Shuo Yu

Jie Ouyang, Yucong Luo, Mingyue Cheng et al.

This paper presents the solution of our team APEX in the Meta KDD CUP 2024: CRAG Comprehensive RAG Benchmark Challenge. The CRAG benchmark addresses the limitations of existing QA benchmarks in evaluating the diverse and dynamic challenges faced by Retrieval-Augmented Generation (RAG) systems. It provides a more comprehensive assessment of RAG performance and contributes to advancing research in this field. We propose a routing-based domain and dynamic adaptive RAG pipeline, which performs specific processing for the diverse and dynamic nature of the question in all three stages: retrieval, augmentation, and generation. Our method achieved superior performance on CRAG and ranked 2nd for Task 2&3 on the final competition leaderboard. Our implementation is available at this link: https://github.com/USTCAGI/CRAG-in-KDD-Cup2024.

Shuo Yu, Mingyue Cheng, Qi Liu et al.

Retrieval-augmented generation (RAG) is increasingly recognized as an effective approach to mitigating the hallucination of large language models (LLMs) through the integration of external knowledge. While numerous efforts, most studies focus on a single type of external knowledge source. However, in real-world applications, most situations involve diverse knowledge from various sources, yet this area has been less explored. The main dilemma is the lack of a suitable dataset containing multiple knowledge sources and pre-exploration of the associated issues. To address these challenges, we standardize a benchmark dataset that combines structured and unstructured knowledge across diverse and complementary domains. Based on this dataset, we further develop a plug-and-play RAG framework, \textbf{PruningRAG}, whose main characteristic is the use of multi-granularity pruning strategies to optimize the integration of relevant information while minimizing misleading context. It consistently improves performance across various existing RAG variants, demonstrating its robustness and broad applicability. Building upon the standardized dataset and PruningRAG, we also report a series of experimental results, as well as insightful findings. Our dataset and code are publicly available\footnote{https://github.com/USTCAGI/PruningRAG}, with the aim of advancing future research in the RAG community.

Feng Xia, Shuo Yu, Chengfei Liu et al.

Clustering a group of vertices in networks facilitates applications across different domains, such as social computing and Internet of Things. However, challenges arises for clustering networks with increased scale. This paper proposes a solution which consists of two motif clustering techniques: standard acceleration CHIEF-ST and approximate acceleration CHIEF-AP. Both algorithms first find the maximal k-edge-connected subgraphs within the target networks to lower the network scale, then employ higher-order motifs in clustering. In the first procedure, we propose to lower the network scale by optimizing the network structure with maximal k-edge-connected subgraphs. For CHIEF-ST, we illustrate that all target motifs will be kept after this procedure when the minimum node degree of the target motif is equal or greater than k. For CHIEF-AP, we prove that the eigenvalues of the adjacency matrix and the Laplacian matrix are relatively stable after this step. That is, CHIEF-ST has no influence on motif clustering, whereas CHIEF-AP introduces limited yet acceptable impact. In the second procedure, we employ higher-order motifs, i.e., heterogeneous four-node motifs clustering in higher-order dense networks. The contributions of CHIEF are two-fold: (1) improved efficiency of motif clustering for big networks; (2) verification of higher-order motif significance. The proposed solutions are found to outperform baseline approaches according to experiments on real and synthetic networks, which demonstrates CHIEF's strength in large network analysis. Meanwhile, higher-order motifs are proved to perform better than traditional triangle motifs in clustering.

Xiaoyu Tao, Mingyue Cheng, Ze Guo et al.

Time series forecasting (TSF) plays a critical role in decision-making for many real-world applications. Recently, LLM-based forecasters have made promising advancements. Despite their effectiveness, existing methods often lack explicit experience accumulation and continual evolution. In this work, we propose MemCast, a learning-to-memory framework that reformulates TSF as an experience-conditioned reasoning task. Specifically, we learn experience from the training set and organize it into a hierarchical memory. This is achieved by summarizing prediction results into historical patterns, distilling inference trajectories into reasoning wisdom, and inducing extracted temporal features into general laws. Furthermore, during inference, we leverage historical patterns to guide the reasoning process and utilize reasoning wisdom to select better trajectories, while general laws serve as criteria for reflective iteration. Additionally, to enable continual evolution, we design a dynamic confidence adaptation strategy that updates the confidence of individual entries without leaking the test set distribution. Extensive experiments on multiple datasets demonstrate that MemCast consistently outperforms previous methods, validating the effectiveness of our approach. Our code is available at https://github.com/Xiaoyu-Tao/MemCast-TS.

Mingyue Cheng, Daoyu Wang, Qi Liu et al.

Synthesizing informative commercial reports from massive and noisy web sources is critical for high-stakes business decisions. Although current deep research agents achieve notable progress, their reports still remain limited in terms of quality, reliability, and coverage. In this work, we propose Mind2Report, a cognitive deep research agent that emulates the commercial analyst to synthesize expert-level reports. Specifically, it first probes fine-grained intent, then searches web sources and records distilled information on the fly, and subsequently iteratively synthesizes the report. We design Mind2Report as a training-free agentic workflow that augments general large language models (LLMs) with dynamic memory to support these long-form cognitive processes. To rigorously evaluate Mind2Report, we further construct QRC-Eval comprising 200 real-world commercial tasks and establish a holistic evaluation strategy to assess report quality, reliability, and coverage. Experiments demonstrate that Mind2Report outperforms leading baselines, including OpenAI and Gemini deep research agents. Although this is a preliminary study, we expect it to serve as a foundation for advancing the future design of commercial deep research agents. Our code and data are available at https://github.com/Melmaphother/Mind2Report.

Daoyu Wang, Qingchuan Li, Mingyue Cheng et al.

General agents have given rise to phenomenal applications such as OpenClaw and Claude Code. As these agent systems (a.k.a. Harnesses) strive for bolder goals, they demand increasingly stronger agentic capabilities from foundation Large Language Models (LLMs). Agentic Reinforcement Learning (RL) is emerging as a central post-training paradigm for empowering LLMs with these capabilities and is playing an increasingly pivotal role in agent training. Unlike single-turn token-level alignment or reasoning enhancement, as in RLHF and RLVR, Agentic RL targets multi-turn interactive settings, where the goal is to optimize core agentic capabilities such as decision making and tool use while addressing new challenges including delayed and sparse rewards, as well as long and variable context. As a result, the token-centric modeling and optimization paradigm inherited from traditional LLM RL is becoming increasingly inadequate for capturing real LLM agent behavior. In this paper, we present StepPO as a position on step-level Agentic RL. We argue that the conventional token-level Markov Decision Process (MDP) should be advanced to a step-level MDP formulation, and that the step, rather than the token, should be regarded as the proper action representation for LLM agents. We then propose step-level credit assignment as the natural optimization counterpart of this formulation, thereby aligning policy optimization and reward propagation with the granularity of agent decisions. Finally, we discuss the key systems designs required to realize step-level Agentic RL in practice and preliminary experiments provide initial evidence for the effectiveness of this perspective. We hope that the step-aligned, step-level paradigm embodied in StepPO offers the Agentic RL community a useful lens for understanding agent behavior and helps advance LLMs toward stronger general-agent capabilities.

Ahsan Shehzad, Feng Xia, Shagufta Abid et al.

Graph transformers are a recent advancement in machine learning, offering a new class of neural network models for graph-structured data. The synergy between transformers and graph learning demonstrates strong performance and versatility across various graph-related tasks. This survey provides an in-depth review of recent progress and challenges in graph transformer research. We begin with foundational concepts of graphs and transformers. We then explore design perspectives of graph transformers, focusing on how they integrate graph inductive biases and graph attention mechanisms into the transformer architecture. Furthermore, we propose a taxonomy classifying graph transformers based on depth, scalability, and pre-training strategies, summarizing key principles for effective development of graph transformer models. Beyond technical analysis, we discuss the applications of graph transformer models for node-level, edge-level, and graph-level tasks, exploring their potential in other application scenarios as well. Finally, we identify remaining challenges in the field, such as scalability and efficiency, generalization and robustness, interpretability and explainability, dynamic and complex graphs, as well as data quality and diversity, charting future directions for graph transformer research.

Shuo Yu, Huafei Huang, Minh N. Dao et al.

Graph Augmentation Learning (GAL) provides outstanding solutions for graph learning in handling incomplete data, noise data, etc. Numerous GAL methods have been proposed for graph-based applications such as social network analysis and traffic flow forecasting. However, the underlying reasons for the effectiveness of these GAL methods are still unclear. As a consequence, how to choose optimal graph augmentation strategy for a certain application scenario is still in black box. There is a lack of systematic, comprehensive, and experimentally validated guideline of GAL for scholars. Therefore, in this survey, we in-depth review GAL techniques from macro (graph), meso (subgraph), and micro (node/edge) levels. We further detailedly illustrate how GAL enhance the data quality and the model performance. The aggregation mechanism of augmentation strategies and graph learning models are also discussed by different application scenarios, i.e., data-specific, model-specific, and hybrid scenarios. To better show the outperformance of GAL, we experimentally validate the effectiveness and adaptability of different GAL strategies in different downstream tasks. Finally, we share our insights on several open issues of GAL, including heterogeneity, spatio-temporal dynamics, scalability, and generalization.

Feng Xia, Xin Chen, Shuo Yu et al.

Multivariate time series anomaly detection (MTAD) plays a vital role in a wide variety of real-world application domains. Over the past few years, MTAD has attracted rapidly increasing attention from both academia and industry. Many deep learning and graph learning models have been developed for effective anomaly detection in multivariate time series data, which enable advanced applications such as smart surveillance and risk management with unprecedented capabilities. Nevertheless, MTAD is facing critical challenges deriving from the dependencies among sensors and variables, which often change over time. To address this issue, we propose a coupled attention-based neural network framework (CAN) for anomaly detection in multivariate time series data featuring dynamic variable relationships. We combine adaptive graph learning methods with graph attention to generate a global-local graph that can represent both global correlations and dynamic local correlations among sensors. To capture inter-sensor relationships and temporal dependencies, a convolutional neural network based on the global-local graph is integrated with a temporal self-attention module to construct a coupled attention module. In addition, we develop a multilevel encoder-decoder architecture that accommodates reconstruction and prediction tasks to better characterize multivariate time series data. Extensive experiments on real-world datasets have been conducted to evaluate the performance of the proposed CAN approach, and the results show that CAN significantly outperforms state-of-the-art baselines.

Shuo Yu, Ciyuan Peng, Yingbo Wang et al.

Quantum theory has shown its superiority in enhancing machine learning. However, facilitating quantum theory to enhance graph learning is in its infancy. This survey investigates the current advances in quantum graph learning (QGL) from three perspectives, i.e., underlying theories, methods, and prospects. We first look at QGL and discuss the mutualism of quantum theory and graph learning, the specificity of graph-structured data, and the bottleneck of graph learning, respectively. A new taxonomy of QGL is presented, i.e., quantum computing on graphs, quantum graph representation, and quantum circuits for graph neural networks. Pitfall traps are then highlighted and explained. This survey aims to provide a brief but insightful introduction to this emerging field, along with a detailed discussion of frontiers and outlook yet to be investigated.

Renqiang Luo, Dong Zhang, Yupeng Gao et al.

Semantic understanding of popularity bias is a crucial yet underexplored challenge in recommender systems, where popular items are often favored at the expense of niche content. Most existing debiasing methods treat the semantic understanding of popularity bias as a matter of diversity enhancement or long-tail coverage, neglecting the deeper semantic layer that embodies the causal origins of the bias itself. Consequently, such shallow interpretations limit both their debiasing effectiveness and recommendation accuracy. In this paper, we propose FairLRM, a novel framework that bridges the gap in the semantic understanding of popularity bias with Recommendation via Large Language Model (RecLLM). FairLRM decomposes popularity bias into item-side and user-side components, using structured instruction-based prompts to enhance the model's comprehension of both global item distributions and individual user preferences. Unlike traditional methods that rely on surface-level features such as "diversity" or "debiasing", FairLRM improves the model's ability to semantically interpret and address the underlying bias. Through empirical evaluation, we show that FairLRM significantly enhances both fairness and recommendation accuracy, providing a more semantically aware and trustworthy approach to enhance the semantic understanding of popularity bias. The implementation is available at https://github.com/LuoRenqiang/FairLRM.

Shaoyuan Chen, Linlin You, Rui Liu et al.

The training of large models, involving fine-tuning, faces the scarcity of high-quality data. Compared to the solutions based on centralized data centers, updating large models in the Internet of Things (IoT) faces challenges in coordinating knowledge from distributed clients by using their private and heterogeneous data. To tackle such a challenge, we propose KOALA (Federated Knowledge Transfer Fine-tuning Large Server Model with Resource-Constrained IoT Clients) to impel the training of large models in IoT. Since the resources obtained by IoT clients are limited and restricted, it is infeasible to locally execute large models and also update them in a privacy-preserving manner. Therefore, we leverage federated learning and knowledge distillation to update large models through collaboration with their small models, which can run locally at IoT clients to process their private data separately and enable large-small model knowledge transfer through iterative learning between the server and clients. Moreover, to support clients with similar or different computing capacities, KOALA is designed with two kinds of large-small model joint learning modes, namely to be homogeneous or heterogeneous. Experimental results demonstrate that compared to the conventional approach, our method can not only achieve similar training performance but also significantly reduce the need for local storage and computing power resources.

Shuo Yu, Shan Jin, Ming Li et al.

Understanding communication and information processing among brain regions of interest (ROIs) is highly dependent on long-range connectivity, which plays a crucial role in facilitating diverse functional neural integration across the entire brain. However, previous studies generally focused on the short-range dependencies within brain networks while neglecting the long-range dependencies, limiting an integrated understanding of brain-wide communication. To address this limitation, we propose Adaptive Long-range aware TransformER (ALTER), a brain graph transformer to capture long-range dependencies between brain ROIs utilizing biased random walk. Specifically, we present a novel long-range aware strategy to explicitly capture long-range dependencies between brain ROIs. By guiding the walker towards the next hop with higher correlation value, our strategy simulates the real-world brain-wide communication. Furthermore, by employing the transformer framework, ALERT adaptively integrates both short- and long-range dependencies between brain ROIs, enabling an integrated understanding of multi-level communication across the entire brain. Extensive experiments on ABIDE and ADNI datasets demonstrate that ALTER consistently outperforms generalized state-of-the-art graph learning methods (including SAN, Graphormer, GraphTrans, and LRGNN) and other graph learning based brain network analysis methods (including FBNETGEN, BrainNetGNN, BrainGNN, and BrainNETTF) in neurological disease diagnosis. Cases of long-range dependencies are also presented to further illustrate the effectiveness of ALTER. The implementation is available at https://github.com/yushuowiki/ALTER.

Daoyu Wang, Mingyue Cheng, Shuo Yu et al.

Understanding and reasoning on the web-scale scientific literature is a crucial touchstone for large language model (LLM) based agents designed to support complex knowledge-intensive tasks. However, existing works are mainly restricted to tool-free tasks within isolated papers, largely due to the lack of a benchmark for cross-paper reasoning and multi-tool orchestration in real research scenarios. In this work, we propose PaperArena, an evaluation benchmark for agents to address real-world research questions that typically require integrating information across multiple papers with the assistance of external tools. Given a research question, agents should integrate diverse formats across multiple papers through reasoning and interacting with appropriate tools, thereby producing a well-grounded answer. To support standardized evaluation, we provide a modular and extensible platform for agent execution, offering tools such as multimodal parsing, context retrieval, and programmatic computation. Experimental results reveal that even the most advanced LLM powering a well-established agent system achieves merely 38.78% average accuracy. On the hard subset, accuracy drops to only 18.47%, highlighting great potential for improvement. We also present several empirical findings, including that all agents tested exhibit inefficient tool usage, often invoking more tools than necessary to solve a task. We invite the community to adopt PaperArena to develop and evaluate more capable agents for scientific discovery. Our code and data are available https://github.com/Melmaphother/PaperArena.

Shuo Yu, Mingyue Cheng, Daoyu Wang et al.

The primary form of user-internet engagement is shifting from leveraging implicit feedback signals, such as browsing and clicks, to harnessing the rich explicit feedback provided by textual interactive behaviors. This shift unlocks a rich source of user textual history, presenting a profound opportunity for a deeper form of personalization. However, prevailing approaches offer only a shallow form of personalization, as they treat user history as a flat list of texts for retrieval and fail to model the rich temporal and semantic structures reflecting dynamic nature of user interests. In this work, we propose \textbf{MemWeaver}, a framework that weaves the user's entire textual history into a hierarchical memory to power deeply personalized generation. The core innovation of our memory lies in its ability to capture both the temporal evolution of interests and the semantic relationships between different activities. To achieve this, MemWeaver builds two complementary memory components that both integrate temporal and semantic information, but at different levels of abstraction: behavioral memory, which captures specific user actions, and cognitive memory, which represents long-term preferences. This dual-component memory serves as a unified representation of the user, allowing large language models (LLMs) to reason over both concrete behaviors and abstracted traits. Experiments on the Language Model Personalization (LaMP) benchmark validate the efficacy of MemWeaver. Our code is available\footnote{https://github.com/fishsure/MemWeaver}.

Mingyue Cheng, Shuo Yu, Chuang Jiang et al.

Table reasoning requires models to jointly perform semantic understanding and precise numerical operations. Most existing methods rely on a single-turn reasoning paradigm over tables which suffers from context overflow and weak numerical sensitivity. To address these limitations, we previously proposed TableMind as a tuning-based autonomous programmatic agent that simulates human-like interaction within a lightweight large language model (LLM). TableMind internalizes planning, action, and reflection through a two-stage training strategy involving supervised fine-tuning (SFT) on filtered high-quality data and reinforcement learning (RL) via a multi-perspective reward and the Rank-Aware Policy Optimization (RAPO) algorithm. While TableMind establishes a solid foundation for programmatic agents, the inherent stochasticity of LLMs remains a critical challenge that leads to hallucinations. In this paper, we extend this foundation to TableMind++ by introducing a novel uncertainty-aware inference framework to mitigate hallucinations. Specifically, we propose memory-guided plan pruning to retrieve historical trajectories for validating and filtering out logically flawed plans to address epistemic uncertainty. To ensure execution precision, we introduce confidence-based action refinement which monitors token-level probabilities to detect and self-correct syntactic noise for aleatoric uncertainty mitigation. Finally, we employ dual-weighted trajectory aggregation to synthesize a robust consensus from multiple reasoning paths. Extensive experiments on diverse benchmarks demonstrate that TableMind++ consistently outperforms previous baselines and proprietary models to validate the effectiveness of integrating autonomous training with uncertainty quantification. Our code is available.

Tingyue Pan, Jie Ouyang, Mingyue Cheng et al.

Academic paper search is a fundamental task in scientific research, yet most existing approaches rely on rigid, predefined workflows that struggle with complex, conditional queries. To address this limitation, we propose PaperScout, an autonomous agent that reformulates paper search as a sequential decision-making process. Unlike static workflows, PaperScout dynamically decides whether, when, and how to invoke search and expand tools based on accumulated retrieval context. However, training such agents presents a fundamental challenge: standard reinforcement learning methods, typically designed for single-turn tasks, suffer from a granularity mismatch when applied to multi-turn agentic tasks, where token-level optimization diverges from the granularity of sequence-level interactions, leading to noisy credit assignment. We introduce Proximal Sequence Policy Optimization (PSPO), a process-aware, sequence-level policy optimization method that aligns optimization with agent-environment interaction. Comprehensive experiments on both synthetic and real-world benchmarks demonstrate that PaperScout significantly outperforms strong workflow-driven and RL baselines in both recall and relevance, validating the effectiveness of our adaptive agentic framework and optimization strategy.

Jing Ren, Bowen Li, Ziqi Xu et al.

Large Language Models (LLMs) are increasingly used for toxicity assessment in online moderation systems, where fairness across demographic groups is essential for equitable treatment. However, LLMs often produce inconsistent toxicity judgements for subtle expressions, particularly those involving implicit hate speech, revealing underlying biases that are difficult to correct through standard training. This raises a key question that existing approaches often overlook: when should corrective mechanisms be invoked to ensure fair and reliable assessments? To address this, we propose FairToT, an inference-time framework that enhances LLM fairness through prompt-guided toxicity assessment. FairToT identifies cases where demographic-related variation is likely to occur and determines when additional assessment should be applied. In addition, we introduce two interpretable fairness indicators that detect such cases and improve inference consistency without modifying model parameters. Experiments on benchmark datasets show that FairToT reduces group-level disparities while maintaining stable and reliable toxicity predictions, demonstrating that inference-time refinement offers an effective and practical approach for fairness improvement in LLM-based toxicity assessment systems. The source code can be found at https://aisuko.github.io/fair-tot/.

Feng Ding, Tingting Wang, Yupeng Gao et al.

Outdated facts in temporal knowledge graphs (TKGs) result from exceeding the expiration date of facts, which negatively impact reasoning performance on TKGs. However, existing reasoning methods primarily focus on positive importance of historical facts, neglecting adverse effects of outdated facts. Besides, training on these outdated facts yields extra computational cost. To address these challenges, we propose an outdated fact filtering framework named HALO, which quantifies the temporal validity of historical facts by exploring the half-life theory to filter outdated facts in TKGs. HALO consists of three modules: the temporal fact attention module, the dynamic relation-aware encoder module, and the outdated fact filtering module. Firstly, the temporal fact attention module captures the evolution of historical facts over time to identify relevant facts. Secondly, the dynamic relation-aware encoder module is designed for efficiently predicting the half life of each fact. Finally, we construct a time decay function based on the half-life theory to quantify the temporal validity of facts and filter outdated facts. Experimental results show that HALO outperforms the state-of-the-art TKG reasoning methods on three public datasets, demonstrating its effectiveness in detecting and filtering outdated facts (Codes are available at https://github.com/yushuowiki/K-Half/tree/main ).

Erkang Jing, Yezheng Liu, Yidong Chai et al.

Music recommender systems play a critical role in music streaming platforms by providing users with music that they are likely to enjoy. Recent studies have shown that user emotions can influence users' preferences for music moods. However, existing emotion-aware music recommender systems (EMRSs) explicitly or implicitly assume that users' actual emotional states expressed through identical emotional words are homogeneous. They also assume that users' music mood preferences are homogeneous under the same emotional state. In this article, we propose four types of heterogeneity that an EMRS should account for: emotion heterogeneity across users, emotion heterogeneity within a user, music mood preference heterogeneity across users, and music mood preference heterogeneity within a user. We further propose a Heterogeneity-aware Deep Bayesian Network (HDBN) to model these assumptions. The HDBN mimics a user's decision process of choosing music with four components: personalized prior user emotion distribution modeling, posterior user emotion distribution modeling, user grouping, and Bayesian neural network-based music mood preference prediction. We constructed two datasets, called EmoMusicLJ and EmoMusicLJ-small, to validate our method. Extensive experiments demonstrate that our method significantly outperforms baseline approaches on metrics of HR, Precision, NDCG, and MRR. Ablation studies and case studies further validate the effectiveness of our HDBN. The source code and datasets are available at https://github.com/jingrk/HDBN.

Yicong Li, Shan Jin, Qi Liu et al.

In social recommenders, the inherent nonlinearity and opacity of synergistic effects across multiple social networks hinders users from understanding how diverse information is leveraged for recommendations, consequently diminishing explainability. However, existing explainers can only identify the topological information in social networks that significantly influences recommendations, failing to further explain the synergistic effects among this information. Inspired by existing findings that synergistic effects enhance mutual information between inputs and predictions to generate information gain, we extend this discovery to graph data. We quantify graph information gain to identify subgraphs embodying synergistic effects. Based on the theoretical insights, we propose SemExplainer, which explains synergistic effects by identifying subgraphs that embody them. SemExplainer first extracts explanatory subgraphs from multi-view social networks to generate preliminary importance explanations for recommendations. A conditional entropy optimization strategy to maximize information gain is developed, thereby further identifying subgraphs that embody synergistic effects from explanatory subgraphs. Finally, SemExplainer searches for paths from users to recommended items within the synergistic subgraphs to generate explanations for the recommendations. Extensive experiments on three datasets demonstrate the superiority of SemExplainer over baseline methods, providing superior explanations of synergistic effects.

Mingyue Cheng, Yucong Luo, Jie Ouyang et al.

Retrieval-Augmented Generation (RAG) has gained significant attention in recent years for its potential to enhance natural language understanding and generation by combining large-scale retrieval systems with generative models. RAG leverages external knowledge sources, such as documents, databases, or structured data, to improve model performance and generate more accurate and contextually relevant outputs. This survey aims to provide a comprehensive overview of RAG by examining its fundamental components, including retrieval mechanisms, generation processes, and the integration between the two. We discuss the key characteristics of RAG, such as its ability to augment generative models with dynamic external knowledge, and the challenges associated with aligning retrieved information with generative objectives. We also present a taxonomy that categorizes RAG methods, ranging from basic retrieval-augmented approaches to more advanced models incorporating multi-modal data and reasoning capabilities. Additionally, we review the evaluation benchmarks and datasets commonly used to assess RAG systems, along with a detailed exploration of its applications in fields such as question answering, summarization, and information retrieval. Finally, we highlight emerging research directions and opportunities for improving RAG systems, such as enhanced retrieval efficiency, model interpretability, and domain-specific adaptations. This paper concludes by outlining the prospects for RAG in addressing real-world challenges and its potential to drive further advancements in natural language processing.

Renqiang Luo, Huafei Huang, Shuo Yu et al.

The design of Graph Transformers (GTs) generally neglects considerations for fairness, resulting in biased outcomes against certain sensitive subgroups. Since GTs encode graph information without relying on message-passing mechanisms, conventional fairness-aware graph learning methods cannot be directly applicable to address these issues. To tackle this challenge, we propose FairGT, a Fairness-aware Graph Transformer explicitly crafted to mitigate fairness concerns inherent in GTs. FairGT incorporates a meticulous structural feature selection strategy and a multi-hop node feature integration method, ensuring independence of sensitive features and bolstering fairness considerations. These fairness-aware graph information encodings seamlessly integrate into the Transformer framework for downstream tasks. We also prove that the proposed fair structural topology encoding with adjacency matrix eigenvector selection and multi-hop integration are theoretically effective. Empirical evaluations conducted across five real-world datasets demonstrate FairGT's superiority in fairness metrics over existing graph transformers, graph neural networks, and state-of-the-art fairness-aware graph learning approaches.

Huiling Tu, Shuo Yu, Vidya Saikrishna et al.

Knowledge graphs (KGs) have garnered significant attention for their vast potential across diverse domains. However, the issue of outdated facts poses a challenge to KGs, affecting their overall quality as real-world information evolves. Existing solutions for outdated fact detection often rely on manual recognition. In response, this paper presents DEAN (Deep outdatEd fAct detectioN), a novel deep learning-based framework designed to identify outdated facts within KGs. DEAN distinguishes itself by capturing implicit structural information among facts through comprehensive modeling of both entities and relations. To effectively uncover latent out-of-date information, DEAN employs a contrastive approach based on a pre-defined Relations-to-Nodes (R2N) graph, weighted by the number of entities. Experimental results demonstrate the effectiveness and superiority of DEAN over state-of-the-art baseline methods.

Bokai Pan, Mingyue Cheng, Zhiding Liu et al.

Recently, large language models (LLMs) have shown great promise in time series forecasting. However, most existing LLM-based forecasting methods still follow a static generative paradigm that directly maps historical observations to future values in a single pass. Under this paradigm, forecasting is constrained by limited temporal pattern extraction, single-round acquisition of contextual features, one-shot forecast generation, and lack of support from ensemble forecasts. To address these limitations, in this work, we propose CastFlow, a dynamic agentic forecasting framework that enables multi-view temporal pattern extraction, multi-round contextual features acquisition, iterative forecast refinement, and forecasting with ensemble forecasts. First, CastFlow organizes the forecasting process into planning, action, forecasting, and reflection, establishing an agentic workflow. Second, this workflow is supported by a memory module that retrieves prior experience and a multi-view toolkit that constructs diagnostic evidence and provides a reliable ensemble forecast baseline. Third, CastFlow adopts a role-specialized design that combines general-purpose reasoning with specialized numerical forecasting. Under this design, a frozen LLM preserves general-purpose reasoning, while a fine-tuned domain-specific LLM performs evidence-guided numerical forecasting based on the ensemble forecast baseline, rather than from scratch. To optimize a fine-tuned domain-specific LLM, we further develop a two-stage workflow-oriented training that combines supervised fine-tuning (SFT) and reinforcement learning with verifiable rewards (RLVR). To evaluate the effectiveness of CastFlow, we conduct extensive experiments on diverse datasets and show that it achieves superior overall results against strong baselines. We hope that this work can serve as a step toward more adaptive and accurate time series forecasting.

Wei Ruan, Yanjun Lyu, Jing Zhang et al.

With the rapid advancements in large language model (LLM) technology and the emergence of bioinformatics-specific language models (BioLMs), there is a growing need for a comprehensive analysis of the current landscape, computational characteristics, and diverse applications. This survey aims to address this need by providing a thorough review of BioLMs, focusing on their evolution, classification, and distinguishing features, alongside a detailed examination of training methodologies, datasets, and evaluation frameworks. We explore the wide-ranging applications of BioLMs in critical areas such as disease diagnosis, drug discovery, and vaccine development, highlighting their impact and transformative potential in bioinformatics. We identify key challenges and limitations inherent in BioLMs, including data privacy and security concerns, interpretability issues, biases in training data and model outputs, and domain adaptation complexities. Finally, we highlight emerging trends and future directions, offering valuable insights to guide researchers and clinicians toward advancing BioLMs for increasingly sophisticated biological and clinical applications.

Ciyuan Peng, Yuelong Huang, Qichao Dong et al.

State-of-the-art brain graph analysis methods fail to fully encode the small-world architecture of brain graphs (accompanied by the presence of hubs and functional modules), and therefore lack biological plausibility to some extent. This limitation hinders their ability to accurately represent the brain's structural and functional properties, thereby restricting the effectiveness of machine learning models in tasks such as brain disorder detection. In this work, we propose a novel Biologically Plausible Brain Graph Transformer (BioBGT) that encodes the small-world architecture inherent in brain graphs. Specifically, we present a network entanglement-based node importance encoding technique that captures the structural importance of nodes in global information propagation during brain graph communication, highlighting the biological properties of the brain structure. Furthermore, we introduce a functional module-aware self-attention to preserve the functional segregation and integration characteristics of brain graphs in the learned representations. Experimental results on three benchmark datasets demonstrate that BioBGT outperforms state-of-the-art models, enhancing biologically plausible brain graph representations for various brain graph analytical tasks

Shuo Yu, Yingbo Wang, Ruolin Li et al.

Graphs are data structures used to represent irregular networks and are prevalent in numerous real-world applications. Previous methods directly model graph structures and achieve significant success. However, these methods encounter bottlenecks due to the inherent irregularity of graphs. An innovative solution is converting graphs into textual representations, thereby harnessing the powerful capabilities of Large Language Models (LLMs) to process and comprehend graphs. In this paper, we present a comprehensive review of methodologies for applying LLMs to graphs, termed LLM4graph. The core of LLM4graph lies in transforming graphs into texts for LLMs to understand and analyze. Thus, we propose a novel taxonomy of LLM4graph methods in the view of the transformation. Specifically, existing methods can be divided into two paradigms: Graph2text and Graph2token, which transform graphs into texts or tokens as the input of LLMs, respectively. We point out four challenges during the transformation to systematically present existing methods in a problem-oriented perspective. For practical concerns, we provide a guideline for researchers on selecting appropriate models and LLMs for different graphs and hardware constraints. We also identify five future research directions for LLM4graph.

Yicong Li, Kuanjiu Zhou, Shuo Yu et al.

Comprehensible neural network explanations are foundations for a better understanding of decisions, especially when the input data are infused with malicious perturbations. Existing solutions generally mitigate the impact of perturbations through adversarial training, yet they fail to generate comprehensible explanations under unknown perturbations. To address this challenge, we propose AGAIN, a fActor GrAph-based Interpretable neural Network, which is capable of generating comprehensible explanations under unknown perturbations. Instead of retraining like previous solutions, the proposed AGAIN directly integrates logical rules by which logical errors in explanations are identified and rectified during inference. Specifically, we construct the factor graph to express logical rules between explanations and categories. By treating logical rules as exogenous knowledge, AGAIN can identify incomprehensible explanations that violate real-world logic. Furthermore, we propose an interactive intervention switch strategy rectifying explanations based on the logical guidance from the factor graph without learning perturbations, which overcomes the inherent limitation of adversarial training-based methods in defending only against known perturbations. Additionally, we theoretically demonstrate the effectiveness of employing factor graph by proving that the comprehensibility of explanations is strongly correlated with factor graph. Extensive experiments are conducted on three datasets and experimental results illustrate the superior performance of AGAIN compared to state-of-the-art baselines.

Mingyue Cheng, Jie Ouyang, Shuo Yu et al.

Large Language Models (LLMs) are increasingly being explored for building Agents capable of active environmental interaction (e.g., via tool use) to solve complex problems. Reinforcement Learning (RL) is considered a key technology with significant potential for training such Agents; however, the effective application of RL to LLM Agents is still in its nascent stages and faces considerable challenges. Currently, this emerging field lacks in-depth exploration into RL approaches specifically tailored for the LLM Agent context, alongside a scarcity of flexible and easily extensible training frameworks designed for this purpose. To help advance this area, this paper first revisits and clarifies Reinforcement Learning methodologies for LLM Agents by systematically extending the Markov Decision Process (MDP) framework to comprehensively define the key components of an LLM Agent. Secondly, we introduce Agent-R1, a modular, flexible, and user-friendly training framework for RL-based LLM Agents, designed for straightforward adaptation across diverse task scenarios and interactive environments. We conducted experiments on Multihop QA benchmark tasks, providing initial validation for the effectiveness of our proposed methods and framework.

Ciyuan Peng, Nguyen Linh Dan Le, Shan Jin et al.

Brain graph learning has demonstrated significant achievements in the fields of neuroscience and artificial intelligence. However, existing methods struggle to selectively learn disease-related knowledge, leading to heavy parameters and computational costs. This challenge diminishes their efficiency, as well as limits their practicality for real-world clinical applications. To this end, we propose a lightweight Brain PathoGraph Learning (BrainPoG) model that enables efficient brain graph learning by pathological pattern filtering and pathological feature distillation. Specifically, BrainPoG first contains a filter to extract the pathological pattern formulated by highly disease-relevant subgraphs, achieving graph pruning and lesion localization. A PathoGraph is therefore constructed by dropping less disease-relevant subgraphs from the whole brain graph. Afterwards, a pathological feature distillation module is designed to reduce disease-irrelevant noise features and enhance pathological features of each node in the PathoGraph. BrainPoG can exclusively learn informative disease-related knowledge while avoiding less relevant information, achieving efficient brain graph learning. Extensive experiments on four benchmark datasets demonstrate that BrainPoG exhibits superiority in both model performance and computational efficiency across various brain disease detection tasks.

Feng Xia, Ciyuan Peng, Jing Ren et al.

Graph learning has rapidly evolved into a critical subfield of machine learning and artificial intelligence (AI). Its development began with early graph-theoretic methods, gaining significant momentum with the advent of graph neural networks (GNNs). Over the past decade, progress in scalable architectures, dynamic graph modeling, multimodal learning, generative AI, explainable AI (XAI), and responsible AI has broadened the applicability of graph learning to various challenging environments. Graph learning is significant due to its ability to model complex, non-Euclidean relationships that traditional machine learning struggles to capture, thus better supporting real-world applications ranging from drug discovery and fraud detection to recommender systems and scientific reasoning. However, challenges like scalability, generalization, heterogeneity, interpretability, and trustworthiness must be addressed to unlock its full potential. This survey provides a comprehensive introduction to graph learning, focusing on key dimensions including scalable, temporal, multimodal, generative, explainable, and responsible graph learning. We review state-of-the-art techniques for efficiently handling large-scale graphs, capturing dynamic temporal dependencies, integrating heterogeneous data modalities, generating novel graph samples, and enhancing interpretability to foster trust and transparency. We also explore ethical considerations, such as privacy and fairness, to ensure responsible deployment of graph learning models. Additionally, we identify and discuss emerging topics, highlighting recent integration of graph learning and other AI paradigms and offering insights into future directions. This survey serves as a valuable resource for researchers and practitioners seeking to navigate the rapidly evolving landscape of graph learning.

Shuo Yu, Feng Xia, Yueru Wang et al.

COVID-19 as a global pandemic causes a massive disruption to social stability that threatens human life and the economy. Policymakers and all elements of society must deliver measurable actions based on the pandemic's severity to minimize the detrimental impact of COVID-19. A proper forecasting system is arguably important to provide an early signal of the risk of COVID-19 infection so that the authorities are ready to protect the people from the worst. However, making a good forecasting model for infection risks in different cities or regions is not an easy task, because it has a lot of influential factors that are difficult to be identified manually. To address the current limitations, we propose a deep graph learning model, called PANDORA, to predict the infection risks of COVID-19, by considering all essential factors and integrating them into a geographical network. The framework uses geographical position relations and transportation frequency as higher-order structural properties formulated by higher-order network structures (i.e., network motifs). Moreover, four significant node attributes (i.e., multiple features of a particular area, including climate, medical condition, economy, and human mobility) are also considered. We propose three different aggregators to better aggregate node attributes and structural features, namely, Hadamard, Summation, and Connection. Experimental results over real data show that PANDORA outperforms the baseline method with higher accuracy and faster convergence speed, no matter which aggregator is chosen. We believe that PANDORA using deep graph learning provides a promising approach to get superior performance in infection risk level forecasting and help humans battle the COVID-19 crisis.

Zhen Cai, Tao Tang, Shuo Yu et al.

Federated recommender systems have been crucially enhanced through data sharing and continuous model updates, attributed to the pervasive connectivity and distributed computing capabilities of Internet of Things (IoT) devices. Given the sensitivity of IoT data, transparent data processing in data sharing and model updates is paramount. However, existing methods fall short in tracing the flow of shared data and the evolution of model updates. Consequently, data sharing is vulnerable to exploitation by malicious entities, raising significant data privacy concerns, while excluding data sharing will result in sub-optimal recommendations. To mitigate these concerns, we present LIBERATE, a privacy-traceable federated recommender system. We design a blockchain-based traceability mechanism, ensuring data privacy during data sharing and model updates. We further enhance privacy protection by incorporating local differential privacy in user-server communication. Extensive evaluations with the real-world dataset corroborate LIBERATE's capabilities in ensuring data privacy during data sharing and model update while maintaining efficiency and performance. Results underscore blockchain-based traceability mechanism as a promising solution for privacy-preserving in federated recommender systems.

Shuo Yu, Fayez Alqahtani, Amr Tolba et al.

Scientific collaboration is a significant behavior in knowledge creation and idea exchange. To tackle large and complex research questions, a trend of team formation has been observed in recent decades. In this study, we focus on recognizing collaborative teams and exploring inner patterns using scholarly big graph data. We propose a collaborative team recognition (CORE) model with a "core + extension" team structure to recognize collaborative teams in large academic networks. In CORE, we combine an effective evaluation index called the collaboration intensity index with a series of structural features to recognize collaborative teams in which members are in close collaboration relationships. Then, CORE is used to guide the core team members to their extension members. CORE can also serve as the foundation for team-based research. The simulation results indicate that CORE reveals inner patterns of scientific collaboration: senior scholars have broad collaborative relationships and fixed collaboration patterns, which are the underlying mechanisms of team assembly. The experimental results demonstrate that CORE is promising compared with state-of-the-art methods.

Xu Yuan, Na Zhou, Shuo Yu et al.

Anomaly detection (such as telecom fraud detection and medical image detection) has attracted the increasing attention of people. The complex interaction between multiple entities widely exists in the network, which can reflect specific human behavior patterns. Such patterns can be modeled by higher-order network structures, thus benefiting anomaly detection on attributed networks. However, due to the lack of an effective mechanism in most existing graph learning methods, these complex interaction patterns fail to be applied in detecting anomalies, hindering the progress of anomaly detection to some extent. In order to address the aforementioned issue, we present a higher-order structure based anomaly detection (GUIDE) method. We exploit attribute autoencoder and structure autoencoder to reconstruct node attributes and higher-order structures, respectively. Moreover, we design a graph attention layer to evaluate the significance of neighbors to nodes through their higher-order structure differences. Finally, we leverage node attribute and higher-order structure reconstruction errors to find anomalies. Extensive experiments on five real-world datasets (i.e., ACM, Citation, Cora, DBLP, and Pubmed) are implemented to verify the effectiveness of GUIDE. Experimental results in terms of ROC-AUC, PR-AUC, and Recall@K show that GUIDE significantly outperforms the state-of-art methods.

Lei Liu, Shuo Yu, Runze Wang et al.

While Large Language Models (LLMs) dominate tasks like natural language processing and computer vision, harnessing their power for spatial-temporal forecasting remains challenging. The disparity between sequential text and complex spatial-temporal data hinders this application. To address this issue, this paper introduces STG-LLM, an innovative approach empowering LLMs for spatial-temporal forecasting. We tackle the data mismatch by proposing: 1) STG-Tokenizer: This spatial-temporal graph tokenizer transforms intricate graph data into concise tokens capturing both spatial and temporal relationships; 2) STG-Adapter: This minimalistic adapter, consisting of linear encoding and decoding layers, bridges the gap between tokenized data and LLM comprehension. By fine-tuning only a small set of parameters, it can effectively grasp the semantics of tokens generated by STG-Tokenizer, while preserving the original natural language understanding capabilities of LLMs. Extensive experiments on diverse spatial-temporal benchmark datasets show that STG-LLM successfully unlocks LLM potential for spatial-temporal forecasting. Remarkably, our approach achieves competitive performance on par with dedicated SOTA methods.

Shuo Yu, Hongyan Xue, Xiang Ao et al.

In the field of quantitative trading, it is common practice to transform raw historical stock data into indicative signals for the market trend. Such signals are called alpha factors. Alphas in formula forms are more interpretable and thus favored by practitioners concerned with risk. In practice, a set of formulaic alphas is often used together for better modeling precision, so we need to find synergistic formulaic alpha sets that work well together. However, most traditional alpha generators mine alphas one by one separately, overlooking the fact that the alphas would be combined later. In this paper, we propose a new alpha-mining framework that prioritizes mining a synergistic set of alphas, i.e., it directly uses the performance of the downstream combination model to optimize the alpha generator. Our framework also leverages the strong exploratory capabilities of reinforcement learning~(RL) to better explore the vast search space of formulaic alphas. The contribution to the combination models' performance is assigned to be the return used in the RL process, driving the alpha generator to find better alphas that improve upon the current set. Experimental evaluations on real-world stock market data demonstrate both the effectiveness and the efficiency of our framework for stock trend forecasting. The investment simulation results show that our framework is able to achieve higher returns compared to previous approaches.

Feng Xia, Ke Sun, Shuo Yu et al.

Graphs are widely used as a popular representation of the network structure of connected data. Graph data can be found in a broad spectrum of application domains such as social systems, ecosystems, biological networks, knowledge graphs, and information systems. With the continuous penetration of artificial intelligence technologies, graph learning (i.e., machine learning on graphs) is gaining attention from both researchers and practitioners. Graph learning proves effective for many tasks, such as classification, link prediction, and matching. Generally, graph learning methods extract relevant features of graphs by taking advantage of machine learning algorithms. In this survey, we present a comprehensive overview on the state-of-the-art of graph learning. Special attention is paid to four categories of existing graph learning methods, including graph signal processing, matrix factorization, random walk, and deep learning. Major models and algorithms under these categories are reviewed respectively. We examine graph learning applications in areas such as text, images, science, knowledge graphs, and combinatorial optimization. In addition, we discuss several promising research directions in this field.

Ke Sun, Jiaying Liu, Shuo Yu et al.

Features representation leverages the great power in network analysis tasks. However, most features are discrete which poses tremendous challenges to effective use. Recently, increasing attention has been paid on network feature learning, which could map discrete features to continued space. Unfortunately, current studies fail to fully preserve the structural information in the feature space due to random negative sampling strategy during training. To tackle this problem, we study the problem of feature learning and novelty propose a force-based graph learning model named GForce inspired by the spring-electrical model. GForce assumes that nodes are in attractive forces and repulsive forces, thus leading to the same representation with the original structural information in feature learning. Comprehensive experiments on benchmark datasets demonstrate the effectiveness of the proposed framework. Furthermore, GForce opens up opportunities to use physics models to model node interaction for graph learning.

Shuo Yu, Feng Xia, Jin Xu et al.

Aiming at better representing multivariate relationships, this paper investigates a motif dimensional framework for higher-order graph learning. The graph learning effectiveness can be improved through OFFER. The proposed framework mainly aims at accelerating and improving higher-order graph learning results. We apply the acceleration procedure from the dimensional of network motifs. Specifically, the refined degree for nodes and edges are conducted in two stages: (1) employ motif degree of nodes to refine the adjacency matrix of the network; and (2) employ motif degree of edges to refine the transition probability matrix in the learning process. In order to assess the efficiency of the proposed framework, four popular network representation algorithms are modified and examined. By evaluating the performance of OFFER, both link prediction results and clustering results demonstrate that the graph representation learning algorithms enhanced with OFFER consistently outperform the original algorithms with higher efficiency.

Jin Xu, Shuo Yu, Ke Sun et al.

Multivariate relations are general in various types of networks, such as biological networks, social networks, transportation networks, and academic networks. Due to the principle of ternary closures and the trend of group formation, the multivariate relationships in social networks are complex and rich. Therefore, in graph learning tasks of social networks, the identification and utilization of multivariate relationship information are more important. Existing graph learning methods are based on the neighborhood information diffusion mechanism, which often leads to partial omission or even lack of multivariate relationship information, and ultimately affects the accuracy and execution efficiency of the task. To address these challenges, this paper proposes the multivariate relationship aggregation learning (MORE) method, which can effectively capture the multivariate relationship information in the network environment. By aggregating node attribute features and structural features, MORE achieves higher accuracy and faster convergence speed. We conducted experiments on one citation network and five social networks. The experimental results show that the MORE model has higher accuracy than the GCN (Graph Convolutional Network) model in node classification tasks, and can significantly reduce time cost.

Hayat Dino Bedru, Shuo Yu, Xinru Xiao et al.

A network is a typical expressive form of representing complex systems in terms of vertices and links, in which the pattern of interactions amongst components of the network is intricate. The network can be static that does not change over time or dynamic that evolves through time. The complication of network analysis is different under the new circumstance of network size explosive increasing. In this paper, we introduce a new network science concept called big network. Big networks are generally in large-scale with a complicated and higher-order inner structure. This paper proposes a guideline framework that gives an insight into the major topics in the area of network science from the viewpoint of a big network. We first introduce the structural characteristics of big networks from three levels, which are micro-level, meso-level, and macro-level. We then discuss some state-of-the-art advanced topics of big network analysis. Big network models and related approaches, including ranking methods, partition approaches, as well as network embedding algorithms are systematically introduced. Some typical applications in big networks are then reviewed, such as community detection, link prediction, recommendation, etc. Moreover, we also pinpoint some critical open issues that need to be investigated further.