arXiv subjects

Da Zheng

Publications and source records attributed to Da Zheng.

At least 55 records · Page 3Linked to original sources

arXiv2023

Train Your Own GNN Teacher: Graph-Aware Distillation on Textual Graphs

How can we learn effective node representations on textual graphs? Graph Neural Networks (GNNs) that use Language Models (LMs) to encode textual information of graphs achieve state-of-the-art performance in many node classification tasks. Yet, combining GNNs with LMs has not been widely explored for practical deployments due to its scalability issues. In this work, we tackle this challenge by developing a Graph-Aware Distillation framework (GRAD) to encode graph structures into an LM for graph-free, fast inference. Different from conventional knowledge distillation, GRAD jointly optimizes a GNN teacher and a graph-free student over the graph's nodes via a shared LM. This encourages the graph-free student to exploit graph information encoded by the GNN teacher while at the same time, enables the GNN teacher to better leverage textual information from unlabeled nodes. As a result, the teacher and the student models learn from each other to improve their overall performance. Experiments in eight node classification benchmarks in both transductive and inductive settings showcase GRAD's superiority over existing distillation approaches for textual graphs.

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arXiv2023

OrthoReg: Improving Graph-regularized MLPs via Orthogonality Regularization

Graph Neural Networks (GNNs) are currently dominating in modeling graph-structure data, while their high reliance on graph structure for inference significantly impedes them from widespread applications. By contrast, Graph-regularized MLPs (GR-MLPs) implicitly inject the graph structure information into model weights, while their performance can hardly match that of GNNs in most tasks. This motivates us to study the causes of the limited performance of GR-MLPs. In this paper, we first demonstrate that node embeddings learned from conventional GR-MLPs suffer from dimensional collapse, a phenomenon in which the largest a few eigenvalues dominate the embedding space, through empirical observations and theoretical analysis. As a result, the expressive power of the learned node representations is constrained. We further propose OrthoReg, a novel GR-MLP model to mitigate the dimensional collapse issue. Through a soft regularization loss on the correlation matrix of node embeddings, OrthoReg explicitly encourages orthogonal node representations and thus can naturally avoid dimensionally collapsed representations. Experiments on traditional transductive semi-supervised classification tasks and inductive node classification for cold-start scenarios demonstrate its effectiveness and superiority.

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arXiv2022

From Local to Global: Spectral-Inspired Graph Neural Networks

Graph Neural Networks (GNNs) are powerful deep learning methods for Non-Euclidean data. Popular GNNs are message-passing algorithms (MPNNs) that aggregate and combine signals in a local graph neighborhood. However, shallow MPNNs tend to miss long-range signals and perform poorly on some heterophilous graphs, while deep MPNNs can suffer from issues like over-smoothing or over-squashing. To mitigate such issues, existing works typically borrow normalization techniques from training neural networks on Euclidean data or modify the graph structures. Yet these approaches are not well-understood theoretically and could increase the overall computational complexity. In this work, we draw inspirations from spectral graph embedding and propose $\texttt{PowerEmbed}$ -- a simple layer-wise normalization technique to boost MPNNs. We show $\texttt{PowerEmbed}$ can provably express the top-$k$ leading eigenvectors of the graph operator, which prevents over-smoothing and is agnostic to the graph topology; meanwhile, it produces a list of representations ranging from local features to global signals, which avoids over-squashing. We apply $\texttt{PowerEmbed}$ in a wide range of simulated and real graphs and demonstrate its competitive performance, particularly for heterophilous graphs.

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arXiv2022

TGL: A General Framework for Temporal GNN Training on Billion-Scale Graphs

Many real world graphs contain time domain information. Temporal Graph Neural Networks capture temporal information as well as structural and contextual information in the generated dynamic node embeddings. Researchers have shown that these embeddings achieve state-of-the-art performance in many different tasks. In this work, we propose TGL, a unified framework for large-scale offline Temporal Graph Neural Network training where users can compose various Temporal Graph Neural Networks with simple configuration files. TGL comprises five main components, a temporal sampler, a mailbox, a node memory module, a memory updater, and a message passing engine. We design a Temporal-CSR data structure and a parallel sampler to efficiently sample temporal neighbors to formtraining mini-batches. We propose a novel random chunk scheduling technique that mitigates the problem of obsolete node memory when training with a large batch size. To address the limitations of current TGNNs only being evaluated on small-scale datasets, we introduce two large-scale real-world datasets with 0.2 and 1.3 billion temporal edges. We evaluate the performance of TGL on four small-scale datasets with a single GPU and the two large datasets with multiple GPUs for both link prediction and node classification tasks. We compare TGL with the open-sourced code of five methods and show that TGL achieves similar or better accuracy with an average of 13x speedup. Our temporal parallel sampler achieves an average of 173x speedup on a multi-core CPU compared with the baselines. On a 4-GPU machine, TGL can train one epoch of more than one billion temporal edges within 1-10 hours. To the best of our knowledge, this is the first work that proposes a general framework for large-scale Temporal Graph Neural Networks training on multiple GPUs.

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arXiv2022

TraverseNet: Unifying Space and Time in Message Passing for Traffic Forecasting

This paper aims to unify spatial dependency and temporal dependency in a non-Euclidean space while capturing the inner spatial-temporal dependencies for traffic data. For spatial-temporal attribute entities with topological structure, the space-time is consecutive and unified while each node's current status is influenced by its neighbors' past states over variant periods of each neighbor. Most spatial-temporal neural networks for traffic forecasting study spatial dependency and temporal correlation separately in processing, gravely impaired the spatial-temporal integrity, and ignore the fact that the neighbors' temporal dependency period for a node can be delayed and dynamic. To model this actual condition, we propose TraverseNet, a novel spatial-temporal graph neural network, viewing space and time as an inseparable whole, to mine spatial-temporal graphs while exploiting the evolving spatial-temporal dependencies for each node via message traverse mechanisms. Experiments with ablation and parameter studies have validated the effectiveness of the proposed TraverseNet, and the detailed implementation can be found from https://github.com/nnzhan/TraverseNet.

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arXiv2022

Efficient and effective training of language and graph neural network models

Can we combine heterogenous graph structure with text to learn high-quality semantic and behavioural representations? Graph neural networks (GNN)s encode numerical node attributes and graph structure to achieve impressive performance in a variety of supervised learning tasks. Current GNN approaches are challenged by textual features, which typically need to be encoded to a numerical vector before provided to the GNN that may incur some information loss. In this paper, we put forth an efficient and effective framework termed language model GNN (LM-GNN) to jointly train large-scale language models and graph neural networks. The effectiveness in our framework is achieved by applying stage-wise fine-tuning of the BERT model first with heterogenous graph information and then with a GNN model. Several system and design optimizations are proposed to enable scalable and efficient training. LM-GNN accommodates node and edge classification as well as link prediction tasks. We evaluate the LM-GNN framework in different datasets performance and showcase the effectiveness of the proposed approach. LM-GNN provides competitive results in an Amazon query-purchase-product application.

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arXiv2022

Nimble GNN Embedding with Tensor-Train Decomposition

This paper describes a new method for representing embedding tables of graph neural networks (GNNs) more compactly via tensor-train (TT) decomposition. We consider the scenario where (a) the graph data that lack node features, thereby requiring the learning of embeddings during training; and (b) we wish to exploit GPU platforms, where smaller tables are needed to reduce host-to-GPU communication even for large-memory GPUs. The use of TT enables a compact parameterization of the embedding, rendering it small enough to fit entirely on modern GPUs even for massive graphs. When combined with judicious schemes for initialization and hierarchical graph partitioning, this approach can reduce the size of node embedding vectors by 1,659 times to 81,362 times on large publicly available benchmark datasets, achieving comparable or better accuracy and significant speedups on multi-GPU systems. In some cases, our model without explicit node features on input can even match the accuracy of models that use node features.

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arXiv2022

Distributed Hybrid CPU and GPU training for Graph Neural Networks on Billion-Scale Graphs

Graph neural networks (GNN) have shown great success in learning from graph-structured data. They are widely used in various applications, such as recommendation, fraud detection, and search. In these domains, the graphs are typically large and heterogeneous, containing many millions or billions of vertices and edges of different types. To tackle this challenge, we develop DistDGLv2, a system that extends DistDGL for training GNNs on massive heterogeneous graphs in a mini-batch fashion, using distributed hybrid CPU/GPU training. DistDGLv2 places graph data in distributed CPU memory and performs mini-batch computation in GPUs. For ease of use, DistDGLv2 adopts API compatible with Deep Graph Library (DGL)'s mini-batch training and heterogeneous graph API, which enables distributed training with almost no code modification. To ensure model accuracy, DistDGLv2 follows a synchronous training approach and allows ego-networks forming mini-batches to include non-local vertices. To ensure data locality and load balancing, DistDGLv2 partitions heterogeneous graphs by using a multi-level partitioning algorithm with min-edge cut and multiple balancing constraints. DistDGLv2 deploys an asynchronous mini-batch generation pipeline that makes computation and data access asynchronous to fully utilize all hardware (CPU, GPU, network, PCIe). The combination allows DistDGLv2 to train high-quality models while achieving high parallel efficiency and memory scalability. We demonstrate DistDGLv2 on various GNN workloads. Our results show that DistDGLv2 achieves 2-3X speedup over DistDGL and 18X speedup over Euler. It takes only 5-10 seconds to complete an epoch on graphs with hundreds of millions of vertices on a cluster with 64 GPUs.

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arXiv2021

Dr. Top-k: Delegate-Centric Top-k on GPUs

Recent top-$k$ computation efforts explore the possibility of revising various sorting algorithms to answer top-$k$ queries on GPUs. These endeavors, unfortunately, perform significantly more work than needed. This paper introduces Dr. Top-k, a Delegate-centric top-$k$ system on GPUs that can reduce the top-$k$ workloads significantly. Particularly, it contains three major contributions: First, we introduce a comprehensive design of the delegate-centric concept, including maximum delegate, delegate-based filtering, and $β$ delegate mechanisms to help reduce the workload for top-$k$ up to more than 99%. Second, due to the difficulty and importance of deriving a proper subrange size, we perform a rigorous theoretical analysis, coupled with thorough experimental validations to identify the desirable subrange size. Third, we introduce four key system optimizations to enable fast multi-GPU top-$k$ computation. Taken together, this work constantly outperforms the state-of-the-art.

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arXiv2021

DistDGL: Distributed Graph Neural Network Training for Billion-Scale Graphs

Graph neural networks (GNN) have shown great success in learning from graph-structured data. They are widely used in various applications, such as recommendation, fraud detection, and search. In these domains, the graphs are typically large, containing hundreds of millions of nodes and several billions of edges. To tackle this challenge, we develop DistDGL, a system for training GNNs in a mini-batch fashion on a cluster of machines. DistDGL is based on the Deep Graph Library (DGL), a popular GNN development framework. DistDGL distributes the graph and its associated data (initial features and embeddings) across the machines and uses this distribution to derive a computational decomposition by following an owner-compute rule. DistDGL follows a synchronous training approach and allows ego-networks forming the mini-batches to include non-local nodes. To minimize the overheads associated with distributed computations, DistDGL uses a high-quality and light-weight min-cut graph partitioning algorithm along with multiple balancing constraints. This allows it to reduce communication overheads and statically balance the computations. It further reduces the communication by replicating halo nodes and by using sparse embedding updates. The combination of these design choices allows DistDGL to train high-quality models while achieving high parallel efficiency and memory scalability. We demonstrate our optimizations on both inductive and transductive GNN models. Our results show that DistDGL achieves linear speedup without compromising model accuracy and requires only 13 seconds to complete a training epoch for a graph with 100 million nodes and 3 billion edges on a cluster with 16 machines. DistDGL is now publicly available as part of DGL:https://github.com/dmlc/dgl/tree/master/python/dgl/distributed.

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arXiv2021

Global Neighbor Sampling for Mixed CPU-GPU Training on Giant Graphs

Graph neural networks (GNNs) are powerful tools for learning from graph data and are widely used in various applications such as social network recommendation, fraud detection, and graph search. The graphs in these applications are typically large, usually containing hundreds of millions of nodes. Training GNN models on such large graphs efficiently remains a big challenge. Despite a number of sampling-based methods have been proposed to enable mini-batch training on large graphs, these methods have not been proved to work on truly industry-scale graphs, which require GPUs or mixed-CPU-GPU training. The state-of-the-art sampling-based methods are usually not optimized for these real-world hardware setups, in which data movement between CPUs and GPUs is a bottleneck. To address this issue, we propose Global Neighborhood Sampling that aims at training GNNs on giant graphs specifically for mixed-CPU-GPU training. The algorithm samples a global cache of nodes periodically for all mini-batches and stores them in GPUs. This global cache allows in-GPU importance sampling of mini-batches, which drastically reduces the number of nodes in a mini-batch, especially in the input layer, to reduce data copy between CPU and GPU and mini-batch computation without compromising the training convergence rate or model accuracy. We provide a highly efficient implementation of this method and show that our implementation outperforms an efficient node-wise neighbor sampling baseline by a factor of 2X-4X on giant graphs. It outperforms an efficient implementation of LADIES with small layers by a factor of 2X-14X while achieving much higher accuracy than LADIES.We also theoretically analyze the proposed algorithm and show that with cached node data of a proper size, it enjoys a comparable convergence rate as the underlying node-wise sampling method.

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arXiv2021

Schema-Aware Deep Graph Convolutional Networks for Heterogeneous Graphs

Graph convolutional network (GCN) based approaches have achieved significant progress for solving complex, graph-structured problems. GCNs incorporate the graph structure information and the node (or edge) features through message passing and computes 'deep' node representations. Despite significant progress in the field, designing GCN architectures for heterogeneous graphs still remains an open challenge. Due to the schema of a heterogeneous graph, useful information may reside multiple hops away. A key question is how to perform message passing to incorporate information of neighbors multiple hops away while avoiding the well-known over-smoothing problem in GCNs. To address this question, we propose our GCN framework 'Deep Heterogeneous Graph Convolutional Network (DHGCN)', which takes advantage of the schema of a heterogeneous graph and uses a hierarchical approach to effectively utilize information many hops away. It first computes representations of the target nodes based on their 'schema-derived ego-network' (SEN). It then links the nodes of the same type with various pre-defined metapaths and performs message passing along these links to compute final node representations. Our design choices naturally capture the way a heterogeneous graph is generated from the schema. The experimental results on real and synthetic datasets corroborate the design choice and illustrate the performance gains relative to competing alternatives.

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arXiv2021

PanRep: Graph neural networks for extracting universal node embeddings in heterogeneous graphs

Learning unsupervised node embeddings facilitates several downstream tasks such as node classification and link prediction. A node embedding is universal if it is designed to be used by and benefit various downstream tasks. This work introduces PanRep, a graph neural network (GNN) model, for unsupervised learning of universal node representations for heterogenous graphs. PanRep consists of a GNN encoder that obtains node embeddings and four decoders, each capturing different topological and node feature properties. Abiding to these properties the novel unsupervised framework learns universal embeddings applicable to different downstream tasks. PanRep can be furthered fine-tuned to account for possible limited labels. In this operational setting PanRep is considered as a pretrained model for extracting node embeddings of heterogenous graph data. PanRep outperforms all unsupervised and certain supervised methods in node classification and link prediction, especially when the labeled data for the supervised methods is small. PanRep-FT (with fine-tuning) outperforms all other supervised approaches, which corroborates the merits of pretraining models. Finally, we apply PanRep-FT for discovering novel drugs for Covid-19. We showcase the advantage of universal embeddings in drug repurposing and identify several drugs used in clinical trials as possible drug candidates.

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arXiv2021

Supervised Dimensionality Reduction for Big Data

To solve key biomedical problems, experimentalists now routinely measure millions or billions of features (dimensions) per sample, with the hope that data science techniques will be able to build accurate data-driven inferences. Because sample sizes are typically orders of magnitude smaller than the dimensionality of these data, valid inferences require finding a low-dimensional representation that preserves the discriminating information (e.g., whether the individual suffers from a particular disease). There is a lack of interpretable supervised dimensionality reduction methods that scale to millions of dimensions with strong statistical theoretical guarantees.We introduce an approach, XOX, to extending principal components analysis by incorporating class-conditional moment estimates into the low-dimensional projection. The simplest ver-sion, "Linear Optimal Low-rank" projection (LOL), incorporates the class-conditional means. We prove, and substantiate with both synthetic and real data benchmarks, that LOL and its generalizations in the XOX framework lead to improved data representations for subsequent classification, while maintaining computational efficiency and scalability. Using multiple brain imaging datasets consisting of >150 million features, and several genomics datasets with>500,000 features, LOL outperforms other scalable linear dimensionality reduction techniques in terms of accuracy, while only requiring a few minutes on a standard desktop computer.

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arXiv2021

Learning over Families of Sets -- Hypergraph Representation Learning for Higher Order Tasks

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.

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arXiv2021

clusterNOR: A NUMA-Optimized Clustering Framework

Clustering algorithms are iterative and have complex data access patterns that result in many small random memory accesses. The performance of parallel implementations suffer from synchronous barriers for each iteration and skewed workloads. We rethink the parallelization of clustering for modern non-uniform memory architectures (NUMA) to maximizes independent, asynchronous computation. We eliminate many barriers, reduce remote memory accesses, and maximize cache reuse. We implement the 'Clustering NUMA Optimized Routines' (clusterNOR) extensible parallel framework that provides algorithmic building blocks. The system is generic, we demonstrate nine modern clustering algorithms that have simple implementations. clusterNOR includes (i) in-memory, (ii) semi-external memory, and (iii) distributed memory execution, enabling computation for varying memory and hardware budgets. For algorithms that rely on Euclidean distance, clusterNOR defines an updated Elkan's triangle inequality pruning algorithm that uses asymptotically less memory so that it works on billion-point data sets. clusterNOR extends and expands the scope of the 'knor' library for k-means clustering by generalizing underlying principles, providing a uniform programming interface and expanding the scope to hierarchical and linear algebraic classes of algorithms. The compound effect of our optimizations is an order of magnitude improvement in speed over other state-of-the-art solutions, such as Spark's MLlib and Apple's Turi.

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arXiv2020

FeatGraph: A Flexible and Efficient Backend for Graph Neural Network Systems

Graph neural networks (GNNs) are gaining increasing popularity as a promising approach to machine learning on graphs. Unlike traditional graph workloads where each vertex/edge is associated with a scalar, GNNs attach a feature tensor to each vertex/edge. This additional feature dimension, along with consequently more complex vertex- and edge-wise computations, has enormous implications on locality and parallelism, which existing graph processing systems fail to exploit. This paper proposes FeatGraph to accelerate GNN workloads by co-optimizing graph traversal and feature dimension computation. FeatGraph provides a flexible programming interface to express diverse GNN models by composing coarse-grained sparse templates with fine-grained user-defined functions (UDFs) on each vertex/edge. FeatGraph incorporates optimizations for graph traversal into the sparse templates and allows users to specify optimizations for UDFs with a feature dimension schedule (FDS). FeatGraph speeds up end-to-end GNN training and inference by up to 32x on CPU and 7x on GPU.

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arXiv2020

Deep Graph Library: A Graph-Centric, Highly-Performant Package for Graph Neural Networks

Advancing research in the emerging field of deep graph learning requires new tools to support tensor computation over graphs. In this paper, we present the design principles and implementation of Deep Graph Library (DGL). DGL distills the computational patterns of GNNs into a few generalized sparse tensor operations suitable for extensive parallelization. By advocating graph as the central programming abstraction, DGL can perform optimizations transparently. By cautiously adopting a framework-neutral design, DGL allows users to easily port and leverage the existing components across multiple deep learning frameworks. Our evaluation shows that DGL significantly outperforms other popular GNN-oriented frameworks in both speed and memory consumption over a variety of benchmarks and has little overhead for small scale workloads.

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