ICML 2024 Papers

Most real-world networks are noisy and incomplete samples from an unknown target distribution. Refining them by correcting corruptions or inferring unobserved regions typically improves downstream performance. Inspired by the impressive generative capabilities that have been used to correct corruptions in images, and the similarities between "in-painting" and filling in missing nodes and edges conditioned on the observed graph, we propose a novel graph generative framework, SGDM, which is based on subgraph diffusion. Our framework not only improves the scalability and fidelity of graph diffusion models, but also leverages the reverse process to perform novel, conditional generation tasks. In particular, through extensive empirical analysis and a set of novel metrics, we demonstrate that our proposed model effectively supports the following refinement tasks for partially observable networks: (T1) denoising extraneous subgraphs, (T2) expanding existing subgraphs and (T3) performing ``style" transfer by regenerating a particular subgraph to match the characteristics of a different node or subgraph.

Predicting the binding sites of target proteins plays a fundamental role in drug discovery. Most existing deep-learning methods consider a protein as a 3D image by spatially clustering its atoms into voxels and then feed the voxelized protein into a 3D CNN for prediction. However, the CNN-based methods encounter several critical issues: 1) defective in representing irregular protein structures; 2) sensitive to rotations; 3) insufficient to characterize the protein surface; 4) unaware of protein size shift. To address the above issues, this work proposes EquiPocket, an E(3)-equivariant Graph Neural Network (GNN) for binding site prediction, which comprises three modules: the first one to extract local geometric information for each surface atom, the second one to model both the chemical and spatial structure of protein and the last one to capture the geometry of the surface via equivariant message passing over the surface atoms. We further propose a dense attention output layer to alleviate the effect incurred by variable protein size. Extensive experiments on several representative benchmarks demonstrate the superiority of our framework to the state-of-the-art methods.

Relieving the reliance of neural network training on a global back-propagation (BP) has emerged as a notable research topic due to the biological implausibility and huge memory consumption caused by BP. Among the existing solutions, local learning optimizes gradient-isolated modules of a neural network with local errors and has been proved to be effective even on large-scale datasets. However, the reconciliation among local errors has never been investigated. In this paper, we first theoretically study non-greedy layer-wise training and show that the convergence cannot be assured when the local gradient in a module w.r.t. its input is not reconciled with the local gradient in the previous module w.r.t. its output. Inspired by the theoretical result, we further propose a local training strategy that successively regularizes the gradient reconciliation between neighboring modules without breaking gradient isolation or introducing any learnable parameters. Our method can be integrated into both local-BP and BP-free settings. In experiments, we achieve significant performance improvements compared to previous methods. Particularly, our method for CNN and Transformer architectures on ImageNet is able to attain a competitive performance with global BP, saving more than 40% memory consumption.

The Transformer architecture has recently gained considerable attention in the field of graph representation learning, as it naturally overcomes several limitations of Graph Neural Networks (GNNs) with customized attention mechanisms or positional and structural encodings. Despite making some progress, existing works tend to overlook external information of graphs, specifically the correlation between graphs. Intuitively, graphs with similar structures should have similar representations. Therefore, we propose Graph External Attention (GEA) --- a novel attention mechanism that leverages multiple external node/edge key-value units to capture inter-graph correlations implicitly. On this basis, we design an effective architecture called Graph External Attention Enhanced Transformer (GEAET), which integrates local structure and global interaction information for more comprehensive graph representations. Extensive experiments on benchmark datasets demonstrate that GEAET achieves state-of-the-art empirical performance. The source code is available for reproducibility at: https://github.com/icm1018/GEAET.

We investigate the trade-off between the representation power of graph generative models and model *overlap*, i.e., the degree to which the model generates diverse outputs versus regurgitating its training data. In particular, we delineate a nested hierarchy of graph generative models categorized into three levels of complexity: edge independent, node independent, and arbitrarily dependent models. This hierarchy encapsulates a wide range of prevalent methods. We derive theoretical bounds on the number of triangles and other short-length cycles producible by each level of the hierarchy, finding that more complex dependency structure allows an improved trade-off between representation power and overlap. We provide instances demonstrating the asymptotic optimality of our bounds. Furthermore, we introduce new generative models for each of the three hierarchical levels, leveraging dense subgraph discovery. Our evaluation, conducted on real-world datasets, focuses on assessing the output quality and overlap of our proposed models in comparison to other popular models. Our results indicate that our simple, interpretable models provide competitive baselines to popular generative models. Through this investigation, we offer a structured and robust evaluation scheme, thereby facilitating the development of models capable of generating accurate and edge-diverse graphs.

Graph neural networks (GNNs) have exhibited superb power in many graph related tasks. Existing GNNs can be categorized into spatial GNNs and spectral GNNs. The spatial GNNs primarily capture the local information around each node, while the spectral GNNs are able to operate on the frequency signals of the entire graph. However, most, if not all, existing spectral GNNs are faced with two limitations: (1) the polynomial limitation that for most spectral GNNs, the expressive power in the spectral domain is limited to polynomial filters; and (2) the transductive limitation that most spectral GNNs can only be applied to the transductive setting on relatively small-scale graphs. In this paper, we propose a novel spectral graph neural network named SLOG to solve the above two limitations. For the polynomial limitation, SLOG proposes a novel real-valued filter with geometric interpretability, mathematical feasibility and adaptive filtering ability to go beyond polynomial. For the transductive limitation, SLOG combines the subgraph sampling technique in spatial GNNs and the signal processing technique in spectral GNNs together to make itself tailored to the inductive setting on large-scale graphs. Extensive experimental results on 16 datasets demonstrate the superiority of SLOG in inductive homophilic and heterophilic node classification task.

We study the optimal transport (OT) problem for measures supported on a graph metric space. Recently, Le et al. (2022) leverage the graph structure and propose a variant of OT, namely Sobolev transport (ST), which yields a closed-form expression for a fast computation. However, ST is essentially coupled with the $L^p$ geometric structure within its definition which makes it nontrivial to utilize ST for other prior structures. In contrast, the classic OT has the flexibility to adapt to various geometric structures by modifying the underlying cost function. An important instance is the Orlicz-Wasserstein (OW) which moves beyond the $L^p$ structure by leveraging the *Orlicz geometric structure*. Comparing to the usage of standard $p$-order Wasserstein, OW remarkably helps to advance certain machine learning approaches. Nevertheless, OW brings up a new challenge on its computation due to its two-level optimization formulation. In this work, we leverage a specific class of convex functions for Orlicz structure to propose the generalized Sobolev transport (GST). GST encompasses the ST as its special case, and can be utilized for prior structures beyond the $L^p$ geometry. In connection with the OW, we show that one only needs to simply solve a univariate optimization problem to compute the GST, unlike the complex two-level optimization problem in OW. We empirically illustrate that GST is several-order faster than the OW. Moreover, we provide preliminary evidences on the advantages of GST for document classification and for several tasks in topological data analysis.