ICLR 2023 论文列表

Structural information of phylogenetic tree topologies plays an important role in phylogenetic inference. However, finding appropriate topological structures for specific phylogenetic inference tasks often requires significant design effort and domain expertise. In this paper, we propose a novel structural representation method for phylogenetic inference based on learnable topological features. By combining the raw node features that minimize the Dirichlet energy with modern graph representation learning techniques, our learnable topological features can provide efficient structural information of phylogenetic trees that automatically adapts to different downstream tasks without requiring domain expertise. We demonstrate the effectiveness and efficiency of our method on a simulated data tree probability estimation task and a benchmark of challenging real data variational Bayesian phylogenetic inference problems.

Gaussian processes (GPs) are an attractive class of machine learning models because of their simplicity and flexibility as building blocks of more complex Bayesian models. Meanwhile, graph neural networks (GNNs) emerged recently as a promising class of models for graph-structured data in semi-supervised learning and beyond. Their competitive performance is often attributed to a proper capturing of the graph inductive bias. In this work, we introduce this inductive bias into GPs to improve their predictive performance for graph-structured data. We show that a prominent example of GNNs, the graph convolutional network, is equivalent to some GP when its layers are infinitely wide; and we analyze the kernel universality and the limiting behavior in depth. We further present a programmable procedure to compose covariance kernels inspired by this equivalence and derive example kernels corresponding to several interesting members of the GNN family. We also propose a computationally efficient approximation of the covariance matrix for scalable posterior inference with large-scale data. We demonstrate that these graph-based kernels lead to competitive classification and regression performance, as well as advantages in computation time, compared with the respective GNNs.

Lottery Ticket Hypothesis (LTH) claims the existence of a winning ticket (i.e., a properly pruned sub-network together with original weight initialization) that can achieve competitive performance to the original dense network. A recent work, called UGS, extended LTH to prune graph neural networks (GNNs) for effectively accelerating GNN inference. UGS simultaneously prunes the graph adjacency matrix and the model weights using the same masking mechanism, but since the roles of the graph adjacency matrix and the weight matrices are very different, we find that their sparsifications lead to different performance characteristics. Specifically, we find that the performance of a sparsified GNN degrades significantly when the graph sparsity goes beyond a certain extent. Therefore, we propose two techniques to improve GNN performance when the graph sparsity is high. First, UGS prunes the adjacency matrix using a loss formulation which, however, does not properly involve all elements of the adjacency matrix; in contrast, we add a new auxiliary loss head to better guide the edge pruning by involving the entire adjacency matrix. Second, by regarding unfavorable graph sparsification as adversarial data perturbations, we formulate the pruning process as a min-max optimization problem to gain the robustness of lottery tickets when the graph sparsity is high. We further investigate the question: Can the ``retrainable'' winning ticket of a GNN be also effective for graph transferring learning? We call it the transferable graph lottery ticket (GLT) hypothesis. Extensive experiments were conducted which demonstrate the superiority of our proposed sparsification method over UGS, and which empirically verified our transferable GLT hypothesis.

With the adoption of recent laws ensuring the ``right to be forgotten'', the problem of machine unlearning has become of significant importance. This is particularly the case for graph-structured data, and learning tools specialized for such data, including graph neural networks (GNNs). This work introduces the first known approach for \emph{approximate graph unlearning} with provable theoretical guarantees. The challenges in addressing the problem are two-fold. First, there exist multiple different types of unlearning requests that need to be considered, including node feature, edge and node unlearning. Second, to establish provable performance guarantees, one needs to carefully evaluate the process of feature mixing during propagation. We focus on analyzing Simple Graph Convolutions (SGC) and their generalized PageRank (GPR) extensions, thereby laying the theoretical foundations for unlearning GNNs. Empirical evaluations of six benchmark datasets demonstrate excellent performance/complexity/privacy trade-offs of our approach compared to complete retraining and general methods that do not leverage graph information. For example, unlearning $200$ out of $1208$ training nodes of the Cora dataset only leads to a $0.1\%$ loss in test accuracy, but offers a $4$-fold speed-up compared to complete retraining with a $(\epsilon,\delta)=(1,10^{-4})$ ``privacy cost''. We also exhibit a $12\%$ increase in test accuracy for the same dataset when compared to unlearning methods that do not leverage graph information, with comparable time complexity and the same privacy guarantee.

Graph neural networks (GNNs), as the de-facto model class for representation learning on graphs, are built upon the multi-layer perceptrons (MLP) architecture with additional message passing layers to allow features to flow across nodes. While conventional wisdom commonly attributes the success of GNNs to their advanced expressivity, we conjecture that this is not the main cause of GNNs' superiority in node-level prediction tasks. This paper pinpoints the major source of GNNs' performance gain to their intrinsic generalization capability, by introducing an intermediate model class dubbed as P(ropagational)MLP, which is identical to standard MLP in training, but then adopts GNN's architecture in testing. Intriguingly, we observe that PMLPs consistently perform on par with (or even exceed) their GNN counterparts, while being much more efficient in training. This finding provides a new perspective for understanding the learning behavior of GNNs, and can be used as an analytic tool for dissecting various GNN-related research problems including expressivity, generalization, over-smoothing and heterophily. As an initial step to analyze PMLP, we show its essential difference to MLP at infinite-width limit lies in the NTK feature map in the post-training stage. Moreover, through extrapolation analysis (i.e., generalization under distribution shifts), we find that though most GNNs and their PMLP counterparts cannot extrapolate non-linear functions for extreme out-of-distribution data, they have greater potential to generalize to testing data near the training data support as natural advantages of the GNN architecture used for inference.

Learning to optimize is a rapidly growing area that aims to solve optimization problems or improve existing optimization algorithms using machine learning (ML). In particular, the graph neural network (GNN) is considered a suitable ML model for optimization problems whose variables and constraints are permutation--invariant, for example, the linear program (LP). While the literature has reported encouraging numerical results, this paper establishes the theoretical foundation of applying GNNs to solving LPs. Given any size limit of LPs, we construct a GNN that maps different LPs to different outputs. We show that properly built GNNs can reliably predict feasibility, boundedness, and an optimal solution for each LP in a broad class. Our proofs are based upon the recently--discovered connections between the Weisfeiler--Lehman isomorphism test and the GNN. To validate our results, we train a simple GNN and present its accuracy in mapping LPs to their feasibilities and solutions.

Recurrent neural network (RNN) and self-attention mechanism (SAM) are the de facto methods to extract spatial-temporal information for temporal graph learning. Interestingly, we found that although both RNN and SAM could lead to a good performance, in practice neither of them is always necessary. In this paper, we propose GraphMixer, a conceptually and technically simple architecture that consists of three components: (1) a link-encoder that is only based on multi-layer perceptrons (MLP) to summarize the information from temporal links, (2) a node-encoder that is only based on neighbor mean-pooling to summarize node information, and (3) an MLP-based link classifier that performs link prediction based on the outputs of the encoders. Despite its simplicity, GraphMixer attains an outstanding performance on temporal link prediction benchmarks with faster convergence and better generalization performance. These results motivate us to rethink the importance of simpler model architecture.

This work establishes rigorous, novel and widely applicable stability guarantees and transferability bounds for general graph convolutional networks -- without reference to any underlying limit object or statistical distribution. Crucially, utilized graph-shift operators are not necessarily assumed to be normal, allowing for the treatment of networks on both directed- and undirected graphs within the developed framework. In the undirected setting, stability to node-level perturbations is related to an 'adequate spectral covering' property of the filters in each layer. Stability to edge-level perturbations is discussed and related to properties of the utilized filters such as their Lipschitz constants. Results on stability to vertex-set non-preserving perturbations are obtained by utilizing recently developed mathematical-physics based tools. As an exemplifying application of the developed theory, it is showcased that general graph convolutional networks utilizing the un-normalized graph Laplacian as graph-shift-operator can be rendered stable to collapsing strong edges in the underlying graph if filters are mandated to be constant at infinity. These theoretical results are supported by corresponding numerical investigations showcasing the response of filters and networks to such perturbations.

Graph unlearning, which involves deleting graph elements such as nodes, node labels, and relationships from a trained graph neural network (GNN) model, is crucial for real-world applications where data elements may become irrelevant, inaccurate, or privacy-sensitive. However, existing methods for graph unlearning either deteriorate model weights shared across all nodes or fail to effectively delete edges due to their strong dependence on local graph neighborhoods. To address these limitations, we introduce GNNDelete, a novel model-agnostic layer-wise operator that optimizes two critical properties, namely, Deleted Edge Consistency and Neighborhood Influence, for graph unlearning. Deleted Edge Consistency ensures that the influence of deleted elements is removed from both model weights and neighboring representations, while Neighborhood Influence guarantees that the remaining model knowledge is preserved after deletion. GNNDelete updates representations to delete nodes and edges from the model while retaining the rest of the learned knowledge. We conduct experiments on seven real-world graphs, showing that GNNDelete outperforms existing approaches by up to 38.8% (AUC) on edge, node, and node feature deletion tasks, and 32.2% on distinguishing deleted edges from non-deleted ones. Additionally, GNNDelete is efficient, taking 12.3x less time and 9.3x less space than retraining GNN from scratch on WordNet18.

Existing Graph Neural Networks (GNNs) compute the message exchange between nodes by either aggregating uniformly (convolving) the features of all the neighbor- ing nodes, or by applying a non-uniform score (attending) to the features. Recent works have shown the strengths and weaknesses of the resulting GNN architectures, respectively, GCNs and GATs. In this work, we aim at exploiting the strengths of both approaches to their full extent. To this end, we first introduce the graph convolutional attention layer (CAT), which relies on convolutions to compute the attention scores. Unfortunately, as in the case of GCNs and GATs, we show that there exists no clear winner between the three—neither theoretically nor in practice—as their performance directly depends on the nature of the data (i.e., of the graph and features). This result brings us to the main contribution of our work, the learnable graph convolutional attention network (L-CAT): a GNN architecture that automatically interpolates between GCN, GAT and CAT in each layer, by adding only two scalar parameters. Our results demonstrate that L-CAT is able to efficiently combine different GNN layers along the network, outperforming competing methods in a wide range of datasets, and resulting in a more robust model that reduces the need of cross-validating.

Output reachability and adversarial robustness are among the most relevant safety properties of neural networks. We show that in the context of Message Passing Neural Networks (MPNN), a common Graph Neural Network (GNN) model, formal verification is impossible. In particular, we show that output reachability of graph-classifier MPNN, working over graphs of unbounded size, non-trivial degree and sufficiently expressive node labels, cannot be verified formally: there is no algorithm that answers correctly (with yes or no), given an MPNN, whether there exists some valid input to the MPNN such that the corresponding output satisfies a given specification. However, we also show that output reachability and adversarial robustness of node-classifier MPNN can be verified formally when a limit on the degree of input graphs is given a priori. We discuss the implications of these results, for the purpose of obtaining a complete picture of the principle possibility to formally verify GNN, depending on the expressiveness of the involved GNN models and input-output specifications.

A soft tree is an actively studied variant of a decision tree that updates splitting rules using the gradient method. Although soft trees can take various architectures, their impact is not theoretically well known. In this paper, we formulate and analyze the Neural Tangent Kernel (NTK) induced by soft tree ensembles for arbitrary tree architectures. This kernel leads to the remarkable finding that only the number of leaves at each depth is relevant for the tree architecture in ensemble learning with an infinite number of trees. In other words, if the number of leaves at each depth is fixed, the training behavior in function space and the generalization performance are exactly the same across different tree architectures, even if they are not isomorphic. We also show that the NTK of asymmetric trees like decision lists does not degenerate when they get infinitely deep. This is in contrast to the perfect binary trees, whose NTK is known to degenerate and leads to worse generalization performance for deeper trees.

Strategic classification studies learning in settings where users can modify their features to obtain favorable predictions. Most current works focus on simple classifiers that trigger independent user responses. Here we examine the implications of learning with more elaborate models that break the independence assumption. Motivated by the idea that applications of strategic classification are often social in nature, we focus on graph neural networks, which make use of social relations between users to improve predictions. Using a graph for learning introduces inter-user dependencies in prediction; our key point is that strategic users can exploit these to promote their goals. As we show through analysis and simulation, this can work either against the system---or for it. Based on this, we propose a differentiable framework for strategically-robust learning of graph-based classifiers. Experiments on several real networked datasets demonstrate the utility of our approach.

Serving a GNN model online is challenging --- in many applications when testing nodes are connected to training nodes, one has to propagate information from training nodes to testing nodes to achieve the best performance, and storing the whole training set (including training graph and node features) during inference stage is prohibitive for large-scale problems. In this paper, we study graph compression to reduce the storage requirement for GNN in serving. Given a GNN model to be served, we propose to construct a compressed graph with a smaller number of nodes. In serving time, one just needs to replace the original training set graph by this compressed graph, without the need of changing the actual GNN model and the forward pass. We carefully analyze the error in the forward pass and derive simple ways to construct the compressed graph to minimize the approximation error. Experimental results on semi-supervised node classification demonstrate that the proposed method can significantly reduce the serving space requirement for GNN inference.

Training graph neural networks (GNNs) on large graphs is complex and extremely time consuming. This is attributed to overheads caused by sparse matrix multiplication, which are sidestepped when training multi-layer perceptrons (MLPs) with only node features. MLPs, by ignoring graph context, are simple and faster for graph data, however they usually sacrifice prediction accuracy, limiting their applications for graph data. We observe that for most message passing-based GNNs, we can trivially derive an analog MLP (we call this a PeerMLP) with an equivalent weight space, by setting the trainable parameters with the same shapes, making us curious about how do GNNs using weights from a fully trained PeerMLP perform? Surprisingly, we find that GNNs initialized with such weights significantly outperform their PeerMLPs, motivating us to use PeerMLP training as a precursor, initialization step to GNN training. To this end, we propose an embarrassingly simple, yet hugely effective initialization method for GNN training acceleration, called \mlpinit. Our extensive experiments on multiple large-scale graph datasets with diverse GNN architectures validate that MLPInit can accelerate the training of GNNs (up to 33× speedup on OGB-Products) and often improve prediction performance (e.g., up to $7.97\%$ improvement for GraphSAGE across $7$ datasets for node classification, and up to $17.81\%$ improvement across $4$ datasets for link prediction on metric Hits@10). The code is available at https://github.com/snap-research/MLPInit-for-GNNs.

Graph Convolutional Networks (GCNs) are one of the most popular architectures that are used to solve classification problems accompanied by graphical information. We present a rigorous theoretical understanding of the effects of graph convolutions in multi-layer networks. We study these effects through the node classification problem of a non-linearly separable Gaussian mixture model coupled with a stochastic block model. First, we show that a single graph convolution expands the regime of the distance between the means where multi-layer networks can classify the data by a factor of at least $1/\sqrt[4]{\rm deg}$, where ${\rm deg}$ denotes the expected degree of a node. Second, we show that with a slightly stronger graph density, two graph convolutions improve this factor to at least $1/\sqrt[4]{n}$, where $n$ is the number of nodes in the graph. Finally, we provide both theoretical and empirical insights into the performance of graph convolutions placed in different combinations among the layers of a neural network, concluding that the performance is mutually similar for all combinations of the placement. We present extensive experiments on both synthetic and real-world data that illustrate our results.

Transfer learning on graphs drawn from varied distributions (domains) is in great demand across many applications. Emerging methods attempt to learn domain-invariant representations using graph neural networks (GNNs), yet the empirical performances vary and the theoretical foundation is limited. This paper aims at designing theory-grounded algorithms for graph domain adaptation (GDA). (i) As the first attempt, we derive a model-based GDA bound closely related to two GNN spectral properties: spectral smoothness (SS) and maximum frequency response (MFR). This is achieved by cross-pollinating between the OT-based (optimal transport) DA and graph filter theories. (ii) Inspired by the theoretical results, we propose algorithms regularizing spectral properties of SS and MFR to improve GNN transferability. We further extend the GDA theory into the more challenging scenario of conditional shift, where spectral regularization still applies. (iii) More importantly, our analyses of the theory reveal which regularization would improve performance of what transfer learning scenario, (iv) with numerical agreement with extensive real-world experiments: SS and MFR regularizations bring more benefits to the scenarios of node transfer and link transfer, respectively. In a nutshell, our study paves the way toward explicitly constructing and training GNNs that can capture more transferable representations across graph domains. Codes are released at https://github.com/Shen-Lab/GDA-SpecReg.

The electronic design automation of analog circuits has been a longstanding challenge in the integrated circuit field due to the huge design space and complex design trade-offs among circuit specifications. In the past decades, intensive research efforts have only been paid to automate the transistor sizing with a given circuit topology. By recognizing the graph nature of circuits, this paper presents a Circuit Graph Neural Network (CktGNN) that simultaneously automates the circuit topology generation and device sizing based on the encoder-dependent optimization subroutines. Particularly, CktGNN encodes circuit graphs using a two-level GNN framework (of nested GNN) where circuits are represented as combinations of subgraphs in a known subgraph basis. In this way, it significantly improves efficiency by reducing the number of subgraphs to perform message passing. Nonetheless, another critical roadblock to advancing learning-assisted circuit design automation is a lack of public benchmarks to perform canonical assessment and reproducible research. To tackle the challenge, we introduce Open Circuit Benchmark (OCB), an open-sourced dataset that contains $10$K distinct operational amplifiers with carefully-extracted circuit specifications from physical implementations. OCB also equips with communicative circuit generation and evaluation capabilities such that it can be used to generalize the applicability of CktGNN to design various analog circuits by efficiently producing corresponding datasets. Experiments on OCB show the extraordinary advantages of CktGNN through representation-based optimization frameworks over other recent powerful GNN baselines and manual design from human experts. Our work paves the way toward a learning-based open-sourced design automation flow for analog circuits.

Graph neural networks (GNNs) for temporal graphs have recently attracted increasing attentions, where a common assumption is that the class set for nodes is closed. However, in real-world scenarios, it often faces the open set problem with the dynamically increased class set as the time passes by. This will bring two big challenges to the existing dynamic GNN methods: (i) How to dynamically propagate appropriate information in an open temporal graph, where new class nodes are often linked to old class nodes. This case will lead to a sharp contradiction. This is because typical GNNs are prone to make the embeddings of connected nodes become similar, while we expect the embeddings of these two interactive nodes to be distinguishable since they belong to different classes. (ii) How to avoid catastrophic knowledge forgetting over old classes when learning new classes occurred in temporal graphs. In this paper, we propose a general and principled learning approach for open temporal graphs, called OTGNet, with the goal of addressing the above two challenges. We assume the knowledge of a node can be disentangled into class-relevant and class-agnostic one, and thus explore a new message passing mechanism by extending the information bottleneck principle to only propagate class-agnostic knowledge between nodes of different classes, avoiding aggregating conflictive information. Moreover, we devise a strategy to select both important and diverse triad sub-graph structures for effective class-incremental learning. Extensive experiments on three real-world datasets of different domains demonstrate the superiority of our method, compared to the baselines.