Xiang Song

Hongkuan Zhou, Da Zheng, Israt Nisa et al.

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.

Arpandeep Khatua, Vikram Sharma Mailthody, Bhagyashree Taleka et al.

Graph neural networks (GNNs) have shown high potential for a variety of real-world, challenging applications, but one of the major obstacles in GNN research is the lack of large-scale flexible datasets. Most existing public datasets for GNNs are relatively small, which limits the ability of GNNs to generalize to unseen data. The few existing large-scale graph datasets provide very limited labeled data. This makes it difficult to determine if the GNN model's low accuracy for unseen data is inherently due to insufficient training data or if the model failed to generalize. Additionally, datasets used to train GNNs need to offer flexibility to enable a thorough study of the impact of various factors while training GNN models. In this work, we introduce the Illinois Graph Benchmark (IGB), a research dataset tool that the developers can use to train, scrutinize and systematically evaluate GNN models with high fidelity. IGB includes both homogeneous and heterogeneous academic graphs of enormous sizes, with more than 40% of their nodes labeled. Compared to the largest graph datasets publicly available, the IGB provides over 162X more labeled data for deep learning practitioners and developers to create and evaluate models with higher accuracy. The IGB dataset is a collection of academic graphs designed to be flexible, enabling the study of various GNN architectures, embedding generation techniques, and analyzing system performance issues for node classification tasks. IGB is open-sourced, supports DGL and PyG frameworks, and comes with releases of the raw text that we believe foster emerging language models and GNN research projects. An early public version of IGB is available at https://github.com/IllinoisGraphBenchmark/IGB-Datasets.

Vassilis N. Ioannidis, Xiang Song, Da Zheng et al. · amazon-science

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.

Han Xie, Da Zheng, Jun Ma et al. · amazon-science

Model pre-training on large text corpora has been demonstrated effective for various downstream applications in the NLP domain. In the graph mining domain, a similar analogy can be drawn for pre-training graph models on large graphs in the hope of benefiting downstream graph applications, which has also been explored by several recent studies. However, no existing study has ever investigated the pre-training of text plus graph models on large heterogeneous graphs with abundant textual information (a.k.a. large graph corpora) and then fine-tuning the model on different related downstream applications with different graph schemas. To address this problem, we propose a framework of graph-aware language model pre-training (GALM) on a large graph corpus, which incorporates large language models and graph neural networks, and a variety of fine-tuning methods on downstream applications. We conduct extensive experiments on Amazon's real internal datasets and large public datasets. Comprehensive empirical results and in-depth analysis demonstrate the effectiveness of our proposed methods along with lessons learned.

Shichang Zhang, Jiani Zhang, Xiang Song et al.

Transparency and accountability have become major concerns for black-box machine learning (ML) models. Proper explanations for the model behavior increase model transparency and help researchers develop more accountable models. Graph neural networks (GNN) have recently shown superior performance in many graph ML problems than traditional methods, and explaining them has attracted increased interest. However, GNN explanation for link prediction (LP) is lacking in the literature. LP is an essential GNN task and corresponds to web applications like recommendation and sponsored search on web. Given existing GNN explanation methods only address node/graph-level tasks, we propose Path-based GNN Explanation for heterogeneous Link prediction (PaGE-Link) that generates explanations with connection interpretability, enjoys model scalability, and handles graph heterogeneity. Qualitatively, PaGE-Link can generate explanations as paths connecting a node pair, which naturally captures connections between the two nodes and easily transfer to human-interpretable explanations. Quantitatively, explanations generated by PaGE-Link improve AUC for recommendation on citation and user-item graphs by 9 - 35% and are chosen as better by 78.79% of responses in human evaluation.

Hongkuan Zhou, Da Zheng, Xiang Song et al.

Memory-based Temporal Graph Neural Networks are powerful tools in dynamic graph representation learning and have demonstrated superior performance in many real-world applications. However, their node memory favors smaller batch sizes to capture more dependencies in graph events and needs to be maintained synchronously across all trainers. As a result, existing frameworks suffer from accuracy loss when scaling to multiple GPUs. Evenworse, the tremendous overhead to synchronize the node memory make it impractical to be deployed to distributed GPU clusters. In this work, we propose DistTGL -- an efficient and scalable solution to train memory-based TGNNs on distributed GPU clusters. DistTGL has three improvements over existing solutions: an enhanced TGNN model, a novel training algorithm, and an optimized system. In experiments, DistTGL achieves near-linear convergence speedup, outperforming state-of-the-art single-machine method by 14.5% in accuracy and 10.17x in training throughput.

Jing Zhu, Xiang Song, Vassilis N. Ioannidis et al.

How can we enhance the node features acquired from Pretrained Models (PMs) to better suit downstream graph learning tasks? Graph Neural Networks (GNNs) have become the state-of-the-art approach for many high-impact, real-world graph applications. For feature-rich graphs, a prevalent practice involves utilizing a PM directly to generate features, without incorporating any domain adaptation techniques. Nevertheless, this practice is suboptimal because the node features extracted from PM are graph-agnostic and prevent GNNs from fully utilizing the potential correlations between the graph structure and node features, leading to a decline in GNNs performance. In this work, we seek to improve the node features obtained from a PM for downstream graph tasks and introduce TOUCHUP-G, which has several advantages. It is (a) General: applicable to any downstream graph task, including link prediction which is often employed in recommender systems; (b) Multi-modal: able to improve raw features of any modality (e.g. images, texts, audio); (c) Principled: it is closely related to a novel metric, feature homophily, which we propose to quantify the potential correlations between the graph structure and node features and we show that TOUCHUP-G can effectively shrink the discrepancy between the graph structure and node features; (d) Effective: achieving state-of-the-art results on four real-world datasets spanning different tasks and modalities.

Cong Wan, Yuhang He, Xiang Song et al.

Diffusion models have revolutionized customized text-to-image generation, allowing for efficient synthesis of photos from personal data with textual descriptions. However, these advancements bring forth risks including privacy breaches and unauthorized replication of artworks. Previous researches primarily center around using prompt-specific methods to generate adversarial examples to protect personal images, yet the effectiveness of existing methods is hindered by constrained adaptability to different prompts. In this paper, we introduce a Prompt-Agnostic Adversarial Perturbation (PAP) method for customized diffusion models. PAP first models the prompt distribution using a Laplace Approximation, and then produces prompt-agnostic perturbations by maximizing a disturbance expectation based on the modeled distribution. This approach effectively tackles the prompt-agnostic attacks, leading to improved defense stability. Extensive experiments in face privacy and artistic style protection, demonstrate the superior generalization of PAP in comparison to existing techniques. Our project page is available at https://github.com/vancyland/Prompt-Agnostic-Adversarial-Perturbation-for-Customized-Diffusion-Models.github.io.

Jing Zhu, Yuhang Zhou, Vassilis N. Ioannidis et al.

While Graph Neural Networks (GNNs) are remarkably successful in a variety of high-impact applications, we demonstrate that, in link prediction, the common practices of including the edges being predicted in the graph at training and/or test have outsized impact on the performance of low-degree nodes. We theoretically and empirically investigate how these practices impact node-level performance across different degrees. Specifically, we explore three issues that arise: (I1) overfitting; (I2) distribution shift; and (I3) implicit test leakage. The former two issues lead to poor generalizability to the test data, while the latter leads to overestimation of the model's performance and directly impacts the deployment of GNNs. To address these issues in a systematic way, we introduce an effective and efficient GNN training framework, SpotTarget, which leverages our insight on low-degree nodes: (1) at training time, it excludes a (training) edge to be predicted if it is incident to at least one low-degree node; and (2) at test time, it excludes all test edges to be predicted (thus, mimicking real scenarios of using GNNs, where the test data is not included in the graph). SpotTarget helps researchers and practitioners adhere to best practices for learning from graph data, which are frequently overlooked even by the most widely-used frameworks. Our experiments on various real-world datasets show that SpotTarget makes GNNs up to 15x more accurate in sparse graphs, and significantly improves their performance for low-degree nodes in dense graphs.

Kezhao Huang, Haitian Jiang, Minjie Wang et al.

A key performance bottleneck when training graph neural network (GNN) models on large, real-world graphs is loading node features onto a GPU. Due to limited GPU memory, expensive data movement is necessary to facilitate the storage of these features on alternative devices with slower access (e.g. CPU memory). Moreover, the irregularity of graph structures contributes to poor data locality which further exacerbates the problem. Consequently, existing frameworks capable of efficiently training large GNN models usually incur a significant accuracy degradation because of the currently-available shortcuts involved. To address these limitations, we instead propose FreshGNN, a general-purpose GNN mini-batch training framework that leverages a historical cache for storing and reusing GNN node embeddings instead of re-computing them through fetching raw features at every iteration. Critical to its success, the corresponding cache policy is designed, using a combination of gradient-based and staleness criteria, to selectively screen those embeddings which are relatively stable and can be cached, from those that need to be re-computed to reduce estimation errors and subsequent downstream accuracy loss. When paired with complementary system enhancements to support this selective historical cache, FreshGNN is able to accelerate the training speed on large graph datasets such as ogbn-papers100M and MAG240M by 3.4x up to 20.5x and reduce the memory access by 59%, with less than 1% influence on test accuracy.

Jiarui Jin, Yangkun Wang, Weinan Zhang et al.

Graph Neural Networks (GNNs), originally proposed for node classification, have also motivated many recent works on edge prediction (a.k.a., link prediction). However, existing methods lack elaborate design regarding the distinctions between two tasks that have been frequently overlooked: (i) edges only constitute the topology in the node classification task but can be used as both the topology and the supervisions (i.e., labels) in the edge prediction task; (ii) the node classification makes prediction over each individual node, while the edge prediction is determinated by each pair of nodes. To this end, we propose a novel edge prediction paradigm named Edge-aware Message PassIng neuRal nEtworks (EMPIRE). Concretely, we first introduce an edge splitting technique to specify use of each edge where each edge is solely used as either the topology or the supervision (named as topology edge or supervision edge). We then develop a new message passing mechanism that generates the messages to source nodes (through topology edges) being aware of target nodes (through supervision edges). In order to emphasize the differences between pairs connected by supervision edges and pairs unconnected, we further weight the messages to highlight the relative ones that can reflect the differences. In addition, we design a novel negative node-pair sampling trick that efficiently samples 'hard' negative instances in the supervision instances, and can significantly improve the performance. Experimental results verify that the proposed method can significantly outperform existing state-of-the-art models regarding the edge prediction task on multiple homogeneous and heterogeneous graph datasets.

Zhikai Chen, Han Xie, Jian Zhang et al.

Predictive modeling over relational databases (RDBs) powers applications, yet remains challenging due to capturing both cross-table dependencies and complex feature interactions. Relational Deep Learning (RDL) methods automate feature engineering via message passing, while classical approaches like Deep Feature Synthesis (DFS) rely on predefined non-parametric aggregators. Despite performance gains, the comparative advantages of RDL over DFS and the design principles for selecting effective architectures remain poorly understood. We present a comprehensive study that unifies RDL and DFS in a shared design space and conducts architecture-centric searches across diverse RDB tasks. Our analysis yields three key findings: (1) RDL does not consistently outperform DFS, with performance being highly task-dependent; (2) no single architecture dominates across tasks, underscoring the need for task-aware model selection; and (3) validation accuracy is an unreliable guide for architecture choice. This search yields a model performance bank that links architecture configurations to their performance; leveraging this bank, we analyze the drivers of the RDL-DFS performance gap and introduce two task signals -- RDB task homophily and an affinity embedding that captures size, path, feature, and temporal structure -- whose correlation with the gap enables principled routing. Guided by these signals, we propose Relatron, a task embedding-based meta-selector that chooses between RDL and DFS and prunes the within-family search. Lightweight loss-landscape metrics further guard against brittle checkpoints by preferring flatter optima. In experiments, Relatron resolves the "more tuning, worse performance" effect and, in joint hyperparameter-architecture optimization, achieves up to 18.5% improvement over strong baselines with 10x lower cost than Fisher information-based alternatives.

Jiahang Li, Yakun Song, Xiang Song et al.

Graph Neural Networks (GNNs) have displayed considerable promise in graph representation learning across various applications. The core learning process requires the initialization of model weight matrices within each GNN layer, which is typically accomplished via classic initialization methods such as Xavier initialization. However, these methods were originally motivated to stabilize the variance of hidden embeddings and gradients across layers of Feedforward Neural Networks (FNNs) and Convolutional Neural Networks (CNNs) to avoid vanishing gradients and maintain steady information flow. In contrast, within the GNN context classical initializations disregard the impact of the input graph structure and message passing on variance. In this paper, we analyze the variance of forward and backward propagation across GNN layers and show that the variance instability of GNN initializations comes from the combined effect of the activation function, hidden dimension, graph structure and message passing. To better account for these influence factors, we propose a new initialization method for Variance Instability Reduction within GNN Optimization (Virgo), which naturally tends to equate forward and backward variances across successive layers. We conduct comprehensive experiments on 15 datasets to show that Virgo can lead to superior model performance and more stable variance at initialization on node classification, link prediction and graph classification tasks. Codes are in https://github.com/LspongebobJH/virgo_icml2023.

Bo He, Xiang Song, Vincent Gao et al.

Low-quality listings and bad actor behavior in online retail websites threatens e-commerce business as these result in sub-optimal buying experience and erode customer trust. When a new listing is created, how to tell it has good-quality? Is the method effective, fast, and scalable? Previous approaches often have three limitations/challenges: (1) unable to handle cold start problems where new sellers/listings lack sufficient selling histories. (2) inability of scoring hundreds of millions of listings at scale, or compromise performance for scalability. (3) has space challenges from large-scale graph with giant e-commerce business size. To overcome these limitations/challenges, we proposed ColdGuess, an inductive graph-based risk predictor built upon a heterogeneous seller product graph, which effectively identifies risky seller/product/listings at scale. ColdGuess tackles the large-scale graph by consolidated nodes, and addresses the cold start problems using homogeneous influence1. The evaluation on real data demonstrates that ColdGuess has stable performance as the number of unknown features increases. It outperforms the lightgbm2 by up to 34 pcp ROC-AUC in a cold start case when a new seller sells a new product . The resulting system, ColdGuess, is effective, adaptable to changing risky seller behavior, and is already in production

Daniil Vankov, Nikita Ivkin, Kyle Ulrich et al.

Mixture-of-Experts (MoE) architectures are increasingly used to efficiently scale large language models. However, in production inference, request batching and speculative decoding significantly amplify expert activation, eroding these efficiency benefits. We address this issue by modeling batch-aware expert selection as a modular optimization problem and designing efficient greedy algorithms for different deployment settings. The proposed method, namely XShare, requires no retraining and dynamically adapts to each batch by maximizing the total gating score of selected experts. It reduces expert activation by up to 30% under standard batching, cuts peak GPU load by up to 3x in expert-parallel deployments, and achieves up to 14% throughput gains in speculative decoding via hierarchical, correlation-aware expert selection even if requests in a batch drawn from heterogeneous datasets.

Jiading Gai, Shuai Zhang, Xiang Song et al.

Modern RL post-training methods such as GRPO and DAPO train on $N$ response sequences of $R$ tokens sampled from a shared prompt of $P$ tokens, but standard FlashAttention replicates all $P$ prompt tokens $N$ times across both forward and backward passes -- duplicating compute and memory on identical hidden states. In large-rollout, long-context RL training ($N{\geq}16$, $P{\geq}8\text{K}$), this redundancy dominates the policy update cost. We observe that in decoder-only models, causal masking makes prompt representations invariant across sequences at every layer, so all per-token operations (norms, projections, MLP) and attention can process the prompt once -- a property not yet exploited at the kernel level for training. We propose \textbf{DualKV}, the first FlashAttention kernel variant that eliminates shared-prompt replication during RL training, via (1)~fused CUDA forward and backward kernels that iterate over two disjoint KV regions -- shared context and per-sequence response -- in a single kernel launch, and (2)~a data-pipeline redesign in veRL that repacks $N(P{+}R)$ tokens into $P{+}NR$ tokens per micro-batch, extending the token reduction from attention to the entire model by a factor $ρ= N(P{+}R)/(P{+}NR)$. DualKV is mathematically equivalent to standard attention and introduces no approximation. On Qwen3-8B GRPO training with 8$\times$H100 GPUs ($N{=}32$, 8K-context), DualKV achieves $1.63$--$2.09\times$ policy-update speedup, enables $2\times$ larger micro-batches, and raises MFU from $36\%$ to $76\%$. Similar gains hold for DAPO ($2.47\times$ speedup, $77\%$ MFU). At 30B MoE scale on 16$\times$H100, DualKV achieves $3.82\times$ policy-update and $3.38\times$ end-to-end step speedup over FlashAttention (which requires 4-way Ulysses sequence parallelism to avoid OOM).

Qiang Wang, Xiang Song, Yuhang He et al.

Deep neural networks (DNNs) often underperform in real-world, dynamic settings where data distributions change over time. Domain Incremental Learning (DIL) offers a solution by enabling continual model adaptation, with Parameter-Isolation DIL (PIDIL) emerging as a promising paradigm to reduce knowledge conflicts. However, existing PIDIL methods struggle with parameter selection accuracy, especially as the number of domains and corresponding classes grows. To address this, we propose SOYO, a lightweight framework that improves domain selection in PIDIL. SOYO introduces a Gaussian Mixture Compressor (GMC) and Domain Feature Resampler (DFR) to store and balance prior domain data efficiently, while a Multi-level Domain Feature Fusion Network (MDFN) enhances domain feature extraction. Our framework supports multiple Parameter-Efficient Fine-Tuning (PEFT) methods and is validated across tasks such as image classification, object detection, and speech enhancement. Experimental results on six benchmarks demonstrate SOYO's consistent superiority over existing baselines, showcasing its robustness and adaptability in complex, evolving environments. The codes will be released in https://github.com/qwangcv/SOYO.

Karish Grover, Haiyang Yu, Xiang Song et al.

Can integrating spectral and curvature signals unlock new potential in graph representation learning? Non-Euclidean geometries, particularly Riemannian manifolds such as hyperbolic (negative curvature) and spherical (positive curvature), offer powerful inductive biases for embedding complex graph structures like scale-free, hierarchical, and cyclic patterns. Meanwhile, spectral filtering excels at processing signal variations across graphs, making it effective in homophilic and heterophilic settings. Leveraging both can significantly enhance the learned representations. To this end, we propose Spectro-Riemannian Graph Neural Networks (CUSP) - the first graph representation learning paradigm that unifies both CUrvature (geometric) and SPectral insights. CUSP is a mixed-curvature spectral GNN that learns spectral filters to optimize node embeddings in products of constant-curvature manifolds (hyperbolic, spherical, and Euclidean). Specifically, CUSP introduces three novel components: (a) Cusp Laplacian, an extension of the traditional graph Laplacian based on Ollivier-Ricci curvature, designed to capture the curvature signals better; (b) Cusp Filtering, which employs multiple Riemannian graph filters to obtain cues from various bands in the eigenspectrum; and (c) Cusp Pooling, a hierarchical attention mechanism combined with a curvature-based positional encoding to assess the relative importance of differently curved substructures in our graph. Empirical evaluation across eight homophilic and heterophilic datasets demonstrates the superiority of CUSP in node classification and link prediction tasks, with a gain of up to 5.3% over state-of-the-art models. The code is available at: https://github.com/amazon-science/cusp.

Zhikai Chen, Han Xie, Jian Zhang et al.

Recent years have witnessed significant advancements in graph machine learning (GML), with its applications spanning numerous domains. However, the focus of GML has predominantly been on developing powerful models, often overlooking a crucial initial step: constructing suitable graphs from common data formats, such as tabular data. This construction process is fundamental to applying graph-based models, yet it remains largely understudied and lacks formalization. Our research aims to address this gap by formalizing the graph construction problem and proposing an effective solution. We identify two critical challenges to achieve this goal: 1. The absence of dedicated datasets to formalize and evaluate the effectiveness of graph construction methods, and 2. Existing automatic construction methods can only be applied to some specific cases, while tedious human engineering is required to generate high-quality graphs. To tackle these challenges, we present a two-fold contribution. First, we introduce a set of datasets to formalize and evaluate graph construction methods. Second, we propose an LLM-based solution, AutoG, automatically generating high-quality graph schemas without human intervention. The experimental results demonstrate that the quality of constructed graphs is critical to downstream task performance, and AutoG can generate high-quality graphs that rival those produced by human experts. Our code can be accessible from https://github.com/amazon-science/Automatic-Table-to-Graph-Generation.

Da Zheng, Xiang Song, Qi Zhu et al.

Graph machine learning (GML) is effective in many business applications. However, making GML easy to use and applicable to industry applications with massive datasets remain challenging. We developed GraphStorm, which provides an end-to-end solution for scalable graph construction, graph model training and inference. GraphStorm has the following desirable properties: (a) Easy to use: it can perform graph construction and model training and inference with just a single command; (b) Expert-friendly: GraphStorm contains many advanced GML modeling techniques to handle complex graph data and improve model performance; (c) Scalable: every component in GraphStorm can operate on graphs with billions of nodes and can scale model training and inference to different hardware without changing any code. GraphStorm has been used and deployed for over a dozen billion-scale industry applications after its release in May 2023. It is open-sourced in Github: https://github.com/awslabs/graphstorm.

Da Zheng, Chao Ma, Minjie Wang et al.

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.

Yang Liu, Jiahua Xiao, Xiang Song et al.

Effectively modeling global context information in hyperspectral image (HSI) denoising is crucial, but prevailing methods using convolution or transformers still face localized or computational efficiency limitations. Inspired by the emerging Selective State Space Model (Mamba) with nearly linear computational complexity and efficient long-term modeling, we present a novel HSI denoising network named HSIDMamba (HSDM). HSDM is tailored to exploit the capture of potential spatial-spectral dependencies effectively and efficiently for HSI denoising. In particular, HSDM comprises multiple Hyperspectral Continuous Scan Blocks (HCSB) to strengthen spatial-spectral interactions. HCSB links forward and backward scans and enhances information from eight directions through the State Space Model (SSM), strengthening the context representation learning of HSDM and improving denoising performance more effectively. In addition, to enhance the utilization of spectral information and mitigate the degradation problem caused by long-range scanning, spectral attention mechanism. Extensive evaluations against HSI denoising benchmarks validate the superior performance of HSDM, achieving state-of-the-art performance and surpassing the efficiency of the transformer method SERT by 31%.

Qiang Wang, Yuhang He, SongLin Dong et al.

Domain-Incremental Learning (DIL) enables vision models to adapt to changing conditions in real-world environments while maintaining the knowledge acquired from previous domains. Given privacy concerns and training time, Rehearsal-Free DIL (RFDIL) is more practical. Inspired by the incremental cognitive process of the human brain, we design Dual-level Concept Prototypes (DualCP) for each class to address the conflict between learning new knowledge and retaining old knowledge in RFDIL. To construct DualCP, we propose a Concept Prototype Generator (CPG) that generates both coarse-grained and fine-grained prototypes for each class. Additionally, we introduce a Coarse-to-Fine calibrator (C2F) to align image features with DualCP. Finally, we propose a Dual Dot-Regression (DDR) loss function to optimize our C2F module. Extensive experiments on the DomainNet, CDDB, and CORe50 datasets demonstrate the effectiveness of our method.

Tengfei Ma, Xiang song, Wen Tao et al. · gatech

Knowledge graph completion (KGC) aims to alleviate the inherent incompleteness of knowledge graphs (KGs), which is a critical task for various applications, such as recommendations on the web. Although knowledge graph embedding (KGE) models have demonstrated superior predictive performance on KGC tasks, these models infer missing links in a black-box manner that lacks transparency and accountability, preventing researchers from developing accountable models. Existing KGE-based explanation methods focus on exploring key paths or isolated edges as explanations, which is information-less to reason target prediction. Additionally, the missing ground truth leads to these explanation methods being ineffective in quantitatively evaluating explored explanations. To overcome these limitations, we propose KGExplainer, a model-agnostic method that identifies connected subgraph explanations and distills an evaluator to assess them quantitatively. KGExplainer employs a perturbation-based greedy search algorithm to find key connected subgraphs as explanations within the local structure of target predictions. To evaluate the quality of the explored explanations, KGExplainer distills an evaluator from the target KGE model. By forwarding the explanations to the evaluator, our method can examine the fidelity of them. Extensive experiments on benchmark datasets demonstrate that KGExplainer yields promising improvement and achieves an optimal ratio of 83.3% in human evaluation.

Qi Zhu, Da Zheng, Xiang Song et al.

Text-rich graphs, which exhibit rich textual information on nodes and edges, are prevalent across a wide range of real-world business applications. Large Language Models (LLMs) have demonstrated remarkable abilities in understanding text, which also introduced the potential for more expressive modeling in text-rich graphs. Despite these capabilities, efficiently applying LLMs to representation learning on graphs presents significant challenges. Recently, parameter-efficient fine-tuning methods for LLMs have enabled efficient new task generalization with minimal time and memory consumption. Inspired by this, we introduce Graph-aware Parameter-Efficient Fine-Tuning - GPEFT, a novel approach for efficient graph representation learning with LLMs on text-rich graphs. Specifically, we utilize a graph neural network (GNN) to encode structural information from neighboring nodes into a graph prompt. This prompt is then inserted at the beginning of the text sequence. To improve the quality of graph prompts, we pre-trained the GNN to assist the frozen LLM in predicting the next token in the node text. Compared with existing joint GNN and LMs, our method directly generate the node embeddings from large language models with an affordable fine-tuning cost. We validate our approach through comprehensive experiments conducted on 8 different text-rich graphs, observing an average improvement of 2% in hit@1 and Mean Reciprocal Rank (MRR) in link prediction evaluations. Our results demonstrate the efficacy and efficiency of our model, showing that it can be smoothly integrated with various large language models, including OPT, LLaMA and Falcon.

Meng-Chieh Lee, Haiyang Yu, Jian Zhang et al.

Given a node-attributed graph, and a graph task (link prediction or node classification), can we tell if a graph neural network (GNN) will perform well? More specifically, do the graph structure and the node features carry enough usable information for the task? Our goals are (1) to develop a fast tool to measure how much information is in the graph structure and in the node features, and (2) to exploit the information to solve the task, if there is enough. We propose NetInfoF, a framework including NetInfoF_Probe and NetInfoF_Act, for the measurement and the exploitation of network usable information (NUI), respectively. Given a graph data, NetInfoF_Probe measures NUI without any model training, and NetInfoF_Act solves link prediction and node classification, while two modules share the same backbone. In summary, NetInfoF has following notable advantages: (a) General, handling both link prediction and node classification; (b) Principled, with theoretical guarantee and closed-form solution; (c) Effective, thanks to the proposed adjustment to node similarity; (d) Scalable, scaling linearly with the input size. In our carefully designed synthetic datasets, NetInfoF correctly identifies the ground truth of NUI and is the only method being robust to all graph scenarios. Applied on real-world datasets, NetInfoF wins in 11 out of 12 times on link prediction compared to general GNN baselines.

Shiyang Chen, Xiang Song, Vasiloudis Theodore et al.

Graph Neural Networks (GNNs) are a new research frontier with various applications and successes. The end-to-end inference for all nodes, is common for GNN embedding models, which are widely adopted in applications like recommendation and advertising. While sharing opportunities arise in GNN tasks (i.e., inference for a few nodes and training), the potential for sharing in full graph end-to-end inference is largely underutilized because traditional efforts fail to fully extract sharing benefits due to overwhelming overheads or excessive memory usage. This paper introduces Deal, a distributed GNN inference system that is dedicated to end-to-end inference for all nodes for graphs with multi-billion edges. First, we unveil and exploit an untapped sharing opportunity during sampling, and maximize the benefits from sharing during subsequent GNN computation. Second, we introduce memory-saving and communication-efficient distributed primitives for lightweight 1-D graph and feature tensor collaborative partitioning-based distributed inference. Third, we introduce partitioned, pipelined communication and fusing feature preparation with the first GNN primitive for end-to-end inference. With Deal, the end-to-end inference time on real-world benchmark datasets is reduced up to 7.70 x and the graph construction time is reduced up to 21.05 x, compared to the state-of-the-art.

Chenhao Ding, Xinyuan Gao, Songlin Dong et al.

With the development of visual-language models (VLM) in downstream task applications, test-time adaptation methods based on VLM have attracted increasing attention for their ability to address changes distribution in test-time. Although prior approaches have achieved some progress, they typically either demand substantial computational resources or are constrained by the limitations of the original feature space, rendering them less effective for test-time adaptation tasks. To address these challenges, we propose a training-free feature space rotation with basis transformation for test-time adaptation. By leveraging the inherent distinctions among classes, we reconstruct the original feature space and map it to a new representation, thereby enhancing the clarity of class differences and providing more effective guidance for the model during testing. Additionally, to better capture relevant information from various classes, we maintain a dynamic queue to store representative samples. Experimental results across multiple benchmarks demonstrate that our method outperforms state-of-the-art techniques in terms of both performance and efficiency.

Mude Hui, Xin Huang, Jaime Campos Salas et al.

Reasoning LLMs produce longer outputs, requiring speculative decoding drafters trained on extended sequences. Parallel drafting - predicting multiple tokens per forward pass - offers latency benefits over sequential generation, but training complexity scales quadratically with the product of sequence length and parallel positions, rendering long-context training impractical. We present P(arallel)-EAGLE, which transforms EAGLE from autoregressive to parallel multi-token prediction via a learnable shared hidden state. To scale training to long contexts, we develop a framework featuring attention mask pre-computation and sequence partitioning techniques, enabling gradient accumulation within individual sequences for parallel-prediction training. We implement P-EAGLE in vLLM and demonstrate speedups of 1.10-1.36x over autoregressive EAGLE-3 across GPT-OSS 120B, 20B, and Qwen3-Coder 30B.

Karish Grover, Theodore Vasiloudis, Han Xie et al.

Can multi-task self-supervised learning on graphs be coordinated without the usual tug-of-war between objectives? Graph self-supervised learning (SSL) offers a growing toolbox of pretext objectives: mutual information, reconstruction, contrastive learning; yet combining them reliably remains a challenge due to objective interference and training instability. Most multi-pretext pipelines use per-update mixing, forcing every parameter update to be a compromise, leading to three failure modes: Disagreement (conflict-induced negative transfer), Drift (nonstationary objective utility), and Drought (hidden starvation of underserved objectives). We argue that coordination is fundamentally a temporal allocation problem: deciding when each objective receives optimization budget, not merely how to weigh them. We introduce ControlG, a control-theoretic framework that recasts multi-objective graph SSL as feedback-controlled temporal allocation by estimating per-objective difficulty and pairwise antagonism, planning target budgets via a Pareto-aware log-hypervolume planner, and scheduling with a Proportional-Integral-Derivative (PID) controller. Across 9 datasets, ControlG consistently outperforms state-of-the-art baselines, while producing an auditable schedule that reveals which objectives drove learning.

Jialin Chen, Houyu Zhang, Seongjun Yun et al.

Retrieval-Augmented Generation (RAG) has significantly mitigated the hallucinations of Large Language Models (LLMs) by grounding the generation with external knowledge. Recent extensions of RAG to graph-based retrieval offer a promising direction, leveraging the structural knowledge for multi-hop reasoning. However, existing graph RAG typically decouples retrieval and reasoning processes, which prevents the retriever from adapting to the reasoning needs of the LLM. They also struggle with scalability when performing multi-hop expansion over large-scale graphs, or depend heavily on annotated ground-truth entities, which are often unavailable in open-domain settings. To address these challenges, we propose a novel graph retriever trained end-to-end with LLM, which features an attention-based growing and pruning mechanism, adaptively navigating multi-hop relevant entities while filtering out noise. Within the extracted subgraph, structural knowledge and semantic features are encoded via soft tokens and the verbalized graph, respectively, which are infused into the LLM together, thereby enhancing its reasoning capability and facilitating interactive joint training of the graph retriever and the LLM reasoner. Experimental results across three QA benchmarks show that our approach consistently achieves state-of-the-art performance, validating the strength of joint graph-LLM optimization for complex reasoning tasks. Notably, our framework eliminates the need for predefined ground-truth entities by directly optimizing the retriever using LLM logits as implicit feedback, making it especially effective in open-domain settings.

Lecheng Kong, Theodore Vasiloudis, Seongjun Yun et al. · amazon-science

Graph incremental learning is a learning paradigm that aims to adapt trained models to continuously incremented graphs and data over time without the need for retraining on the full dataset. However, regular graph machine learning methods suffer from catastrophic forgetting when applied to incremental learning settings, where previously learned knowledge is overridden by new knowledge. Previous approaches have tried to address this by treating the previously trained model as an inseparable unit and using techniques to maintain old behaviors while learning new knowledge. These approaches, however, do not account for the fact that previously acquired knowledge at different timestamps contributes differently to learning new tasks. Some prior patterns can be transferred to help learn new data, while others may deviate from the new data distribution and be detrimental. To address this, we propose a dynamic mixture-of-experts (DyMoE) approach for incremental learning. Specifically, a DyMoE GNN layer adds new expert networks specialized in modeling the incoming data blocks. We design a customized regularization loss that utilizes data sequence information so existing experts can maintain their ability to solve old tasks while helping the new expert learn the new data effectively. As the number of data blocks grows over time, the computational cost of the full mixture-of-experts (MoE) model increases. To address this, we introduce a sparse MoE approach, where only the top-$k$ most relevant experts make predictions, significantly reducing the computation time. Our model achieved 4.92\% relative accuracy increase compared to the best baselines on class incremental learning, showing the model's exceptional power.

Shichang Zhang, Da Zheng, Jiani Zhang et al.

Text-rich graphs, prevalent in data mining contexts like e-commerce and academic graphs, consist of nodes with textual features linked by various relations. Traditional graph machine learning models, such as Graph Neural Networks (GNNs), excel in encoding the graph structural information, but have limited capability in handling rich text on graph nodes. Large Language Models (LLMs), noted for their superior text understanding abilities, offer a solution for processing the text in graphs but face integration challenges due to their limitation for encoding graph structures and their computational complexities when dealing with extensive text in large neighborhoods of interconnected nodes. This paper introduces ``Hierarchical Compression'' (HiCom), a novel method to align the capabilities of LLMs with the structure of text-rich graphs. HiCom processes text in a node's neighborhood in a structured manner by organizing the extensive textual information into a more manageable hierarchy and compressing node text step by step. Therefore, HiCom not only preserves the contextual richness of the text but also addresses the computational challenges of LLMs, which presents an advancement in integrating the text processing power of LLMs with the structural complexities of text-rich graphs. Empirical results show that HiCom can outperform both GNNs and LLM backbones for node classification on e-commerce and citation graphs. HiCom is especially effective for nodes from a dense region in a graph, where it achieves a 3.48% average performance improvement on five datasets while being more efficient than LLM backbones.

Xiang Song, Runjie Ma, Jiahang Li et al.

Graph Neural Networks (GNNs) have shown success in learning from graph structured data containing node/edge feature information, with application to social networks, recommendation, fraud detection and knowledge graph reasoning. In this regard, various strategies have been proposed in the past to improve the expressiveness of GNNs. For example, one straightforward option is to simply increase the parameter size by either expanding the hid-den dimension or increasing the number of GNN layers. However, wider hidden layers can easily lead to overfitting, and incrementally adding more GNN layers can potentially result in over-smoothing.In this paper, we present a model-agnostic methodology, namely Network In Graph Neural Network (NGNN ), that allows arbitrary GNN models to increase their model capacity by making the model deeper. However, instead of adding or widening GNN layers, NGNN deepens a GNN model by inserting non-linear feedforward neural network layer(s) within each GNN layer. An analysis of NGNN as applied to a GraphSage base GNN on ogbn-products data demonstrate that it can keep the model stable against either node feature or graph structure perturbations. Furthermore, wide-ranging evaluation results on both node classification and link prediction tasks show that NGNN works reliably across diverse GNN architectures.For instance, it improves the test accuracy of GraphSage on the ogbn-products by 1.6% and improves the hits@100 score of SEAL on ogbl-ppa by 7.08% and the hits@20 score of GraphSage+Edge-Attr on ogbl-ppi by 6.22%. And at the time of this submission, it achieved two first places on the OGB link prediction leaderboard.

Seung Won Min, Kun Wu, Mert Hidayetoğlu et al.

Graph Neural Networks (GNNs) have shown success in learning from graph-structured data, with applications to fraud detection, recommendation, and knowledge graph reasoning. However, training GNN efficiently is challenging because: 1) GPU memory capacity is limited and can be insufficient for large datasets, and 2) the graph-based data structure causes irregular data access patterns. In this work, we provide a method to statistical analyze and identify more frequently accessed data ahead of GNN training. Our data tiering method not only utilizes the structure of input graph, but also an insight gained from actual GNN training process to achieve a higher prediction result. With our data tiering method, we additionally provide a new data placement and access strategy to further minimize the CPU-GPU communication overhead. We also take into account of multi-GPU GNN training as well and we demonstrate the effectiveness of our strategy in a multi-GPU system. The evaluation results show that our work reduces CPU-GPU traffic by 87-95% and improves the training speed of GNN over the existing solutions by 1.6-2.1x on graphs with hundreds of millions of nodes and billions of edges.

Colby Wise, Vassilis N. Ioannidis, Miguel Romero Calvo et al.

The coronavirus disease (COVID-19) has claimed the lives of over 350,000 people and infected more than 6 million people worldwide. Several search engines have surfaced to provide researchers with additional tools to find and retrieve information from the rapidly growing corpora on COVID-19. These engines lack extraction and visualization tools necessary to retrieve and interpret complex relations inherent to scientific literature. Moreover, because these engines mainly rely upon semantic information, their ability to capture complex global relationships across documents is limited, which reduces the quality of similarity-based article recommendations for users. In this work, we present the COVID-19 Knowledge Graph (CKG), a heterogeneous graph for extracting and visualizing complex relationships between COVID-19 scientific articles. The CKG combines semantic information with document topological information for the application of similar document retrieval. The CKG is constructed using the latent schema of the data, and then enriched with biomedical entity information extracted from the unstructured text of articles using scalable AWS technologies to form relations in the graph. Finally, we propose a document similarity engine that leverages low-dimensional graph embeddings from the CKG with semantic embeddings for similar article retrieval. Analysis demonstrates the quality of relationships in the CKG and shows that it can be used to uncover meaningful information in COVID-19 scientific articles. The CKG helps power www.cord19.aws and is publicly available.

Xiangxiang Zeng, Xiang Song, Tengfei Ma et al.

There have been more than 850,000 confirmed cases and over 48,000 deaths from the human coronavirus disease 2019 (COVID-19) pandemic, caused by novel severe acute respiratory syndrome coronavirus (SARS-CoV-2), in the United States alone. However, there are currently no proven effective medications against COVID-19. Drug repurposing offers a promising way for the development of prevention and treatment strategies for COVID-19. This study reports an integrative, network-based deep learning methodology to identify repurposable drugs for COVID-19 (termed CoV-KGE). Specifically, we built a comprehensive knowledge graph that includes 15 million edges across 39 types of relationships connecting drugs, diseases, genes, pathways, and expressions, from a large scientific corpus of 24 million PubMed publications. Using Amazon AWS computing resources, we identified 41 repurposable drugs (including indomethacin, toremifene and niclosamide) whose therapeutic association with COVID-19 were validated by transcriptomic and proteomic data in SARS-CoV-2 infected human cells and data from ongoing clinical trials. While this study, by no means recommends specific drugs, it demonstrates a powerful deep learning methodology to prioritize existing drugs for further investigation, which holds the potential of accelerating therapeutic development for COVID-19.

Biao Yang, Guocheng Yan, Pin Wang et al.

Pedestrian trajectory prediction in dynamic scenes remains a challenging and critical problem in numerous applications, such as self-driving cars and socially aware robots. Challenges concentrate on capturing pedestrians' motion patterns and social interactions, as well as handling the future uncertainties. Recent studies focus on modeling pedestrians' motion patterns with recurrent neural networks, capturing social interactions with pooling-based or graph-based methods, and handling future uncertainties by using random Gaussian noise as the latent variable. However, they do not integrate specific obstacle avoidance experience (OAE) that may improve prediction performance. For example, pedestrians' future trajectories are always influenced by others in front. Here we propose GTPPO (Graph-based Trajectory Predictor with Pseudo Oracle), an encoder-decoder-based method conditioned on pedestrians' future behaviors. Pedestrians' motion patterns are encoded with a long short-term memory unit, which introduces the temporal attention to highlight specific time steps. Their interactions are captured by a graph-based attention mechanism, which draws OAE into the data-driven learning process of graph attention. Future uncertainties are handled by generating multi-modal outputs with an informative latent variable. Such a variable is generated by a novel pseudo oracle predictor, which minimizes the knowledge gap between historical and ground-truth trajectories. Finally, the GTPPO is evaluated on ETH, UCY and Stanford Drone datasets, and the results demonstrate state-of-the-art performance. Besides, the qualitative evaluations show successful cases of handling sudden motion changes in the future. Such findings indicate that GTPPO can peek into the future.

Minjie Wang, Da Zheng, Zihao Ye et al.

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.