arXiv subjects

Shuiwang Ji

Publications and source records attributed to Shuiwang Ji.

At least 91 records · Page 5Linked to original sources

arXiv2023

Automated Data Augmentations for Graph Classification

Data augmentations are effective in improving the invariance of learning machines. We argue that the core challenge of data augmentations lies in designing data transformations that preserve labels. This is relatively straightforward for images, but much more challenging for graphs. In this work, we propose GraphAug, a novel automated data augmentation method aiming at computing label-invariant augmentations for graph classification. Instead of using uniform transformations as in existing studies, GraphAug uses an automated augmentation model to avoid compromising critical label-related information of the graph, thereby producing label-invariant augmentations at most times. To ensure label-invariance, we develop a training method based on reinforcement learning to maximize an estimated label-invariance probability. Experiments show that GraphAug outperforms previous graph augmentation methods on various graph classification tasks.

cs.LG↗

arXiv2023

Gradient-Guided Importance Sampling for Learning Binary Energy-Based Models

Learning energy-based models (EBMs) is known to be difficult especially on discrete data where gradient-based learning strategies cannot be applied directly. Although ratio matching is a sound method to learn discrete EBMs, it suffers from expensive computation and excessive memory requirements, thereby resulting in difficulties in learning EBMs on high-dimensional data. Motivated by these limitations, in this study, we propose ratio matching with gradient-guided importance sampling (RMwGGIS). Particularly, we use the gradient of the energy function w.r.t. the discrete data space to approximately construct the provably optimal proposal distribution, which is subsequently used by importance sampling to efficiently estimate the original ratio matching objective. We perform experiments on density modeling over synthetic discrete data, graph generation, and training Ising models to evaluate our proposed method. The experimental results demonstrate that our method can significantly alleviate the limitations of ratio matching, perform more effectively in practice, and scale to high-dimensional problems. Our implementation is available at https://github.com/divelab/RMwGGIS.

cs.LG↗

arXiv2023

Generalization in Visual Reinforcement Learning with the Reward Sequence Distribution

Generalization in partially observed markov decision processes (POMDPs) is critical for successful applications of visual reinforcement learning (VRL) in real scenarios. A widely used idea is to learn task-relevant representations that encode task-relevant information of common features in POMDPs, i.e., rewards and transition dynamics. As transition dynamics in the latent state space -- which are task-relevant and invariant to visual distractions -- are unknown to the agents, existing methods alternatively use transition dynamics in the observation space to extract task-relevant information in transition dynamics. However, such transition dynamics in the observation space involve task-irrelevant visual distractions, degrading the generalization performance of VRL methods. To tackle this problem, we propose the reward sequence distribution conditioned on the starting observation and the predefined subsequent action sequence (RSD-OA). The appealing features of RSD-OA include that: (1) RSD-OA is invariant to visual distractions, as it is conditioned on the predefined subsequent action sequence without task-irrelevant information from transition dynamics, and (2) the reward sequence captures long-term task-relevant information in both rewards and transition dynamics. Experiments demonstrate that our representation learning approach based on RSD-OA significantly improves the generalization performance on unseen environments, outperforming several state-of-the-arts on DeepMind Control tasks with visual distractions.

cs.LG↗

arXiv2022

Spherical Message Passing for 3D Graph Networks

We consider representation learning of 3D molecular graphs in which each atom is associated with a spatial position in 3D. This is an under-explored area of research, and a principled message passing framework is currently lacking. In this work, we conduct analyses in the spherical coordinate system (SCS) for the complete identification of 3D graph structures. Based on such observations, we propose the spherical message passing (SMP) as a novel and powerful scheme for 3D molecular learning. SMP dramatically reduces training complexity, enabling it to perform efficiently on large-scale molecules. In addition, SMP is capable of distinguishing almost all molecular structures, and the uncovered cases may not exist in practice. Based on meaningful physically-based representations of 3D information, we further propose the SphereNet for 3D molecular learning. Experimental results demonstrate that the use of meaningful 3D information in SphereNet leads to significant performance improvements in prediction tasks. Our results also demonstrate the advantages of SphereNet in terms of capability, efficiency, and scalability. Our code is publicly available as part of the DIG library (https://github.com/divelab/DIG).

cs.LG↗

arXiv2022

ComENet: Towards Complete and Efficient Message Passing for 3D Molecular Graphs

Many real-world data can be modeled as 3D graphs, but learning representations that incorporates 3D information completely and efficiently is challenging. Existing methods either use partial 3D information, or suffer from excessive computational cost. To incorporate 3D information completely and efficiently, we propose a novel message passing scheme that operates within 1-hop neighborhood. Our method guarantees full completeness of 3D information on 3D graphs by achieving global and local completeness. Notably, we propose the important rotation angles to fulfill global completeness. Additionally, we show that our method is orders of magnitude faster than prior methods. We provide rigorous proof of completeness and analysis of time complexity for our methods. As molecules are in essence quantum systems, we build the \underline{com}plete and \underline{e}fficient graph neural network (ComENet) by combing quantum inspired basis functions and the proposed message passing scheme. Experimental results demonstrate the capability and efficiency of ComENet, especially on real-world datasets that are large in both numbers and sizes of graphs. Our code is publicly available as part of the DIG library (\url{https://github.com/divelab/DIG}).

cs.LG↗

arXiv2022

GOOD: A Graph Out-of-Distribution Benchmark

Out-of-distribution (OOD) learning deals with scenarios in which training and test data follow different distributions. Although general OOD problems have been intensively studied in machine learning, graph OOD is only an emerging area of research. Currently, there lacks a systematic benchmark tailored to graph OOD method evaluation. In this work, we aim at developing an OOD benchmark, known as GOOD, for graphs specifically. We explicitly make distinctions between covariate and concept shifts and design data splits that accurately reflect different shifts. We consider both graph and node prediction tasks as there are key differences in designing shifts. Overall, GOOD contains 11 datasets with 17 domain selections. When combined with covariate, concept, and no shifts, we obtain 51 different splits. We provide performance results on 10 commonly used baseline methods with 10 random runs. This results in 510 dataset-model combinations in total. Our results show significant performance gaps between in-distribution and OOD settings. Our results also shed light on different performance trends between covariate and concept shifts by different methods. Our GOOD benchmark is a growing project and expects to expand in both quantity and variety of resources as the area develops. The GOOD benchmark can be accessed via https://github.com/divelab/GOOD/.

cs.LG↗

arXiv2022

Task-Agnostic Graph Explanations

Graph Neural Networks (GNNs) have emerged as powerful tools to encode graph-structured data. Due to their broad applications, there is an increasing need to develop tools to explain how GNNs make decisions given graph-structured data. Existing learning-based GNN explanation approaches are task-specific in training and hence suffer from crucial drawbacks. Specifically, they are incapable of producing explanations for a multitask prediction model with a single explainer. They are also unable to provide explanations in cases where the GNN is trained in a self-supervised manner, and the resulting representations are used in future downstream tasks. To address these limitations, we propose a Task-Agnostic GNN Explainer (TAGE) that is independent of downstream models and trained under self-supervision with no knowledge of downstream tasks. TAGE enables the explanation of GNN embedding models with unseen downstream tasks and allows efficient explanation of multitask models. Our extensive experiments show that TAGE can significantly speed up the explanation efficiency by using the same model to explain predictions for multiple downstream tasks while achieving explanation quality as good as or even better than current state-of-the-art GNN explanation approaches. Our code is pubicly available as part of the DIG library at https://github.com/divelab/DIG/tree/main/dig/xgraph/TAGE/.

cs.LG↗

arXiv2022

Periodic Graph Transformers for Crystal Material Property Prediction

We consider representation learning on periodic graphs encoding crystal materials. Different from regular graphs, periodic graphs consist of a minimum unit cell repeating itself on a regular lattice in 3D space. How to effectively encode these periodic structures poses unique challenges not present in regular graph representation learning. In addition to being E(3) invariant, periodic graph representations need to be periodic invariant. That is, the learned representations should be invariant to shifts of cell boundaries as they are artificially imposed. Furthermore, the periodic repeating patterns need to be captured explicitly as lattices of different sizes and orientations may correspond to different materials. In this work, we propose a transformer architecture, known as Matformer, for periodic graph representation learning. Our Matformer is designed to be invariant to periodicity and can capture repeating patterns explicitly. In particular, Matformer encodes periodic patterns by efficient use of geometric distances between the same atoms in neighboring cells. Experimental results on multiple common benchmark datasets show that our Matformer outperforms baseline methods consistently. In addition, our results demonstrate the importance of periodic invariance and explicit repeating pattern encoding for crystal representation learning.

cs.LG↗

arXiv2022

Self-Supervised Representation Learning via Latent Graph Prediction

Self-supervised learning (SSL) of graph neural networks is emerging as a promising way of leveraging unlabeled data. Currently, most methods are based on contrastive learning adapted from the image domain, which requires view generation and a sufficient number of negative samples. In contrast, existing predictive models do not require negative sampling, but lack theoretical guidance on the design of pretext training tasks. In this work, we propose the LaGraph, a theoretically grounded predictive SSL framework based on latent graph prediction. Learning objectives of LaGraph are derived as self-supervised upper bounds to objectives for predicting unobserved latent graphs. In addition to its improved performance, LaGraph provides explanations for recent successes of predictive models that include invariance-based objectives. We provide theoretical analysis comparing LaGraph to related methods in different domains. Our experimental results demonstrate the superiority of LaGraph in performance and the robustness to decreasing of training sample size on both graph-level and node-level tasks.

cs.LG↗

arXiv2022

Explainability in Graph Neural Networks: A Taxonomic Survey

Deep learning methods are achieving ever-increasing performance on many artificial intelligence tasks. A major limitation of deep models is that they are not amenable to interpretability. This limitation can be circumvented by developing post hoc techniques to explain the predictions, giving rise to the area of explainability. Recently, explainability of deep models on images and texts has achieved significant progress. In the area of graph data, graph neural networks (GNNs) and their explainability are experiencing rapid developments. However, there is neither a unified treatment of GNN explainability methods, nor a standard benchmark and testbed for evaluations. In this survey, we provide a unified and taxonomic view of current GNN explainability methods. Our unified and taxonomic treatments of this subject shed lights on the commonalities and differences of existing methods and set the stage for further methodological developments. To facilitate evaluations, we generate a set of benchmark graph datasets specifically for GNN explainability. We summarize current datasets and metrics for evaluating GNN explainability. Altogether, this work provides a unified methodological treatment of GNN explainability and a standardized testbed for evaluations.

cs.LG↗

arXiv2022

Learning Task-relevant Representations for Generalization via Characteristic Functions of Reward Sequence Distributions

Generalization across different environments with the same tasks is critical for successful applications of visual reinforcement learning (RL) in real scenarios. However, visual distractions -- which are common in real scenes -- from high-dimensional observations can be hurtful to the learned representations in visual RL, thus degrading the performance of generalization. To tackle this problem, we propose a novel approach, namely Characteristic Reward Sequence Prediction (CRESP), to extract the task-relevant information by learning reward sequence distributions (RSDs), as the reward signals are task-relevant in RL and invariant to visual distractions. Specifically, to effectively capture the task-relevant information via RSDs, CRESP introduces an auxiliary task -- that is, predicting the characteristic functions of RSDs -- to learn task-relevant representations, because we can well approximate the high-dimensional distributions by leveraging the corresponding characteristic functions. Experiments demonstrate that CRESP significantly improves the performance of generalization on unseen environments, outperforming several state-of-the-arts on DeepMind Control tasks with different visual distractions.

cs.LG↗

arXiv2022

GraphFM: Improving Large-Scale GNN Training via Feature Momentum

Training of graph neural networks (GNNs) for large-scale node classification is challenging. A key difficulty lies in obtaining accurate hidden node representations while avoiding the neighborhood explosion problem. Here, we propose a new technique, named feature momentum (FM), that uses a momentum step to incorporate historical embeddings when updating feature representations. We develop two specific algorithms, known as GraphFM-IB and GraphFM-OB, that consider in-batch and out-of-batch data, respectively. GraphFM-IB applies FM to in-batch sampled data, while GraphFM-OB applies FM to out-of-batch data that are 1-hop neighborhood of in-batch data. We provide a convergence analysis for GraphFM-IB and some theoretical insight for GraphFM-OB. Empirically, we observe that GraphFM-IB can effectively alleviate the neighborhood explosion problem of existing methods. In addition, GraphFM-OB achieves promising performance on multiple large-scale graph datasets.

cs.LG↗

arXiv2022

Self-Adaptive Label Augmentation for Semi-supervised Few-shot Classification

Few-shot classification aims to learn a model that can generalize well to new tasks when only a few labeled samples are available. To make use of unlabeled data that are more abundantly available in real applications, Ren et al. \shortcite{ren2018meta} propose a semi-supervised few-shot classification method that assigns an appropriate label to each unlabeled sample by a manually defined metric. However, the manually defined metric fails to capture the intrinsic property in data. In this paper, we propose a \textbf{S}elf-\textbf{A}daptive \textbf{L}abel \textbf{A}ugmentation approach, called \textbf{SALA}, for semi-supervised few-shot classification. A major novelty of SALA is the task-adaptive metric, which can learn the metric adaptively for different tasks in an end-to-end fashion. Another appealing feature of SALA is a progressive neighbor selection strategy, which selects unlabeled data with high confidence progressively through the training phase. Experiments demonstrate that SALA outperforms several state-of-the-art methods for semi-supervised few-shot classification on benchmark datasets.

cs.CV↗

arXiv2022

Lattice Convolutional Networks for Learning Ground States of Quantum Many-Body Systems

Deep learning methods have been shown to be effective in representing ground-state wave functions of quantum many-body systems. Existing methods use convolutional neural networks (CNNs) for square lattices due to their image-like structures. For non-square lattices, existing method uses graph neural network (GNN) in which structure information is not precisely captured, thereby requiring additional hand-crafted sublattice encoding. In this work, we propose lattice convolutions in which a set of proposed operations are used to convert non-square lattices into grid-like augmented lattices on which regular convolution can be applied. Based on the proposed lattice convolutions, we design lattice convolutional networks (LCN) that use self-gating and attention mechanisms. Experimental results show that our method achieves performance on par or better than existing methods on spin 1/2 $J_1$-$J_2$ Heisenberg model over the square, honeycomb, triangular, and kagome lattices while without using hand-crafted encoding.

quant-ph↗

arXiv2022

Augmented Equivariant Attention Networks for Microscopy Image Reconstruction

It is time-consuming and expensive to take high-quality or high-resolution electron microscopy (EM) and fluorescence microscopy (FM) images. Taking these images could be even invasive to samples and may damage certain subtleties in the samples after long or intense exposures, often necessary for achieving high-quality or high resolution in the first place. Advances in deep learning enable us to perform image-to-image transformation tasks for various types of microscopy image reconstruction, computationally producing high-quality images from the physically acquired low-quality ones. When training image-to-image transformation models on pairs of experimentally acquired microscopy images, prior models suffer from performance loss due to their inability to capture inter-image dependencies and common features shared among images. Existing methods that take advantage of shared features in image classification tasks cannot be properly applied to image reconstruction tasks because they fail to preserve the equivariance property under spatial permutations, something essential in image-to-image transformation. To address these limitations, we propose the augmented equivariant attention networks (AEANets) with better capability to capture inter-image dependencies, while preserving the equivariance property. The proposed AEANets captures inter-image dependencies and shared features via two augmentations on the attention mechanism, which are the shared references and the batch-aware attention during training. We theoretically derive the equivariance property of the proposed augmented attention model and experimentally demonstrate its consistent superiority in both quantitative and visual results over the baseline methods.

cs.CV↗

arXiv2022

Generating 3D Molecules for Target Protein Binding

A fundamental problem in drug discovery is to design molecules that bind to specific proteins. To tackle this problem using machine learning methods, here we propose a novel and effective framework, known as GraphBP, to generate 3D molecules that bind to given proteins by placing atoms of specific types and locations to the given binding site one by one. In particular, at each step, we first employ a 3D graph neural network to obtain geometry-aware and chemically informative representations from the intermediate contextual information. Such context includes the given binding site and atoms placed in the previous steps. Second, to preserve the desirable equivariance property, we select a local reference atom according to the designed auxiliary classifiers and then construct a local spherical coordinate system. Finally, to place a new atom, we generate its atom type and relative location w.r.t. the constructed local coordinate system via a flow model. We also consider generating the variables of interest sequentially to capture the underlying dependencies among them. Experiments demonstrate that our GraphBP is effective to generate 3D molecules with binding ability to target protein binding sites. Our implementation is available at https://github.com/divelab/GraphBP.

q-bio.BM↗

arXiv2022

Self-Supervised Learning of Graph Neural Networks: A Unified Review

Deep models trained in supervised mode have achieved remarkable success on a variety of tasks. When labeled samples are limited, self-supervised learning (SSL) is emerging as a new paradigm for making use of large amounts of unlabeled samples. SSL has achieved promising performance on natural language and image learning tasks. Recently, there is a trend to extend such success to graph data using graph neural networks (GNNs). In this survey, we provide a unified review of different ways of training GNNs using SSL. Specifically, we categorize SSL methods into contrastive and predictive models. In either category, we provide a unified framework for methods as well as how these methods differ in each component under the framework. Our unified treatment of SSL methods for GNNs sheds light on the similarities and differences of various methods, setting the stage for developing new methods and algorithms. We also summarize different SSL settings and the corresponding datasets used in each setting. To facilitate methodological development and empirical comparison, we develop a standardized testbed for SSL in GNNs, including implementations of common baseline methods, datasets, and evaluation metrics.

cs.LG↗

arXiv2022

Duality-Induced Regularizer for Semantic Matching Knowledge Graph Embeddings

Semantic matching models -- which assume that entities with similar semantics have similar embeddings -- have shown great power in knowledge graph embeddings (KGE). Many existing semantic matching models use inner products in embedding spaces to measure the plausibility of triples and quadruples in static and temporal knowledge graphs. However, vectors that have the same inner products with another vector can still be orthogonal to each other, which implies that entities with similar semantics may have dissimilar embeddings. This property of inner products significantly limits the performance of semantic matching models. To address this challenge, we propose a novel regularizer -- namely, DUality-induced RegulArizer (DURA) -- which effectively encourages the entities with similar semantics to have similar embeddings. The major novelty of DURA is based on the observation that, for an existing semantic matching KGE model (primal), there is often another distance based KGE model (dual) closely associated with it, which can be used as effective constraints for entity embeddings. Experiments demonstrate that DURA consistently and significantly improves the performance of state-of-the-art semantic matching models on both static and temporal knowledge graph benchmarks.

cs.CL↗