters (NLSFs) that are fully equivariant to graph functional shifts and show that they have universal approximation properties. The proposed NLSFs are based on a new form of spectral domain that is transferable between graphs. We demonstrate the superior performance of NLSFs over existing spectral GNNs in node and graph classification benchmarks.

Federated graph learning (FedGL) is an emerging learning paradigm to collaboratively train graph data from various clients. However, during the development and deployment of FedGL models, they are susceptible to illegal copying and model theft. Backdoor-based watermarking is a well-known method for mitigating these attacks, as it offers ownership verification to the model owner. We take the first step to protect the ownership of FedGL models via backdoor-based watermarking. Existing techniques have challenges in achieving the goal: 1) they either cannot be directly applied or yield unsatisfactory performance; 2) they are vulnerable to watermark removal attacks; and 3) they lack of formal guarantees. To address all the challenges, we propose FedGMark, the first certified robust backdoor-based watermarking for FedGL. FedGMark leverages the unique graph structure and client information in FedGL to learn customized and diverse watermarks. It also designs a novel GL architecture that facilitates defending against both the empirical and theoretically worst-case watermark removal attacks. Extensive experiments validate the promising empirical and provable watermarking performance of FedGMark. Source code is available at: https://github.com/Yuxin104/FedGMark.

Unsupervised Multiplex Graph Learning (UMGL) aims to learn node representations on various edge types without manual labeling. However, existing research overlooks a key factor: the reliability of the graph structure. Real-world data often exhibit a complex nature and contain abundant task-irrelevant noise, severely compromising UMGL's performance. Moreover, existing methods primarily rely on contrastive learning to maximize mutual information across different graphs, limiting them to multiplex graph redundant scenarios and failing to capture view-unique task-relevant information. In this paper, we focus on a more realistic and challenging task: to unsupervisedly learn a fused graph from multiple graphs that preserve sufficient task-relevant information while removing task-irrelevant noise. Specifically, our proposed Information-aware Unsupervised Multiplex Graph Fusion framework (InfoMGF) uses graph structure refinement to eliminate irrelevant noise and simultaneously maximizes view-shared and view-unique task-relevant information, thereby tackling the frontier of non-redundant multiplex graph. Theoretical analyses further guarantee the effectiveness of InfoMGF. Comprehensive experiments against various baselines on different downstream tasks demonstrate its superior performance and robustness. Surprisingly, our unsupervised method even beats the sophisticated supervised approaches. The source code and datasets are available at https://github.com/zxlearningdeep/InfoMGF.

Artificial general intelligence on graphs has shown significant advancements across various applications, yet the traditional `Pre-train \& Fine-tune' paradigm faces inefficiencies and negative transfer issues, particularly in complex and few-shot settings. Graph prompt learning emerges as a promising alternative, leveraging lightweight prompts to manipulate data and fill the task gap by reformulating downstream tasks to the pretext. However, several critical challenges still remain: how to unify diverse graph prompt models, how to evaluate the quality of graph prompts, and to improve their usability for practical comparisons and selection. In response to these challenges, we introduce the first comprehensive benchmark for graph prompt learning. Our benchmark integrates **SIX** pre-training methods and **FIVE** state-of-the-art graph prompt techniques, evaluated across **FIFTEEN** diverse datasets to assess performance, flexibility, and efficiency. We also present 'ProG', an easy-to-use open-source library that streamlines the execution of various graph prompt models, facilitating objective evaluations. Additionally, we propose a unified framework that categorizes existing graph prompt methods into two main approaches: prompts as graphs and prompts as tokens. This framework enhances the applicability and comparison of graph prompt techniques. The code is available at: https://github.com/sheldonresearch/ProG.

In recent years, machine learning has established itself as a powerful tool for high-resolution weather forecasting. While most current machine learning models focus on deterministic forecasts, accurately capturing the uncertainty in the chaotic weather system calls for probabilistic modeling. We propose a probabilistic weather forecasting model called Graph-EFM, combining a flexible latent-variable formulation with the successful graph-based forecasting framework. The use of a hierarchical graph construction allows for efficient sampling of spatially coherent forecasts. Requiring only a single forward pass per time step, Graph-EFM allows for fast generation of arbitrarily large ensembles. We experiment with the model on both global and limited area forecasting. Ensemble forecasts from Graph-EFM achieve equivalent or lower errors than comparable deterministic models, with the added benefit of accurately capturing forecast uncertainty.

Given the damping factor $\alpha$ and precision tolerance $\epsilon$, \citet{andersen2006local} introduced Approximate Personalized PageRank (APPR), the \textit{de facto local method} for approximating the PPR vector, with runtime bounded by $\Theta(1/(\alpha\epsilon))$ independent of the graph size. Recently, Fountoulakis \& Yang asked whether faster local algorithms could be developed using $\tilde{\mathcal{O}}(1/(\sqrt{\alpha}\epsilon))$ operations. By noticing that APPR is a local variant of Gauss-Seidel, this paper explores the question of *whether standard iterative solvers can be effectively localized*. We propose to use the *locally evolving set process*, a novel framework to characterize the algorithm locality, and demonstrate that many standard solvers can be effectively localized. Let $\overline{\operatorname{vol}}{ (\mathcal S_t)}$ and $\overline{\gamma_t}$ be the running average of volume and the residual ratio of active nodes $\textstyle \mathcal{S_t}$ during the process. We show $\overline{\operatorname{vol}}{ (\mathcal S_t)}/\overline{\gamma_t} \leq 1/\epsilon$ and prove APPR admits a new runtime bound $\tilde{\mathcal{O}}(\overline{\operatorname{vol}}(\mathcal S_t)/(\alpha\overline{\gamma_t}))$ mirroring the actual performance. Furthermore, when the geometric mean of residual reduction is $\Theta(\sqrt{\alpha})$, then there exists $c \in (0,2)$ such that the local Chebyshev method has runtime $\tilde{\mathcal{O}}(\overline{\operatorname{vol}}(\mathcal{S_t})/(\sqrt{\alpha}(2-c)))$ without the monotonicity assumption. Numerical results confirm the efficiency of this novel framework and show up to a hundredfold speedup over corresponding standard solvers on real-world graphs.

Fully connected Graph Transformers (GT) have rapidly become prominent in the static graph community as an alternative to Message-Passing models, which suffer from a lack of expressivity, oversquashing, and under-reaching. However, in a dynamic context, by interconnecting all nodes at multiple snapshots with self-attention,GT loose both structural and temporal information. In this work, we introduce Supra-LAplacian encoding for spatio-temporal TransformErs (SLATE), a new spatio-temporal encoding to leverage the GT architecture while keeping spatio-temporal information. Specifically, we transform Discrete Time Dynamic Graphs into multi-layer graphs and take advantage of the spectral properties of their associated supra-Laplacian matrix. Our second contribution explicitly model nodes' pairwise relationships with a cross-attention mechanism, providing an accurate edge representation for dynamic link prediction. SLATE outperforms numerous state-of-the-art methods based on Message-Passing Graph Neural Networks combined with recurrent models (e.g, LSTM), and Dynamic Graph Transformers, on~9 datasets. Code is open-source and available at this link https://github.com/ykrmm/SLATE.

Graph retrieval based on subgraph isomorphism has several real-world applications such as scene graph retrieval, molecular fingerprint detection and circuit design. Roy et al. [35] proposed IsoNet, a late interaction model for subgraph matching, which first computes the node and edge embeddings of each graph independently of paired graph and then computes a trainable alignment map. Here, we present $\texttt{IsoNet++}$, an early interaction graph neural network (GNN), based on several technical innovations. First, we compute embeddings of all nodes by passing messages within and across the two input graphs, guided by an *injective alignment* between their nodes. Second, we update this alignment in a lazy fashion over multiple *rounds*. Within each round, we run a layerwise GNN from scratch, based on the current state of the alignment. After the completion of one round of GNN, we use the last-layer embeddings to update the alignments, and proceed to the next round. Third, $\texttt{IsoNet++}$ incorporates a novel notion of node-pair partner interaction. Traditional early interaction computes attention between a node and its potential partners in the other graph, the attention then controlling messages passed across graphs. We consider *node pairs* (not single nodes) as potential partners. Existence of an edge between the nodes in one graph and non-existence in the other provide vital signals for refining the alignment. Our experiments on several datasets show that the alignments get progressively refined with successive rounds, resulting in significantly better retrieval performance than existing methods. We demonstrate that all three innovations contribute to the enhanced accuracy. Our code and datasets are publicly available at https://github.com/structlearning/isonetpp.

Polynomial-based learnable spectral graph neural networks (GNNs) utilize polynomial to approximate graph convolutions and have achieved impressive performance on graphs. Nevertheless, there are three progressive problems to be solved. Some models use polynomials with better approximation for approximating filters, yet perform worse on real-world graphs. Carefully crafted graph learning methods, sophisticated polynomial approximations, and refined coefficient constraints leaded to overfitting, which diminishes the generalization of the models. How to design a model that retains the ability of polynomial-based spectral GNNs to approximate filters while it possesses higher generalization and performance? In this paper, we propose a spectral GNN with triple filter ensemble (TFE-GNN), which extracts homophily and heterophily from graphs with different levels of homophily adaptively while utilizing the initial features. Specifically, the first and second ensembles are combinations of a set of base low-pass and high-pass filters, respectively, after which the third ensemble combines them with two learnable coefficients and yield a graph convolution (TFE-Conv). Theoretical analysis shows that the approximation ability of TFE-GNN is consistent with that of ChebNet under certain conditions, namely it can learn arbitrary filters. TFE-GNN can be viewed as a reasonable combination of two unfolded and integrated excellent spectral GNNs, which motivates it to perform well. Experiments show that TFE-GNN achieves high generalization and new state-of-the-art performance on various real-world datasets.

Graph Edit Distance (GED) measures the (dis-)similarity between two given graphs in terms of the minimum-cost edit sequence, which transforms one graph to the other. GED is related to other notions of graph similarity, such as graph and subgraph isomorphism, maximum common subgraph, etc. However, the computation of exact GED is NP-Hard, which has recently motivated the design of neural models for GED estimation. However, they do not explicitly account for edit operations with different costs. In response, we propose $\texttt{GraphEdX}$, a neural GED estimator that can work with general costs specified for the four edit operations, viz., edge deletion, edge addition, node deletion, and node addition. We first present GED as a quadratic assignment problem (QAP) that incorporates these four costs. Then, we represent each graph as a set of node and edge embeddings and use them to design a family of neural set divergence surrogates. We replace the QAP terms corresponding to each operation with their surrogates. Computing such neural set divergence requires aligning nodes and edges of the two graphs. We learn these alignments using a Gumbel-Sinkhorn permutation generator, additionally ensuring that the node and edge alignments are consistent with each other. Moreover, these alignments are cognizant of both the presence and absence of edges between node pairs. Through extensive experiments on several datasets, along with a variety of edit cost settings, we show that $\texttt{GraphEdX}$ consistently outperforms state-of-the-art methods and heuristics in terms of prediction error. The code is available at https://github.com/structlearning/GraphEdX.

While tokenized graph Transformers have demonstrated strong performance in node classification tasks, their reliance on a limited subset of nodes with high similarity scores for constructing token sequences overlooks valuable information from other nodes, hindering their ability to fully harness graph information for learning optimal node representations. To address this limitation, we propose a novel graph Transformer called GCFormer. Unlike previous approaches, GCFormer develops a hybrid token generator to create two types of token sequences, positive and negative, to capture diverse graph information. And a tailored Transformer-based backbone is adopted to learn meaningful node representations from these generated token sequences. Additionally, GCFormer introduces contrastive learning to extract valuable information from both positive and negative token sequences, enhancing the quality of learned node representations. Extensive experimental results across various datasets, including homophily and heterophily graphs, demonstrate the superiority of GCFormer in node classification, when compared to representative graph neural networks (GNNs) and graph Transformers.

Survival prediction is a significant challenge in cancer management. Tumor micro-environment is a highly sophisticated ecosystem consisting of cancer cells, immune cells, endothelial cells, fibroblasts, nerves and extracellular matrix. The intratumor heterogeneity and the interaction across multiple tissue types profoundly impacts the prognosis. However, current methods often neglect the fact that the contribution to prognosis differs with tissue types. In this paper, we propose ProtoSurv, a novel heterogeneous graph model for WSI survival prediction. The learning process of ProtoSurv is not only driven by data but also incorporates pathological domain knowledge, including the awareness of tissue heterogeneity, the emphasis on prior knowledge of prognostic-related tissues, and the depiction of spatial interaction across multiple tissues. We validate ProtoSurv across five different cancer types from TCGA (i.e., BRCA, LGG, LUAD, COAD and PAAD), and demonstrate the superiority of our method over the state-of-the-art methods.

We propose Any2graph, a generic framework for end-to-end Supervised Graph Prediction (SGP) i.e. a deep learning model that predicts an entire graph for any kind of input. The framework is built on a novel Optimal Transport loss, the Partially-Masked Fused Gromov-Wasserstein, that exhibits all necessary properties (permutation invariance, differentiability and scalability) and is designed to handle any-sized graphs. Numerical experiments showcase the versatility of the approach that outperform existing competitors on a novel challenging synthetic dataset and a variety of real-world tasks such as map construction from satellite image (Sat2Graph) or molecule prediction from fingerprint (Fingerprint2Graph).

Graph class incremental learning (GCIL) requires the model to classify emerging nodes of new classes while remembering old classes. Existing methods are designed to preserve effective information of old models or graph data to alleviate forgetting, but there is no clear theoretical understanding of what matters in information preservation. In this paper, we consider that present practice suffers from high semantic and structural shifts assessed by two devised shift metrics. We provide insights into information preservation in GCIL and find that maintaining graph information can preserve information of old models in theory to calibrate node semantic and graph structure shifts. We correspond graph information into low-frequency local-global information and high-frequency information in spatial domain. Based on the analysis, we propose a framework, Graph Spatial Information Preservation (GSIP). Specifically, for low-frequency information preservation, the old node representations obtained by inputting replayed nodes into the old model are aligned with the outputs of the node and its neighbors in the new model, and then old and new outputs are globally matched after pooling. For high-frequency information preservation, the new node representations are encouraged to imitate the near-neighbor pair similarity of old node representations. GSIP achieves a 10\% increase in terms of the forgetting metric compared to prior methods on large-scale datasets. Our framework can also seamlessly integrate existing replay designs. The code is available through https://github.com/Jillian555/GSIP.

Interacting systems are prevalent in nature. It is challenging to accurately predict the dynamics of the system if its constituent components are analyzed independently. We develop a graph-based model that unveils the systemic interactions of time series observed at irregular time points, by using a directed acyclic graph to model the conditional dependencies (a form of causal notation) of the system components and learning this graph in tandem with a continuous-time model that parameterizes the solution curves of ordinary differential equations (ODEs). Our technique, a graph neural flow, leads to substantial enhancements over non-graph-based methods, as well as graph-based methods without the modeling of conditional dependencies. We validate our approach on several tasks, including time series classification and forecasting, to demonstrate its efficacy.