Anomaly detection in dynamic graphs is a critical area of research that focuses on identifying abnormal components within evolving graph structures that deviate significantly from typical patterns. Despite advancements in traditional temporal pattern mining and deep learning techniques, a comprehensive benchmarking framework for Dynamic Graph Anomaly Detection (DyGAD) has been lacking. To address this gap, we introduce BAG, the first comprehensive benchmark specifically designed for anomaly detection on dynamic graphs. BAG enables extensive evaluation of 25 leading DyGAD models, covering both classical approaches and advanced Dynamic Graph Neural Networks (DGNNs), across 10 diverse real-world datasets that include both synthetic and naturally occurring anomalies. The framework supports evaluations at both the edge and node levels, offering a robust tool to advance DyGAD research. Our main finding is that Continuous-time Dynamic Graph (CTDG) models demonstrate superior performance and potential in detecting anomalies in dynamic graph edges, compared to Discrete-time Dynamic Graph (DTDG) models. Furthermore, the results reveal that existing methods are less effective at detecting organic anomalies, primarily due to the presence of temporal anomalies and highly imbalanced samples. The proposed BAG benchmark significantly enhances the evaluation of DyGAD methods by improving dataset selection, metric application, and model training. Moreover, BAG supports reproducibility and further exploration in this field by integrating all models, datasets, and evaluation protocols into an open-source repository.

Accurate medical time series (MedTS) classification is essential for effective clinical diagnosis, yet remains challenging due to complex multi-channel temporal dependencies, information redundancy, and label scarcity. While transformer-based models have shown promise in time series analysis, most are designed for forecasting tasks and fail to fully exploit the unique characteristics of MedTS. In this paper, we introduce MedSpaformer, a transformer-based framework tailored for MedTS classification. It incorporates a sparse token-based dual-attention mechanism that enables global context modeling and token sparsification, allowing dynamic feature refinement by focusing on informative tokens while reducing redundancy. This mechanism is integrated into a multi-granularity cross-channel encoding scheme to capture intra- and inter-granularity temporal dependencies and inter-channel correlations, enabling progressive refinement of task-relevant patterns in medical signals. The sparsification design allows our model to flexibly accommodate inputs with variable lengths and channel dimensions. We also introduce an adaptive label encoder to extract label semantics and address cross-dataset label space misalignment. Together, these components enhance the model’s transferability across heterogeneous medical datasets, which helps alleviate the challenge of label scarcity. Our model outperforms 13 baselines across 7 medical datasets under supervised learning. It also excels in few-shot learning and demonstrates zero-shot capability in both in-domain and cross-domain diagnostics. These results highlight MedSpaformer's robustness and its potential as a unified solution for MedTS classification across diverse settings.

Accurate channel prediction is crucial for high-speed railway communications, especially in the 5G/6G era. Existing single-modality methods struggle to capture the intricate temporal and environmental dynamics, leading to suboptimal performance. To address this, we propose ChannelMTS, a novel multi-modal time-series framework that integrates both channel and environmental information to enhance prediction accuracy. First, ChannelMTS represents environmental conditions as snapshots, which are subsequently enhanced by a retrieval-augmented statistical channel module and embedded into an environmental time-series space using a transformer. Then, it aligns the channel and environmental time-series distributions to reduce the modality disparity. Finally, it adaptively fuses both modalities to achieve accurate channel prediction. This design can effectively leverage the complementary strengths of both modalities to enrich single-modality channel time series. Extensive experiments on real-world channel datasets show that ChannelMTS consistently outperforms state-of-the-art baselines. Moreover, online A/B testing reveals a significant 70%-90% performance improvement, and real-world deployment confirms its practical value.

Recently, Graph Foundation Models (GFMs) have emerged as a central focus in the field of graph learning due to their strong generalizability to various unseen graphs. However, existing GFMs typically work under the homophily assumption, and the exploration of universality on heterophilic graphs is still in its early stages. In fact, even in homophilic graphs, there exists limited yet informative heterophilic information that is not fully exploited by current GFMs. Moreover, due to the requirement for universality, the heterophily issue faced by GFMs is more challenging than in classical graph learning, as it requires training a single model to adapt to varying structures, features, and tasks. Classic heterophilic graph learning methods primarily based on the node-level homophily or heterophily. However, we highlight that homophily and heterophily exist not only at the node semantic level, but also at a finer granularity across individual feature dimensions. This finding enables GFMs to adapt to heterophilic graphs and better utilize the small amount of heterophilic information in homophilic graphs. Based on this, we propose Topology-aware Feature Sorting Graph Foundation Model (TFSGFM), which employs a feature-level topology-aware sorting strategy and a dual-channel graph neural network framework, enabling unified modeling of both feature and structure. Extensive experiments demonstrate the strong generalizability of TFSGFM. The source code is available at https://github.com/hedongxiao-tju/TFSGFM.

Graph Retrieval-Augmented Generation (GraphRAG) has shown great effectiveness in enhancing the reasoning abilities of Large Language Models (LLMs) by leveraging graph structures for knowledge representation and modeling complex real-world relationships. However, existing GraphRAG methods still face significant bottlenecks when handling complex problems that require multi-hop reasoning, as their query and retrieval phases are largely based on pre-defined heuristics and do not fully utilize the reasoning potentials of LLMs. To address this problem, we propose GraphRAG-R1, an adaptive GraphRAG framework by training LLMs with process-constrained outcome-based reinforcement learning (RL) to enhance the multi-hop reasoning ability. Our method can decompose complex problems, autonomously invoke retrieval tools to acquire necessary information, and perform effective reasoning. Specifically, we utilize a modified version of Group Relative Policy Optimization (GRPO) that supports rollout-with-thinking capability to train the model. Next, we design two process-constrained reward functions. To handle the shallow retrieval problem, we design a Progressive Retrieval Attenuation (PRA) reward to encourage essential retrievals. Then, to handle the over-thinking problem, we design a Cost-Aware F1 (CAF) reward to balance the model performance with computational costs. We further design a phase-dependent training strategy, containing three training stages corresponding to cold start and these two rewards. These stages empower GraphRAG with format following, behavior shaping, and smartness optimization abilities, respectively. Lastly, our method adopts a hybrid graph-textual retrieval to improve the reasoning capacity. Extensive experimental results demonstrate that GraphRAG-R1 significantly boosts LLM capabilities in solving complex reasoning problems compared to state-of-the-art GraphRAG methods on both in-domain and out-of-domain datasets. Furthermore, our framework can be flexibly integrated with various existing retrieval methods, consistently delivering performance improvements.

Large Language Models (LLMs) have advanced rapidly but face significant memory demands.While quantization could alleviate the memory-bound issue, current methods typically require lengthy training to recover accuracy under low bit width.In that circumstance, deployment across scenarios with different resource constraints necessitates repeated training, amplifying the issue of protracted training.It is beneficial to train a once-for-all (OFA) supernet capable of offering optimal subnets for downstream applications.To extend the oncefor-all setting to LLMs, we decouple the shared weights to mitigate the interference and integrate Low-Rank adapters to enhance training efficiency.Furthermore, it is observed that there is an imbalance in the allocation of training resources due to traditional uniform sampling.A non-parametric scheduler is introduced to adjust the sampling rate for each quantization configuration, thereby achieving a more balanced allocation among subnets with varying demands.We validate the approach on LLaMA families and Mistral on downstream evaluation, demonstrating high performance while significantly reducing deployment time faced with multiple scenarios.1

Recent studies have demonstrated the effectiveness of LLM test-time scaling. However, existing approaches to incentivize LLMs’ deep thinking abilities generally require large-scale data or significant training efforts. Meanwhile, it remains unclear how to improve the thinking abilities of less powerful base models. In this work, we introduce S^2R, an efficient framework that enhances LLM reasoning by teaching models to self-verify and self-correct during inference. Specifically, we first initialize LLMs with iterative self-verification and self-correction behaviors through supervised fine-tuning on carefully curated data. The self-verification and self-correction skills are then further strengthened by outcome-level and process-level reinforcement learning with minimized resource requirements. Our results demonstrate that, with only 3.1k behavior initialization samples, Qwen2.5-math-7B achieves an accuracy improvement from 51.0% to 81.6%, outperforming models trained on an equivalent amount of long-CoT distilled data. We also discuss the effect of different RL strategies on enhancing LLMs’ deep reasoning. Extensive experiments and analysis based on three base models across both in-domain and out-of-domain benchmarks validate the effectiveness of S^2R.

Large Language Models (LLMs) have shown remarkable capabilities in knowledge-intensive tasks, while they remain vulnerable when encountering misinformation. Existing studies have explored the role of LLMs in combating misinformation, but there is still a lack of fine-grained analysis on the specific aspects and extent to which LLMs are influenced by misinformation. To bridge this gap, we present MISBENCH, the current largest and most comprehensive benchmark for evaluating LLMs' behavior and knowledge preference toward misinformation. MISBENCH consists of 10,346,712 pieces of misinformation, which uniquely considers both knowledge-based conflicts and stylistic variations in misinformation. Empirical results reveal that while LLMs demonstrate comparable abilities in discerning misinformation, they still remain susceptible to knowledge conflicts and stylistic variations. Based on these findings, we further propose a novel approach called Reconstruct to Discriminate (RtD) to strengthen LLMs' ability to detect misinformation. Our study provides valuable insights into LLMs' interactions with misinformation, and we believe MISBENCH can serve as an effective benchmark for evaluating LLM-based detectors and enhancing their reliability in real-world applications. Codes and data are available at: https://github.com/GKNL/MisBench.

Existing retrieval-based methods have made significant strides in maintaining long-term conversations. However, these approaches face challenges in memory database management and accurate memory retrieval, hindering their efficacy in dynamic, real-world interactions. This study introduces a novel framework, COmpressive Memory-Enhanced Dialogue sYstems (COMEDY), which eschews traditional retrieval modules and memory databases. Instead, COMEDY adopts a “One-for-All” approach, utilizing a single language model to manage memory generation, compression, and response generation. Central to this framework is the concept of compressive memory, which integrates session-specific summaries, user-bot dynamics, and past events into a concise memory format. To support COMEDY, we collect the biggest Chinese long-term conversation dataset, Dolphin, derived from real user-chatbot interactions. Comparative evaluations demonstrate COMEDY’s superiority over traditional retrieval-based methods in producing more nuanced and human-like conversational experiences.

In the practical use of graph databases, storing graphs separately enhances maintainability, while integrating them into a unified graph facilitates advanced analytics. To address these dual needs, we present a GQL-compatible framework for creating graph views across multiple property graphs. Leveraging insights from commercial graph database environments and user-driven requirements, we identify two key graph transformations—merging and expansion—that significantly boost query efficiency. By incorporating these transformations into view generation, we effectively minimize redundant queries. Furthermore, we streamline view creation through implicit edge creation and automated property merging. To ensure views meet user expectations before full generation, we introduce a preview feature that uses sampling to effectively represent the graph structure. We assess the performance of GalaxyView across diverse workloads, with comprehensive experiments on real-world graphs demonstrating significant improvements in query performance and operational efficiency.

Powder X-ray diffraction (XRD) patterns are highly effective for crystal identification and play a pivotal role in materials discovery. While machine learning (ML) has advanced the analysis of powder XRD patterns, progress has been constrained by the limited availability of training data and established benchmarks. To address this, we introduce SimXRD, the largest open-source simulated XRD pattern dataset to date, aimed at accelerating the development of crystallographic informatics. We developed a novel XRD simulation method that incorporates comprehensive physical interactions, resulting in a high-fidelity database. SimXRD comprises 4,065,346 simulated powder XRD patterns, representing 119,569 unique crystal structures under 33 simulated conditions that reflect real-world variations. We benchmark 21 sequence models in both in-library and out-of-library scenarios and analyze the impact of class imbalance in long-tailed crystal label distributions. Remarkably, we find that: (1) current neural networks struggle with classifying low-frequency crystals, particularly in out-of-library situations; (2) models trained on SimXRD can generalize to real experimental data.

Accurate Subseasonal-to-Seasonal (S2S) climate forecasting is pivotal for decision-making including agriculture planning and disaster preparedness but is known to be challenging due to its chaotic nature. Although recent data-driven models have shown promising results, their performance is limited by inadequate consideration of geometric inductive biases. Usually, they treat the spherical weather data as planar images, resulting in an inaccurate representation of locations and spatial relations. In this work, we propose the geometric-inspired Circular Transformer (CirT) to model the cyclic characteristic of the graticule, consisting of two key designs: (1) Decomposing the weather data by latitude into circular patches that serve as input tokens to the Transformer; (2) Leveraging Fourier transform in self-attention to capture the global information and model the spatial periodicity. Extensive experiments on the Earth Reanalysis 5 (ERA5) reanalysis dataset demonstrate our model yields a significant improvement over the advanced data-driven models, including PanguWeather and GraphCast, as well as skillful ECMWF systems. Additionally, we empirically show the effectiveness of our model designs and high-quality prediction over spatial and temporal dimensions.

Exploring chemical space to find novel molecules that simultaneously satisfy multiple properties is crucial in drug discovery. However, existing methods often struggle with trading off multiple properties due to the conflicting or correlated nature of chemical properties. To tackle this issue, we introduce InversionGNN framework, an effective yet sample-efficient dual-path graph neural network (GNN) for multi-objective drug discovery. In the direct prediction path of InversionGNN, we train the model for multi-property prediction to acquire knowledge of the optimal combination of functional groups. Then the learned chemical knowledge helps the inversion generation path to generate molecules with required properties. In order to decode the complex knowledge of multiple properties in the inversion path, we propose a gradient-based Pareto search method to balance conflicting properties and generate Pareto optimal molecules. Additionally, InversionGNN is able to search the full Pareto front approximately in discrete chemical space. Comprehensive experimental evaluations show that InversionGNN is both effective and sample-efficient in various discrete multi-objective settings including drug discovery.

The ``arms race'' of Large Language Models (LLMs) demands new benchmarks to examine their progresses. In this paper, we introduce GraphArena, a benchmarking tool designed to evaluate LLMs on real-world graph computational problems. It offers a suite of four polynomial-time tasks (e.g., Shortest Distance) and six NP-complete challenges (e.g., Traveling Salesman Problem). GraphArena features a rigorous evaluation framework that classifies LLM outputs as correct, suboptimal (feasible but not optimal), hallucinatory (properly formatted but infeasible), or missing. Evaluation of over 10 LLMs reveals that even top-performing LLMs struggle with larger, more complex graph problems and exhibit hallucination issues. We further explore four potential solutions to address this issue and improve LLMs on graph computation, including chain-of-thought prompting, instruction tuning, code writing, and scaling test-time compute, each demonstrating unique strengths and limitations. GraphArena complements the existing LLM benchmarks and is open-sourced at https://github.com/squareRoot3/GraphArena.

Circuit discovery has recently attracted attention as a potential research direction to explain the non-trivial behaviors of language models. It aims to find the computational subgraphs, also known as circuits, within the model that are responsible for solving specific tasks. However, most existing studies overlook the holistic nature of these circuits and require designing specific corrupted activations for different tasks, which is inaccurate and inefficient. In this work, we propose an end-to-end approach based on the principle of Information Bottleneck, called IBCircuit, to holistically identify informative circuits. In contrast to traditional causal interventions, IBCircuit is an optimization framework for holistic circuit discovery and can be applied to any given task without tediously corrupted activation design. In both the Indirect Object Identification (IOI) and Greater-Than tasks, IBCircuit identifies more faithful and minimal circuits in terms of critical node components and edge components compared to recent related work.

The recent rapid advancements in language models (LMs) have garnered attention in medical time series-text multimodal learning. However, existing contrastive learning-based and prompt-based LM approaches tend to be biased, often assigning a primary role to time series modality while treating text modality as secondary. We classify these approaches under a temporal-primary paradigm, which may overlook the unique and critical task-relevant information embedded in text modality like clinical reports, thus failing to fully leverage mutual benefits and complementarity of different modalities. To fill this gap, we propose a novel textual-temporal multimodal learning paradigm that enables either modality to serve as the primary while being enhanced by the other, thereby effectively capturing modality-specific information and fostering cross-modal interaction. In specific, we design MedualTime, a language model composed of dual adapters to implement temporal-primary and textual-primary modeling simultaneously. Within each adapter, lightweight adaptation tokens are injected into the top layers of LM to encourage high-level modality fusion. The shared LM pipeline by dual adapters not only achieves adapter alignment but also enables efficient fine-tuning, reducing computational resources. Empirically, MedualTime demonstrates superior performance on medical data, achieving notable improvements of 8% accuracy and 12% F1 in supervised settings. Furthermore, MedualTime's transferability is validated by few-shot transfer experiments from coarse-grained to fine-grained medical data.

Recently, Graph Foundation Models (GFMs) have emerged as a significant research topic in graph machine learning. Compared with traditional graph neural networks, GFMs demonstrate impressive zero-shot generalization across different domains and tasks through large-scale pre-training on extensive and diverse graph data. Despite the initial success of pre-training, existing GFMs face challenges such as extreme time consumption and the presence of redundancy and noise in pre-training data. To alleviate these issues, we present the first exploration of data-centric GFM, which aims to optimize pre-training data (i.e., a set of subgraphs) to establish a more efficient GFM while maintaining robust performance across various downstream tasks. We propose DCGFM, a plug-and-play approach for Data-Centric GFM that incorporates the idea of data pruning to remove redundant and less informative subgraphs from the pre-training data, thereby improving both efficiency and effectiveness. Specifically, DCGFM consists of two components: (1) a model-agnostic hard pruning module that filters out subgraphs with lower informativity scores by considering both the semantics and structures of subgraphs; and (2) a model-aware soft pruning module that dynamically prunes subgraphs with lower loss values in each pre-training epoch with a gradient rescaling strategy. Extensive experiments on representative GFM backbones demonstrate DCGFM's efficiency and effectiveness. Remarkably, DCGFM achieves even better performance using only 30% of the pre-training data. Codes and data are available at https://github.com/Yuhan1i/DCGFM.

Accurate weather forecasting on Subseasonal-to-Seasonal (S2S) timescale is critical to human society such as agriculture planning and extreme weather preparation. Although data-driven models have become alternatives to computationally intensive Numerical Weather Prediction (NWP) systems, existing Transformer-based approaches suffer from biases due to planar projections distorting the spherical geometry and inadequate handling of vector-scalar variable interactions (e.g., wind velocity vs. temperature). To address these limitations, we propose a graph-based Equivariant and Invariant Message Passing (EIMP) framework that directly processes spherical grid data. It maintains SO(3) equivariant embeddings for vector data and SO(3) invariant embeddings for scalar data, which are interacted by a shared invariant message embedding. Guaranteed equivariant and invariant message aggregation functions are proposed to update embeddings under strict symmetry constraints. Extensive experiments on the Earth Reanalysis 5 (ERA5) reanalysis dataset of 41 years demonstrate the proposed model achieves significant improvement over advanced data-driven models and skillful numerical ECMWF systems. Additionally, we empirically show that EIMP demonstrates geometrically superior predictions and conduct ablation studies to validate the efficacy of its design.

The LifeTime Value (LTV) prediction, which endeavors to forecast the cumulative purchase contribution of a user to a particular item, remains a vital challenge that advertisers are keen to resolve. A precise LTV prediction system enhances the alignment of user interests with meticulously designed advertisements, thereby generating substantial profits for advertisers. Nonetheless, this issue is complicated by the paucity of data typically observed in real-world advertising scenarios. The purchase rate among registered users is often as critically low as 0.1%, resulting in a dataset where the majority of users make only several purchases. Consequently, there is insufficient supervisory signal for effectively training the LTV prediction model. An additional challenge emerges from the interdependencies among tasks with high correlation. It is a common practice to estimate a user's contribution to a game over a specified temporal interval. Varying the lengths of these intervals corresponds to distinct predictive tasks, which are highly correlated. For instance, predictions over a 7-day period are heavily reliant on forecasts made over a 3-day period, where exceptional cases can adversely affect the accuracy of both tasks. In order to comprehensively address the aforementioned challenges, we introduce an innovative framework denoted as Graph-Represented Pareto-Optimal LifeTime Value prediction (GRePO-LTV). Graph representation learning is initially employed to address the issue of data scarcity. Subsequently, Pareto-Optimization is utilized to manage the interdependence of prediction tasks. Our method is evaluated using a proprietary offline mini-game recommendation dataset in conjunction with an online A/B test. The implementation of our method results in a significant enhancement within the offline dataset. Moreover, the A/B test demonstrates encouraging outcomes, increasing average Gross Merchandise Value (GMV) by 8.4%.

Despite significant advancements in Large Language Models (LLMs), developing advanced reasoning capabilities in LLMs remains a key challenge. Process Reward Models (PRMs) have demonstrated exceptional promise in enhancing reasoning by providing step-wise feedback, particularly in the context of mathematical reasoning. However, their application to broader reasoning domains remains understudied, largely due to the high costs associated with manually creating step-level supervision. In this work, we explore the potential of PRMs in graph reasoning problems - a domain that demands sophisticated multi-step reasoning and offers opportunities for automated step-level data generation using established graph algorithms. We introduce GraphSilo, the largest dataset for graph reasoning problems with fine-grained step-wise label, built using automated Task-oriented Trajectories and Monte Carlo Tree Search (MCTS) to generate detailed reasoning steps with step-wise labels. Building upon this dataset, we train GraphPRM, the first PRM designed for graph reasoning problems, and evaluate its effectiveness in two key settings: inference-time scaling and reinforcement learning via Direct Preference Optimization (DPO). Experimental results show that GraphPRM significantly improves LLM performance across 13 graph reasoning tasks, delivering a 9% gain for Qwen2.5-7B and demonstrating transferability to new graph reasoning datasets and new reasoning domains like mathematical problem-solving. Notably, GraphPRM enhances LLM performance on GSM8K and MATH500, underscoring the cross-domain applicability of graph-based reasoning rewards. Our findings highlight the potential of PRMs in advancing reasoning across diverse domains, paving the way for more versatile and effective LLMs.

Battery Life Prediction (BLP), which relies on time series data produced by battery degradation tests, is crucial for battery utilization, optimization, and production. Despite impressive advancements, this research area faces three key challenges. Firstly, the limited size of existing datasets impedes insights into modern battery life data. Secondly, most datasets are restricted to small-capacity lithium-ion batteries tested under a narrow range of diversity in labs, raising concerns about the generalizability of findings. Thirdly, inconsistent and limited benchmarks across studies obscure the effectiveness of baselines and leave it unclear if models popular in other time series fields are effective for BLP. To address these challenges, we propose BatteryLife, a comprehensive dataset and benchmark for BLP. BatteryLife integrates 16 datasets, offering a 2.5 times sample size compared to the previous largest dataset, and provides the most diverse battery life resource with batteries from 8 formats, 59 chemical systems, 9 operating temperatures, and 421 charge/discharge protocols, including both laboratory and industrial tests. Notably, BatteryLife is the first to release battery life datasets of zinc-ion batteries, sodium-ion batteries, and industry-tested large-capacity lithium-ion batteries. With the comprehensive dataset, we revisit the effectiveness of baselines popular in this and other time series fields. Furthermore, we propose CyclePatch, a plug-in technique that can be employed in various neural networks. Extensive benchmarking of 18 methods reveals that models popular in other time series fields can be unsuitable for BLP, and CyclePatch consistently improves model performance establishing state-of-the-art benchmarks. Moreover, BatteryLife evaluates model performance across aging conditions and domains. BatteryLife is available at https://github.com/Ruifeng-Tan/BatteryLife.

To enhance the generalization ability of graph neural networks (GNNs) in learning and simulation physical dynamics, a series of equivariant GNNs have been developed to incorporate the symmetric inductive bias. However, the existing methods do not take into account the non-stationarity nature of physical dynamics, where the joint distribution changes over time. Moreover, previous approaches for modeling non-stationary time series typically involve normalizing the data, which disrupts the symmetric assumption inherent in physical dynamics. To model the non-stationary physical dynamics while preserving the symmetric inductive bias, we introduce a Non-Stationary Equivariant Graph Neural Network (NS-EGNN) to capture the non-stationarity in physical dynamics while preserving the symmetric property of the model. Specifically, NS-EGNN employs Fourier Transform on segments of physical dynamics to extract time-varying frequency information from the trajectories. It then uses the first and second-order differences to mitigate non-stationarity, followed by pooling for future predictions. Through capturing varying frequency characteristics and alleviate the linear and quadric trend in the raw physical dynamics, NS-EGNN better models the temporal dependencies in the physical dynamics. NS-EGNN has been applied on various types of physical dynamics, including molecular, motion and protein dynamics. In various scenario, NS-EGNN consistently surpasses the performance of existing state-of-the-art algorithms, underscoring its effectiveness. The implementation of NS-EGNN is available at https://github.com/MaojiWEN/NS-EGNN.

Graph neural networks have shown promising results in weather forecasting, which is critical for human activity such as agriculture planning and extreme weather preparation. However, most studies focus on finite and local areas for training, overlooking the influence of broader areas and limiting their ability to generalize effectively. Thus, in this work, we study global weather forecasting that is irregularly distributed and dynamically varying in practice, requiring the model to generalize to unobserved locations. To address such challenges, we propose a general Mesh Interpolation Graph Network (MIGN) that models the irregular weather station forecasting, consisting of two key designs: (1) learning spatially irregular data with regular mesh interpolation network to align the data; (2) leveraging parametric spherical harmonics location embedding to further enhance spatial generalization ability. Extensive experiments on an up-to-date observation dataset show that MIGN significantly outperforms existing data-driven models. Besides, we show that MIGN has spatial generalization ability, and is capable of generalizing to previously unseen stations.

In this work, we discover that causal inference provides a promising approach to capture heterophilic message-passing in Graph Neural Network (GNN). By leveraging cause-effect analysis, we can discern heterophilic edges based on asymmetric node dependency. The learned causal structure offers more accurate relationships among nodes. To reduce the computational complexity, we introduce intervention-based causal inference in graph learning. We first simplify causal analysis on graphs by formulating it as a structural learning model and define the optimization problem within the Bayesian scheme. We then present an analysis of decomposing the optimization target into a consistency penalty and a structure modification based on cause-effect relations. We then estimate this target by conditional entropy and present insights into how conditional entropy quantifies the heterophily. Accordingly, we propose CausalMP, a causal message-passing discovery network for heterophilic graph learning, that iteratively learns the explicit causal structure of input graphs. We conduct extensive experiments in both heterophilic and homophilic graph settings. The result demonstrates that the our model achieves superior link prediction performance. Training on causal structure can also enhance node representation in classification task across different base models.

Explainable recommendation has demonstrated significant advantages in informing users about the logic behind recommendations, thereby increasing system transparency, effectiveness, and trustworthiness. To provide personalized and interpretable explanations, existing works often combine the generation capabilities of large language models (LLMs) with collaborative filtering (CF) information. CF information extracted from the user-item interaction graph captures the user behaviors and preferences, which is crucial for providing informative explanations. However, due to the complexity of graph structure, effectively extracting the CF information from graphs still remains a challenge. Moreover, existing methods often struggle with the integration of extracted CF information with LLMs due to its implicit representation and the modality gap between graph structures and natural language explanations. To address these challenges, we propose G-Refer, a framework using Graph Retrieval-augmented large language models (LLMs) for explainable recommendation. Specifically, we first employ a hybrid graph retrieval mechanism to retrieve explicit CF signals from both structural and semantic perspectives. The retrieved CF information is explicitly formulated as human-understandable text by the proposed graph translation and accounts for the explanations generated by LLMs. To bridge the modality gap, we introduce knowledge pruning and retrieval-augmented fine-tuning to enhance the ability of LLMs to process and utilize the retrieved CF information to generate explanations. Extensive experiments show that G-Refer achieves superior performance compared with existing methods in both explainability and stability. Codes and data are available at https://github.com/Yuhan1i/G-Refer.

Graph databases play a pivotal role in the FinTech industry. However, existing graph benchmarks fail to capture the unique characteristics of financial datasets and workloads, rendering them inadequate for evaluating graph databases in financial scenarios. This paper presents the LDBC Financial Benchmark (FinBench) Transaction Workload, a novel benchmark that adopts a choke point-driven design methodology, emphasizing performance bottlenecks, and incorporates distinct features such as dataset skewness, edge multiplicity, temporal window filtering, recursive path filtering, read-write query patterns, and truncation on hub vertices. Key contributions include a scalable data generator that synthesizes datasets with financial-specific features, a parameter generator that leverages bucketed data statistics for runtime consistency across queries, and a scalable benchmark driver that biases query execution by time windows. Experimental evaluations on graph databases demonstrate the benchmark's capability to reveal novel choke points and provide insights into system performance in financial scenarios.

Graph Edit Distance (GED) is a widely recognized metric for measuring graph similarity, yet its NP-complete nature poses challenges for fast and accurate computation. This paper introduces FGWAlign, an Optimal Transport (OT)-based approach for graph alignment and GED computation. We take the first step to theoretically demonstrate and that computing GED can be transformed into optimizing a particular OT variant—the Fused Gromov-Wasserstein distance. Tailored to the GED problem structure, we further implement three key enhancements to the standard FGW solver: (1) a random exploration scheme to better locate the global optimum, (2) a diverse projection strategy for post-processing the transportation plan to escape local optima, and (3) a novel extension to accommodate multi-relational graphs with edge labels. With O (| V || E |) time complexity and O (| V | 2 ) space complexity, where | V | and | E | are the maximum number of nodes and edges between the two compared graphs, FGWAlign achieves a superior balance of efficiency, accuracy, and scalability. Empirical results show that, compared with 12 representative GED computation methods across different categories on 4 real-world graph datasets, FGWAlign reduces computation errors by over 80% and achieves 15–60× speedup. It also demonstrates promising resutls on downstream applications including labeled graph alignment and graph-level anomaly detection, highlighting its versatility. FGWAlign opens up promising avenues for future applications in graph data management.

Recently, generative models based on the diffusion process have emerged as a promising direction for automating the design of molecules. However, directly adding continuous Gaussian noise to discrete graphs leads to the problem that the generated data do not conform to the discrete graph data distribution in the training set. Current graph diffusion models either corrupt discrete data through a transition matrix or relax the discrete data to continuous space for the diffusion process. These approaches make it hard to perform extensible conditional generation, such as adapting to text-based conditions, due to the lack of embedding representations and require significant computation resources due to the diffusion process of the bond type matrix. This paper introduces the Hierarchical Graph Latent Diffusion Model (HGLDM), a novel variant of latent diffusion models that overcomes the problem of applying continuous diffusion models directly to discrete graph data. Meanwhile, based on the latent diffusion framework, HGLDM avoids the issues of computational consumption and lack of embeddings for extensible conditional generation. In addition, by comparing the HGLDM with its variant, the Graph Latent Diffusion Model (GLDM), which only has graph-level embeddings, we validate the advantage of the hierarchical graph structure for capturing the relationship between structure information and molecular properties. We evaluate the performance of our model through various conditional generation tasks, demonstrating its superior performance.

Data imputation is a crucial task due to the widespread occurrence of missing data. Many methods adopt a two-step approach: initially crafting a preliminary imputation (the "draft") and then refining it to produce the final missing data imputation result, commonly referred to as "draft-then-refine". In our study, we examine this prevalent strategy through the lens of graph Dirichlet energy. We observe that a basic "draft"imputation tends to decrease the Dirichlet energy. Therefore, a subsequent "refine"step is necessary to restore the overall energy balance. Existing refinement techniques, such as the Graph Convolutional Network (GCN), often result in further energy reduction. To address this, we introduce a new framework, the Graph Laplacian Pyramid Network (GLPN). GLPN incorporates a U-shaped autoencoder and residual networks to capture both global and local details effectively. Through extensive experiments on multiple real-world datasets, GLPN consistently outperforms state-of-the-art methods across three different missing data mechanisms. The code is available at https://github.com/liguanlue/GLPN.

Utilizing large language models (LLMs) for data augmentation has yielded encouraging results in mathematical reasoning.However, these approaches face constraints in problem diversity, potentially restricting them to indomain/distribution data generation.To this end, we propose ControlMath, an iterative method involving an equation-generator module and two LLM-based agents.The module creates diverse equations, which the Problem-Crafter agent then transforms into math word problems.The Reverse-Agent filters and selects high-quality data, adhering to the "less is more" principle, achieving better results with fewer data points.This approach enables the generation of diverse math problems, not limited to specific domains or distributions.As a result, we collect ControlMathQA, which involves 190k math word problems.Extensive results prove that combining our dataset with indomain datasets like GSM8K can help improve the model's mathematical ability to generalize, leading to improved performances both within and beyond specific domains.

Structure prediction of large protein complexes (a.k.a., protein multimer mod- elling, PMM) can be achieved through the one-by-one assembly using provided dimer structures and predicted docking paths. However, existing PMM methods struggle with vast search spaces and generalization challenges: (1) The assembly of a N -chain multimer can be depicted using graph structured data, with each chain represented as a node and assembly actions as edges. Thus the assembly graph can be arbitrary acyclic undirected connected graph, leading to the com- binatorial optimization space of N^(N −2) for the PMM problem. (2) Knowledge transfer in the PMM task is non-trivial. The gradually limited data availability as the chain number increases necessitates PMM models that can generalize across multimers of various chains. To address these challenges, we propose GAPN, a Generative Adversarial Policy Network powered by domain-specific rewards and adversarial loss through policy gradient for automatic PMM prediction. Specifi- cally, GAPN learns to efficiently search through the immense assembly space and optimize the direct docking reward through policy gradient. Importantly, we de- sign a adversarial reward function to enhance the receptive field of our model. In this way, GAPN will simultaneously focus on a specific batch of multimers and the global assembly rules learned from multimers with varying chain numbers. Empirically, we have achieved both significant accuracy (measured by RMSD and TM-Score) and efficiency improvements compared to leading complex mod- eling software. GAPN outperforms the state-of-the-art method (MoLPC) with up to 27% improvement in TM-Score, with a speed-up of 600×.

Understanding the 3D structures of protein multimers is crucial, as they play a vital role in regulating various cellular processes. It has been empirically confirmed that the multimer structure prediction (MSP) can be well handled in a step-wise assembly fashion using provided dimer structures and predicted protein-protein interactions (PPIs). However, due to the biological gap in the formation of dimers and larger multimers, directly applying PPI prediction techniques can often cause a poor generalization to the MSP task. To address this challenge, we aim to extend the PPI knowledge to multimers of different scales (i.e., chain numbers). Specifically, we propose PromptMSP, a pre-training and Prompt tuning framework for Multimer Structure Prediction. First, we tailor the source and target tasks for effective PPI knowledge learning and efficient inference, respectively. We design PPI-inspired prompt learning to narrow the gaps of two task formats and generalize the PPI knowledge to multimers of different scales. We provide a meta-learning strategy to learn a reliable initialization of the prompt model, enabling our prompting framework to effectively adapt to limited data for large-scale multimers. Empirically, we achieve both significant accuracy (RMSD and TM-Score) and efficiency improvements compared to advanced MSP models.

Graph Neural Networks (GNNs) with equivariant properties have emerged as powerful tools for modeling complex dynamics of multi-object physical systems. However, their generalization ability is limited by the inadequate consideration of physical inductive biases: (1) Existing studies overlook the continuity of transitions among system states, opting to employ several discrete transformation layers to learn the direct mapping between two adjacent states; (2) Most models only account for first-order velocity information, despite the fact that many physical systems are governed by second-order motion laws. To incorporate these inductive biases, we propose the Second-order Equivariant Graph Neural Ordinary Differential Equation (SEGNO). Specifically, we show how the second-order continuity can be incorporated into GNNs while maintaining the equivariant property. Furthermore, we offer theoretical insights into SEGNO, highlighting that it can learn a unique trajectory between adjacent states, which is crucial for model generalization. Additionally, we prove that the discrepancy between this learned trajectory of SEGNO and the true trajectory is bounded. Extensive experiments on complex dynamical systems including molecular dynamics and motion capture demonstrate that our model yields a significant improvement over the state-of-the-art baselines.

Low-rank adaptation (LoRA) has recently gained much interest in fine-tuning foundation models. It effectively reduces the number of trainable parameters by incorporating low-rank matrices $A$ and $B$ to represent the weight change, i.e., $\Delta W=BA$. Despite LoRA’s progress, it faces storage challenges when handling extensive customization adaptations or larger base models. In this work, we aim to further compress trainable parameters by enjoying the powerful expressiveness of the Fourier transform. Specifically, we introduce FourierFT, which treats $\Delta W$ as a matrix in the spatial domain and learns only a small fraction of its spectral coefficients. With the trained spectral coefficients, we implement the inverse discrete Fourier transform to recover $\Delta W$. Empirically, our FourierFT method shows comparable or better performance with fewer parameters than LoRA on various tasks, including natural language understanding, natural language generation, instruction tuning, and image classification. For example, when performing instruction tuning on the LLaMA2-7B model, FourierFT surpasses LoRA with only 0.064M trainable parameters, compared to LoRA’s 33.5M. Our code is released at this link.

Large language models (LLMs) have achieved impressive success across various domains, but their capability in understanding and resolving complex graph problems is less explored. To bridge this gap, we introduce GraphInstruct, a novel instruction-tuning dataset aimed at enabling language models to tackle a broad spectrum of graph problems through explicit reasoning paths. Utilizing GraphInstruct, we build GraphWiz, an open-source language model capable of solving various graph computational problems while generating clear reasoning processes. To further enhance the model's performance and reliability, we integrate the Direct Preference Optimization (DPO) framework within the graph problem-solving context. The improved model, GraphWiz-DPO, achieves an average accuracy of 65% across nine tasks with different complexity levels, surpassing GPT-4 which has an average accuracy of 43.8%. Our study also investigates the relationship between training data volume and model performance, emphasizing the risk of overfitting as data volume increases. Additionally, we explore the transferability of the proposed model across different tasks and datasets, demonstrating its robust zero-shot generalization capability. GraphWiz offers a new blueprint and valuable insights for developing LLMs specialized in graph reasoning and problem-solving.

With the development of foundation models such as large language models, zero-shot transfer learning has become increasingly significant. This is highlighted by the generative capabilities of NLP models like GPT-4, and the retrieval-based approaches of CV models like CLIP, both of which effectively bridge the gap between seen and unseen data. In the realm of graph learning, the continuous emergence of new graphs and the challenges of human labeling also amplify the necessity for zero-shot transfer learning, driving the exploration of approaches that can generalize across diverse graph data without necessitating dataset-specific and label-specific fine-tuning. In this study, we extend such paradigms to Zero-shot transferability in Graphs by introducing ZeroG, a new framework tailored to enable cross-dataset generalization. Addressing the inherent challenges such as feature misalignment, mismatched label spaces, and negative transfer, we leverage a language model to encode both node attributes and class semantics, ensuring consistent feature dimensions across datasets. We also propose a prompt-based subgraph sampling module that enriches the semantic information and structure information of extracted subgraphs using prompting nodes and neighborhood aggregation, respectively. We further adopt a lightweight fine-tuning strategy that reduces the risk of overfitting and maintains the zero-shot learning efficacy of the language model. The results underscore the effectiveness of our model in achieving significant cross-dataset zero-shot transferability, opening pathways for the development of graph foundation models.

Graph Neural Networks (GNNs) have achieved great success in Knowledge Graph Completion (KGC) by modelling how entities and relations interact in recent years. However, the explanation of the predicted facts has not caught the necessary attention. Proper explanations for the results of GNN-based KGC models increase model transparency and help researchers develop more reliable models. Existing practices for explaining KGC tasks rely on instance/subgraph-based approaches, while in some scenarios, paths can provide more user-friendly and interpretable explanations. Nonetheless, the methods for generating path-based explanations for KGs have not been well-explored. To address this gap, we propose Power-Link, the first path-based KGC explainer that explores GNN-based models. We design a novel simplified graph-powering technique, which enables the generation of path-based explanations with a fully parallelisable and memory-efficient training scheme. We further introduce three new metrics for quantitative evaluation of the explanations, together with a qualitative human evaluation. Extensive experiments demonstrate that Power-Link outperforms the SOTA baselines in interpretability, efficiency, and scalability. The code is available at https://github.com/OUTHIM/power-link

Graph plays a significant role in representing and analyzing complex relationships in real-world applications such as citation networks, social networks, and biological data. Graph intelligence is rapidly becoming a crucial aspect of understanding and exploiting the intricate interconnections within graph data. Recently, large language models (LLMs) and prompt learning techniques have pushed graph intelligence forward, outperforming traditional Graph Neural Network (GNN) pre-training methods and setting new benchmarks for performance. In this tutorial, we begin by offering a comprehensive review and analysis of existing methods that integrate LLMs with graphs. We introduce existing works based on a novel taxonomy that classifies them into three distinct categories according to the roles of LLMs in graph tasks: as enhancers, predictors, or alignment components. Secondly, we introduce a new learning method that utilizes prompting on graphs, offering substantial potential to enhance graph transfer capabilities across diverse tasks and domains. We discuss existing works on graph prompting within a unified framework and introduce our developed tool for executing a variety of graph prompting tasks. Additionally, we discuss the applications of combining Graphs, LLMs, and prompt learning across various tasks, such as urban computing, recommendation systems, and anomaly detection. This lecture-style tutorial is an extension of our original work published in IJCAI 2024[44] and arXiv[77] with the invitation of KDD24.

Large Language Models (LLMs) have revolutionized the fields of computer vision (CV) and natural language processing (NLP). One of the most notable advancements of LLMs is that a single model is trained on vast and diverse datasets spanning multiple domains -- a paradigm we term 'All in One'. This methodology empowers LLMs with super generalization capabilities, facilitating an encompassing comprehension of varied data distributions. Leveraging these capabilities, a single LLM demonstrates remarkable versatility across a variety of domains -- a paradigm we term 'One for All'. However, applying this idea to the graph field remains a formidable challenge, with cross-domain pretraining often resulting in negative transfer. This issue is particularly important in few-shot learning scenarios, where the paucity of training data necessitates the incorporation of external knowledge sources. In response to this challenge, we propose a novel approach called Graph COordinators for PrEtraining (GCOPE), that harnesses the underlying commonalities across diverse graph datasets to enhance few-shot learning. Our novel methodology involves a unification framework that amalgamates disparate graph datasets during the pretraining phase to distill and transfer meaningful knowledge to target tasks. Extensive experiments across multiple graph datasets demonstrate the superior efficacy of our approach. By successfully leveraging the synergistic potential of multiple graph datasets for pretraining, our work stands as a pioneering contribution to the realm of graph foundational model. Code available at https://github.com/cshhzhao/GCOPE.

Incorporating Euclidean symmetries (e.g. rotation equivariance) as inductive biases into graph neural networks has improved their generalization ability and data efficiency in unbounded physical dynamics modeling. However, in various scientific and engineering applications, the symmetries of dynamics are frequently discrete due to the boundary conditions. Thus, existing GNNs either over-look necessary symmetry, resulting in suboptimal representation ability, or impose excessive equivariance, which fails to generalize to unobserved symmetric dynamics. In this work, we propose a general Discrete Equivariant Graph Neural Network (DEGNN) that guarantees equivariance to a given discrete point group. Specifically, we show that such discrete equivariant message passing could be constructed by transforming geometric features into permutation-invariant embeddings. Through relaxing continuous equivariant constraints, DEGNN can employ more geometric feature combinations to approximate unobserved physical object interaction functions. Two implementation approaches of DEGNN are proposed based on ranking or pooling permutation-invariant functions. We apply DEGNN to various physical dynamics, ranging from particle, molecular, crowd to vehicle dynamics. In twenty scenarios, DEGNN significantly outperforms existing state-of-the-art approaches. Moreover, we show that DEGNN is data efficient, learning with less data, and can generalize across scenarios such as unobserved orientation.

The emergence of large language models (LLMs) has revolutionized the way we interact with graphs, leading to a new paradigm called GraphLLM. Despite the rapid development of GraphLLM methods in recent years, the progress and understanding of this field remain unclear due to the lack of a benchmark with consistent experimental protocols. To bridge this gap, we introduce GLBench, the first comprehensive benchmark for evaluating GraphLLM methods in both supervised and zero-shot scenarios. GLBench provides a fair and thorough evaluation of different categories of GraphLLM methods, along with traditional baselines such as graph neural networks. Through extensive experiments on a collection of real-world datasets with consistent data processing and splitting strategies, we have uncovered several key findings. Firstly, GraphLLM methods outperform traditional baselines in supervised settings, with LLM-as-enhancers showing the most robust performance. However, using LLMs as predictors is less effective and often leads to uncontrollable output issues. We also notice that no clear scaling laws exist for current GraphLLM methods. In addition, both structures and semantics are crucial for effective zero-shot transfer, and our proposed simple baseline can even outperform several models tailored for zero-shot scenarios. The data and code of the benchmark can be found at https://github.com/NineAbyss/GLBench.

The knowledge of protein interactions is crucial but challenging for drug discovery applications. This work focuses on protein interface prediction, which aims to determine whether a pair of residues from different proteins interact. Existing data-driven methods have made significant progress in effectively learning protein structures. Nevertheless, they overlook the conformational changes (i.e., flexibility) within proteins upon binding, leading to poor generalization ability. In this paper, we regard the protein flexibility as an attack on the trained model and aim to defend against it for improved generalization. To fulfill this purpose, we propose ATProt, an adversarial training framework for protein representations to robustly defend against the attack of protein flexibility. ATProt can theoretically guarantee protein representation stability under complicated protein flexibility. Experiments on various benchmarks demonstrate that ATProt consistently improves the performance for protein interface prediction. Moreover, our method demonstrates broad applicability, performing the best even when provided with testing structures from structure prediction models like ESMFold and AlphaFold2.

Graph Anomaly Detection (GAD) aims to identify uncommon, deviated, or suspicious objects within graph-structured data. Existing methods generally focus on a single graph object type (node, edge, graph, etc.) and often overlook the inherent connections among different object types of graph anomalies. For instance, a money laundering transaction might involve an abnormal account and the broader community it interacts with. To address this, we present UniGAD, the first unified framework for detecting anomalies at node, edge, and graph levels jointly. Specifically, we develop the Maximum Rayleigh Quotient Subgraph Sampler (MRQSampler) that unifies multi-level formats by transferring objects at each level into graph-level tasks on subgraphs. We theoretically prove that MRQSampler maximizes the accumulated spectral energy of subgraphs (i.e., the Rayleigh quotient) to preserve the most significant anomaly information. To further unify multi-level training, we introduce a novel GraphStitch Network to integrate information across different levels, adjust the amount of sharing required at each level, and harmonize conflicting training goals. Comprehensive experiments show that UniGAD outperforms both existing GAD methods specialized for a single task and graph prompt-based approaches for multiple tasks, while also providing robust zero-shot task transferability.

Delivering precise point and distributional forecasts across a spectrum of prediction horizons represents a significant and enduring challenge in the application of time-series forecasting within various industries.Prior research on developing deep learning models for time-series forecasting has often concentrated on isolated aspects, such as long-term point forecasting or short-term probabilistic estimations. This narrow focus may result in skewed methodological choices and hinder the adaptability of these models to uncharted scenarios.While there is a rising trend in developing universal forecasting models, a thorough understanding of their advantages and drawbacks, especially regarding essential forecasting needs like point and distributional forecasts across short and long horizons, is still lacking.In this paper, we present ProbTS, a benchmark tool designed as a unified platform to evaluate these fundamental forecasting needs and to conduct a rigorous comparative analysis of numerous cutting-edge studies from recent years.We dissect the distinctive data characteristics arising from disparate forecasting requirements and elucidate how these characteristics can skew methodological preferences in typical research trajectories, which often fail to fully accommodate essential forecasting needs.Building on this, we examine the latest models for universal time-series forecasting and discover that our analyses of methodological strengths and weaknesses are also applicable to these universal models.Finally, we outline the limitations inherent in current research and underscore several avenues for future exploration.

Numerous industrial sectors necessitate models capable of providing robust forecasts across various horizons. Despite the recent strides in crafting specific architectures for time-series forecasting and developing pre-trained universal models, a comprehensive examination of their capability in accommodating varied-horizon forecasting during inference is still lacking. This paper bridges this gap through the design and evaluation of the Elastic Time-Series Transformer (ElasTST). The ElasTST model incorporates a non-autoregressive design with placeholders and structured self-attention masks, warranting future outputs that are invariant to adjustments in inference horizons. A tunable version of rotary position embedding is also integrated into ElasTST to capture time-series-specific periods and enhance adaptability to different horizons. Additionally, ElasTST employs a multi-scale patch design, effectively integrating both fine-grained and coarse-grained information. During the training phase, ElasTST uses a horizon reweighting strategy that approximates the effect of random sampling across multiple horizons with a single fixed horizon setting. Through comprehensive experiments and comparisons with state-of-the-art time-series architectures and contemporary foundation models, we demonstrate the efficacy of ElasTST's unique design elements. Our findings position ElasTST as a robust solution for the practical necessity of varied-horizon forecasting.

Artificial general intelligence on graphs has shown significant advancements across various applications, yet the traditional `Pre-train & Fine-tune' paradigm faces inefficiencies and negative transfer issues, particularly in complex and few-shot settings. Graph prompt learning emerges as a promising alternative, leveraging lightweight prompts to manipulate data and fill the task gap by reformulating downstream tasks to the pretext. However, several critical challenges still remain: how to unify diverse graph prompt models, how to evaluate the quality of graph prompts, and to improve their usability for practical comparisons and selection. In response to these challenges, we introduce the first comprehensive benchmark for graph prompt learning. Our benchmark integrates SIX pre-training methods and FIVE state-of-the-art graph prompt techniques, evaluated across FIFTEEN diverse datasets to assess performance, flexibility, and efficiency. We also present 'ProG', an easy-to-use open-source library that streamlines the execution of various graph prompt models, facilitating objective evaluations. Additionally, we propose a unified framework that categorizes existing graph prompt methods into two main approaches: prompts as graphs and prompts as tokens. This framework enhances the applicability and comparison of graph prompt techniques. The code is available at: https://github.com/sheldonresearch/ProG.

Graph Anomaly Detection (GAD) is a technique used to identify abnormal nodes within graphs, finding applications in network security, fraud detection, social media spam detection, and various other domains. A common method for GAD is Graph Auto-Encoders (GAEs), which encode graph data into node representations and identify anomalies by assessing the reconstruction quality of the graphs based on these representations. However, existing GAE models are primarily optimized for direct link reconstruction, resulting in nodes connected in the graph being clustered in the latent space. As a result, they excel at detecting cluster-type structural anomalies but struggle with more complex structural anomalies that do not conform to clusters. To address this limitation, we propose a novel solution called GAD-NR, a new variant of GAE that incorporates neighborhood reconstruction for graph anomaly detection. GAD-NR aims to reconstruct the entire neighborhood of a node, encompassing the local structure, self-attributes, and neighbor attributes, based on the corresponding node representation. By comparing the neighborhood reconstruction loss between anomalous nodes and normal nodes, GAD-NR can effectively detect any anomalies. Extensive experimentation conducted on six real-world datasets validates the effectiveness of GAD-NR, showcasing significant improvements (by up to 30%↑ in AUC) over state-of-the-art competitors. The source code for GAD-NR is openly available. Importantly, the comparative analysis reveals that the existing methods perform well only in detecting one or two types of anomalies out of the three types studied. In contrast, GAD-NR excels at detecting all three types of anomalies across the datasets, demonstrating its comprehensive anomaly detection capabilities.

Anomaly detection (AD) plays a pivotal role in numerous web-based applications, including malware detection, anti-money laundering, device failure detection, and network fault analysis. Most methods, which rely on unsupervised learning, are hard to reach satisfactory detection accuracy due to the lack of labels. Weakly Supervised Anomaly Detection (WSAD) has been introduced with a limited number of labeled anomaly samples to enhance model performance. Nevertheless, it is still challenging for models, trained on an inadequate amount of labeled data, to generalize to unseen anomalies. In this paper, we introduce a novel framework, Knowledge-Data Alignment (KDAlign), to integrate rule knowledge, typically summarized by human experts, to supplement the limited labeled data. Specifically, we transpose these rules into the knowledge space and subsequently recast the incorporation of knowledge as the alignment of knowledge and data. To facilitate this alignment, we employ the Optimal Transport (OT) technique. We then incorporate the OT distance as an additional loss term to the original objective function of WSAD methodologies. Comprehensive experimental results on five real-world datasets demonstrate that our proposed KDAlign framework markedly surpasses its state-of-the-art counterparts, achieving superior performance across various anomaly types. Our codes are released at https://github.com/cshhzhao/KDAlign.

We introduce Galaxybase, a native distributed graph database that addresses the increasing demands for processing large volumes of graph data in diverse industries like finance, manufacturing, and government. Designed to handle the requirements of both transactional and analytical workloads, Galaxybase stands out with its novel data storage and transaction mechanisms. At its core, Galaxybase utilizes a Log-Structured Adjacency List coupled with an Edge Page structure, optimizing read-write operations across a spectrum of tasks such as graph traversals and single edge queries. A notable aspect of Galaxybase is its execution of custom distributed transaction modes tailored for HTAP transactions, allowing for the facilitation of bidirectional and interactive transactions. It ensures data integrity and minimal latency while enabling simultaneous processing of OLTP and OLAP workloads without blocking. Experimental results show that Galaxybase achieves high throughput and low latency in both OLTP and OLAP workloads, across various graph query scenarios and resource conditions. Galaxybase has been deployed in leading banks, education, telecommunication and energy sectors in China, consistently maintaining robust performance for HTAP workloads over the years.

Graph self-supervised learning (SSL) has been vastly employed to learn representations from unlabeled graphs. Existing methods can be roughly divided into predictive learning and contrastive learning, where the latter one attracts more research attention with better empirical performance. We argue that, however, predictive models weaponed with powerful decoder could achieve comparable or even better representation power than contrastive models. In this work, we propose a Wiener Graph Deconvolutional Network (WGDN), an augmentation-adaptive decoder empowered by graph wiener filter to perform information reconstruction. Theoretical analysis proves the superior reconstruction ability of graph wiener filter. Extensive experimental results on various datasets demonstrate the effectiveness of our approach.

Graph neural networks (GNNs) are popular weapons for modeling relational data. Existing GNNs are not specified for attribute-incomplete graphs, making missing attribute imputation a burning issue. Until recently, many works notice that GNNs are coupled with spectral concentration, which means the spectrum obtained by GNNs concentrates on a local part in spectral domain, e.g., low-frequency due to oversmoothing issue. As a consequence, GNNs may be seriously flawed for reconstructing graph attributes as graph spectral concentration tends to cause a low imputation precision. In this work, we present a regularized graph autoencoder for graph attribute imputation, named MEGAE, which aims at mitigating spectral concentration problem by maximizing the graph spectral entropy. Notably, we first present the method for estimating graph spectral entropy without the eigen-decomposition of Laplacian matrix and provide the theoretical upper error bound. A maximum entropy regularization then acts in the latent space, which directly increases the graph spectral entropy. Extensive experiments show that MEGAE outperforms all the other state-of-the-art imputation methods on a variety of benchmark datasets.

Non-Pharmaceutical Interventions (NPIs), such as social gathering restrictions, have shown effectiveness to slow the transmission of COVID-19 by reducing the contact of people. To support policy-makers, multiple studies have first modelled human mobility via macro indicators (e.g., average daily travel distance) and then study the effectiveness of NPIs. In this work, we focus on mobility modelling and, from a micro perspective, aim to predict locations that will be visited by COVID-19 cases. Since NPIs generally cause economic and societal loss, such a prediction benefits governments when they design and evaluate them. However, in real-world situations, strict privacy data protection regulations result in severe data sparsity problems (i.e., limited case and location information). To address these challenges and jointly model variables including a geometric graph, a set of diffusions and a set of locations, we propose a model named Deep Graph Diffusion Infomax (DGDI). We show the maximization of DGDI can be bounded by two tractable components: a univariate Mutual Information (MI) between geometric graph and diffusion representation, and a univariate MI between diffusion representation and location representation. To facilitate the research of COVID-19 prediction, we present two benchmarks that contain geometric graphs and location histories of COVID-19 cases. Extensive experiments on the two benchmarks show that DGDI significantly outperforms other competing methods.

Nuo Chen, Linjun Shou, Jian Pei, Ming Gong, Bowen Cao, Jianhui Chang, Jia Li, Daxin Jiang. Proceedings of the 61st Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). 2023.

In this work, we focus on robust time series representation learning. Our assumption is that real-world time series is noisy and complementary information from different views of the same time series plays an important role while analyzing noisy input. Based on this, we create two views for the input time series through two different encoders. We conduct co-training based contrastive learning iteratively to learn the encoders. Our experiments demonstrate that this co-training approach leads to a significant improvement in performance. Especially, by leveraging the complementary information from different views, our proposed TS-CoT method can mitigate the impact of data noise and corruption. Empirical evaluations on four time series benchmarks in unsupervised and semi-supervised settings reveal that TS-CoT outperforms existing methods. Furthermore, the representations learned by TS-CoT can transfer well to downstream tasks through fine-tuning1.

Many patients with chronic diseases resort to multiple medications to relieve various symptoms, which raises concerns about the safety of multiple medication use, as severe drug-drug antagonism can lead to serious adverse effects or even death. This paper presents a Decision Support System, called DSSDDI, based on drug-drug interactions to support doctors prescribing decisions. DSSDDI contains three modules, Drug-Drug Interaction (DDI) module, Medical Decision (MD) module and Medical Support (MS) module. The DDI module learns safer and more effective drug representations from the drug-drug interactions. To capture the potential causal relationship between DDI and medication use, the MD module considers the representations of patients and drugs as context, DDI and patients’ similarity as treatment, and medication use as outcome to construct counterfactual links for the representation learning. Furthermore, the MS module provides drug candidates to doctors with explanations. Experiments on the chronic data collected from the Hong Kong Chronic Disease Study Project and a public diagnostic data MIMIC-III demonstrate that DSSDDI can be a reliable reference for doctors in terms of safety and efficiency of clinical diagnosis, with significant improvements compared to baseline methods. Source code of the proposed DSSDDI is publicly available at https://github.com/TianBian95/DSSDDI.

Graph alignment, which aims at identifying corresponding entities across multiple networks, has been widely applied in various domains. As the graphs to be aligned are usually constructed from different sources, the inconsistency issues of structures and features between two graphs are ubiquitous in real-world applications. Most existing methods follow the "embed-then-cross-compare" paradigm which computes node embeddings in each graph and then processes node correspondences based on cross-graph embedding comparison. However, we find these methods are unstable and sub-optimal when structure or feature inconsistency appears. To this end, we propose SLOTAlign, an unsupervised graph alignment framework that jointly performs Structure Learning and Optimal Transport Alignment. We convert graph alignment to an optimal transport problem between two intra-graph matrices without the requirement of cross-graph comparison. We further incorporate multi-view structure learning to enhance graph representation power and reduce the effect of structure and feature inconsistency inherited across graphs. Moreover, an alternating scheme based algorithm has been developed to address the joint optimization problem in SLOTAlign and the provable convergence result are also established. Finally, we conduct extensive experiments on six unsupervised graph alignment datasets and the DBP15K knowledge graph (KG) alignment benchmark dataset. The proposed SLOTAlign shows superior performance and strongest robustness over seven unsupervised graph alignment methods and five specialized KG alignment methods.1

Recently, "pre-training and fine-tuning'' has been adopted as a standard workflow for many graph tasks since it can take general graph knowledge to relieve the lack of graph annotations from each application. However, graph tasks with node level, edge level, and graph level are far diversified, making the pre-training pretext often incompatible with these multiple tasks. This gap may even cause a "negative transfer'' to the specific application, leading to poor results. Inspired by the prompt learning in natural language processing (NLP), which has presented significant effectiveness in leveraging prior knowledge for various NLP tasks, we study the prompting topic for graphs with the motivation of filling the gap between pre-trained models and various graph tasks. In this paper, we propose a novel multi-task prompting method for graph models. Specifically, we first unify the format of graph prompts and language prompts with the prompt token, token structure, and inserting pattern. In this way, the prompting idea from NLP can be seamlessly introduced to the graph area. Then, to further narrow the gap between various graph tasks and state-of-the-art pre-training strategies, we further study the task space of various graph applications and reformulate downstream problems to the graph-level task. Afterward, we introduce meta-learning to efficiently learn a better initialization for the multi-task prompt of graphs so that our prompting framework can be more reliable and general for different tasks. We conduct extensive experiments, results from which demonstrate the superiority of our method.

Irregularly sampled multivariate time series are ubiquitous in various fields, particularly in healthcare, and exhibit two key characteristics: intra-series irregularity and inter-series discrepancy. Intra-series irregularity refers to the fact that time-series signals are often recorded at irregular intervals, while inter-series discrepancy refers to the significant variability in sampling rates among diverse series. However, recent advances in irregular time series have primarily focused on addressing intra-series irregularity, overlooking the issue of inter-series discrepancy. To bridge this gap, we present Warpformer, a novel approach that fully considers these two characteristics. In a nutshell, Warpformer has several crucial designs, including a specific input representation that explicitly characterizes both intra-series irregularity and inter-series discrepancy, a warping module that adaptively unifies irregular time series in a given scale, and a customized attention module for representation learning. Additionally, we stack multiple warping and attention modules to learn at different scales, producing multi-scale representations that balance coarse-grained and fine-grained signals for downstream tasks. We conduct extensive experiments on widely used datasets and a new large-scale benchmark built from clinical databases. The results demonstrate the superiority of Warpformer over existing state-of-the-art approaches.

With a long history of traditional Graph Anomaly Detection (GAD) algorithms and recently popular Graph Neural Networks (GNNs), it is still not clear (1) how they perform under a standard comprehensive setting, (2) whether GNNs can outperform traditional algorithms such as tree ensembles, and (3) how about their efficiency on large-scale graphs. In response, we introduce GADBench---a benchmark tool dedicated to supervised anomalous node detection in static graphs. GADBench facilitates a detailed comparison across 29 distinct models on ten real-world GAD datasets, encompassing thousands to millions (~6M) nodes. Our main finding is that tree ensembles with simple neighborhood aggregation can outperform the latest GNNs tailored for the GAD task. We shed light on the current progress of GAD, setting a robust groundwork for subsequent investigations in this domain. GADBench is open-sourced at https://github.com/squareRoot3/GADBench.

Pseudo labeling (PL) is a wide-applied strategy to enlarge the labeled dataset by self-annotating the potential samples during the training process. Several works have shown that it can improve the graph learning model performance in general. However, we notice that the incorrect labels can be fatal to the graph training process. Inappropriate PL may result in the performance degrading, especially on graph data where the noise can propagate. Surprisingly, the corresponding error is seldom theoretically analyzed in the literature. In this paper, we aim to give deep insights of PL on graph learning models. We first present the error analysis of PL strategy by showing that the error is bounded by the confidence of PL threshold and consistency of multi-view prediction. Then, we theoretically illustrate the effect of PL on convergence property. Based on the analysis, we propose a cautious pseudo labeling methodology in which we pseudo label the samples with highest confidence and multi-view consistency. Finally, extensive experiments demonstrate that the proposed strategy improves graph learning process and outperforms other PL strategies on link prediction and node classification tasks.

Graph Neural Networks (GNNs) have demonstrated great success in Knowledge Graph Completion (KGC) by modeling how entities and relations interact in recent years. However, most of them are designed to learn from the observed graph structure, which appears to have imbalanced relation distribution during the training stage. Motivated by the causal relationship among the entities on a knowledge graph, we explore this defect through a counterfactual question: “would the relation still exist if the neighborhood of entities became different from observation?”. With a carefully designed instantiation of a causal model on the knowledge graph, we generate the counterfactual relations to answer the question by regarding the representations of entity pair given relation as context, structural information of relation-aware neighborhood as treatment, and validity of the composed triplet as the outcome. Furthermore, we incorporate the created counterfactual relations with the GNN-based framework on KGs to augment their learning of entity pair representations from both the observed and counterfactual relations. Experiments on benchmarks show that our proposed method outperforms existing methods on the task of KGC, achieving new state-of-the-art results. Moreover, we demonstrate that the proposed counterfactual relations-based augmentation also enhances the interpretability of the GNN-based framework through the path interpretations of predictions.

Node classification and graph classification are two graph learning problems that predict the class label of a node and the class label of a graph respectively. A node of a graph usually represents a real-world entity, e.g., a user in a social network, or a document in a document citation network. In this work, we consider a more challenging but practically useful setting, in which a node itself is a graph instance. This leads to a hierarchical graph perspective which arises in many domains such as social network, biological network and document collection. We study the node classification problem in the hierarchical graph where a "node" is a graph instance. As labels are usually limited, we design a novel semi-supervised solution named SEAL-CI. SEAL-CI adopts an iterative framework that takes turns to update two modules, one working at the graph instance level and the other at the hierarchical graph level. To enforce a consistency among different levels of hierarchical graph, we propose the Hierarchical Graph Mutual Information (HGMI) and further present a way to compute HGMI with theoretical guarantee. We demonstrate the effectiveness of this hierarchical graph modeling and the proposed SEAL-CI method on text and social network data.

Modern sociology has profoundly uncovered many convincing social criteria for behavioral analysis. Unfortunately, many of them are too subjective to be measured and very challenging to be presented in online social networks (OSNs) for the large data volume and complicated environments to be explored. On the other hand, data mining techniques can better find data patterns but many of them leave behind unnatural understanding to humans. Although there are some works trying to integrate social observations for specific tasks, they are still hard to be applied to more general cases. In this paper, we propose a fundamental methodology to support the further fusion of data mining techniques and sociological behavioral criteria. Our highlights are three-fold: First, we propose an effective hypergraph awareness and a fast line graph construction framework. The hypergraph can more profoundly indicate the interactions between individuals and their environments because each edge in the hypergraph (a.k.a hyperedge) contains more than two nodes, which is perfect to describe social. A line graph treats each social environment as a super node with the underlying influence between different environments. In this way, we go beyond traditional pair-wise relations and explore richer patterns under various sociological criteria; Second, we propose a novel hypergraph-based neural network to learn social influence flowing from users to users, users to environments, environment to users, and environments to environments. The neural network can be learned via a task-free method, making our model very flexible to support various data mining tasks and sociological analysis; Third, we propose both qualitative and quantitive solutions to effectively evaluate the most common sociological criteria like social conformity, social equivalence, environmental evolving and social polarization. Our extensive experiments show that our framework can better support both data mining tasks for online user behaviors and sociological analysis.

Graph Neural Networks (GNNs) are widely applied for graph anomaly detection. As one of the key components for GNN design is to select a tailored spectral filter, we take the first step towards analyzing anomalies via the lens of the graph spectrum. Our crucial observation is the existence of anomalies will lead to the ‘right-shift’ phenomenon, that is, the spectral energy distribution concentrates less on low frequencies and more on high frequencies. This fact motivates us to propose the Beta Wavelet Graph Neural Network (BWGNN). Indeed, BWGNN has spectral and spatial localized band-pass filters to better handle the ‘right-shift’ phenomenon in anomalies. We demonstrate the effectiveness of BWGNN on four large-scale anomaly detection datasets. Our code and data are released at https://github.com/squareRoot3/Rethinking-Anomaly-Detection.

In this paper, we consider an inverse problem in graph learning domain -- "given the graph representations smoothed by Graph Convolutional Network (GCN), how can we reconstruct the input graph signal?" We propose Graph Deconvolutional Network (GDN) and motivate the design of GDN via a combination of inverse filters in spectral domain and de-noising layers in wavelet domain, as the inverse operation results in a high frequency amplifier and may amplify the noise. We demonstrate the effectiveness of the proposed method on several tasks including graph feature imputation and graph structure generation.

We present Mask-GVAE, a variational generative model for blind denoising large discrete graphs, in which ”blind denoising” means we don’t require any supervision from clean graphs. We focus on recovering graph structures via deleting irrelevant edges and adding missing edges, which has many applications in real-world scenarios, for example, enhancing the quality of connections in a co-authorship network. Mask-GVAE makes use of the robustness in low eigenvectors of graph Laplacian against random noise and decomposes the input graph into several stable clusters. It then harnesses the huge computations by decoding probabilistic smoothed subgraphs in a variational manner. On a wide variety of benchmarks, Mask-GVAE outperforms competing approaches by a significant margin on PSNR and WL similarity.

Graph Neural Networks (GNN) and Variational Autoencoders (VAEs) have been widely used in modeling and generating graphs with latent factors. However there is no clear explanation of what these latent factors are and why they perform well. In this work, we present Dirichlet Graph Variational Autoencoder (DGVAE) with graph cluster memberships as latent factors. Our study connects VAEs based graph generation and balanced graph cut, and provides a new way to understand and improve the internal mechanism of VAEs based graph generation. Specifically, we first interpret the reconstruction term of DGVAE as balanced graph cut in a principled way. Furthermore, motivated by the low pass characteristics in balanced graph cut, we propose a new variant of GNN named Heatts to encode the input graph into cluster memberships. Heatts utilizes the Taylor series for fast computation of Heat kernels and has better low pass characteristics than Graph Convolutional Networks (GCN). Through experiments on graph generation and graph clustering, we demonstrate the effectiveness of our proposed framework.

It has been demonstrated that adversarial graphs, i.e., graphs with imperceptible perturbations added, can cause deep graph models to fail on node/graph classification tasks. In this paper, we extend adversarial graphs to the problem of community detection which is much more difficult. We focus on black-box attack and aim to hide targeted individuals from the detection of deep graph community detection models, which has many applications in real-world scenarios, for example, protecting personal privacy in social networks and understanding camouflage patterns in transaction networks. We propose an iterative learning framework that takes turns to update two modules: one working as the constrained graph generator and the other as the surrogate community detection model. We also find that the adversarial graphs generated by our method can be transferred to other learning based community detection models.

In this paper we use a time-evolving graph which consists of a sequence of graph snapshots over time to model many real-world networks. We study the path classification problem in a time-evolving graph, which has many applications in real-world scenarios, for example, predicting path failure in a telecommunication network and predicting path congestion in a traffic network in the near future. In order to capture the temporal dependency and graph structure dynamics, we design a novel deep neural network named Long Short-Term Memory R-GCN (LRGCN). LRGCN considers temporal dependency between time-adjacent graph snapshots as a special relation with memory, and uses relational GCN to jointly process both intra-time and inter-time relations. We also propose a new path representation method named self-attentive path embedding (SAPE), to embed paths of arbitrary length into fixed-length vectors. Through experiments on a real-world telecommunication network and a traffic network in California, we demonstrate the superiority of LRGCN to other competing methods in path failure prediction, and prove the effectiveness of SAPE on path representation.

Node classification and graph classification are two graph learning problems that predict the class label of a node and the class label of a graph respectively. A node of a graph usually represents a real-world entity, e.g., a user in a social network, or a protein in a protein-protein interaction network. In this work, we consider a more challenging but practically useful setting, in which a node itself is a graph instance. This leads to a hierarchical graph perspective which arises in many domains such as social network, biological network and document collection. For example, in a social network, a group of people with shared interests forms a user group, whereas a number of user groups are interconnected via interactions or common members. We study the node classification problem in the hierarchical graph where a “node” is a graph instance, e.g., a user group in the above example. As labels are usually limited in real-world data, we design two novel semi-supervised solutions named SEmi-supervised grAph cLassification via Cautious/Active Iteration (or SEAL-C/AI in short). SEAL-C/AI adopt an iterative framework that takes turns to build or update two classifiers, one working at the graph instance level and the other at the hierarchical graph level. To simplify the representation of the hierarchical graph, we propose a novel supervised, self-attentive graph embedding method called SAGE, which embeds graph instances of arbitrary size into fixed-length vectors. Through experiments on synthetic data and Tencent QQ group data, we demonstrate that SEAL-C/AI not only outperform competing methods by a significant margin in terms of accuracy/Macro-F1, but also generate meaningful interpretations of the learned representations.

With the increase of elderly population, Alzheimer's Disease (AD), as the most common cause of dementia among the elderly, is affecting more and more senior people. It is crucial for a patient to receive accurate and timely diagnosis of AD. Current diagnosis relies on doctors' experience and clinical test, which, unfortunately, may not be performed until noticeable AD symptoms are developed. In this work, we present our novel solution named time-aware TICC and CNN (TATC), for predicting AD from actigraphy data. TATC is a multivariate time series classification method using a neural attention-based deep learning approach. It not only performs accurate prediction of AD risk, but also generates meaningful interpretation of daily behavior pattern of subjects. TATC provides an automatic, low-cost solution for continuously monitoring the change of physical activity of subjects in daily living environment. We believe the future deployment of TATC can benefit both doctors and patients in early detection of potential AD risk.