arXiv subjects

Jiliang Tang

Publications and source records attributed to Jiliang Tang.

At least 73 records · Page 4Linked to original sources

arXiv2025

Towards the Effect of Examples on In-Context Learning: A Theoretical Case Study

In-context learning (ICL) has emerged as a powerful capability for large language models (LLMs) to adapt to downstream tasks by leveraging a few (demonstration) examples. Despite its effectiveness, the mechanism behind ICL remains underexplored. To better understand how ICL integrates the examples with the knowledge learned by the LLM during pre-training (i.e., pre-training knowledge) and how the examples impact ICL, this paper conducts a theoretical study in binary classification tasks. In particular, we introduce a probabilistic model extending from the Gaussian mixture model to exactly quantify the impact of pre-training knowledge, label frequency, and label noise on the prediction accuracy. Based on our analysis, when the pre-training knowledge contradicts the knowledge in the examples, whether ICL prediction relies more on the pre-training knowledge or the examples depends on the number of examples. In addition, the label frequency and label noise of the examples both affect the accuracy of the ICL prediction, where the minor class has a lower accuracy, and how the label noise impacts the accuracy is determined by the specific noise level of the two classes. Extensive simulations are conducted to verify the correctness of the theoretical results, and real-data experiments also align with the theoretical insights. Our work reveals the role of pre-training knowledge and examples in ICL, offering a deeper understanding of LLMs' behaviors in classification tasks.

cs.LG↗

arXiv2025

Mixture of Structural-and-Textual Retrieval over Text-rich Graph Knowledge Bases

Text-rich Graph Knowledge Bases (TG-KBs) have become increasingly crucial for answering queries by providing textual and structural knowledge. However, current retrieval methods often retrieve these two types of knowledge in isolation without considering their mutual reinforcement and some hybrid methods even bypass structural retrieval entirely after neighboring aggregation. To fill in this gap, we propose a Mixture of Structural-and-Textual Retrieval (MoR) to retrieve these two types of knowledge via a Planning-Reasoning-Organizing framework. In the Planning stage, MoR generates textual planning graphs delineating the logic for answering queries. Following planning graphs, in the Reasoning stage, MoR interweaves structural traversal and textual matching to obtain candidates from TG-KBs. In the Organizing stage, MoR further reranks fetched candidates based on their structural trajectory. Extensive experiments demonstrate the superiority of MoR in harmonizing structural and textual retrieval with insights, including uneven retrieving performance across different query logics and the benefits of integrating structural trajectories for candidate reranking. Our code is available at https://github.com/Yoega/MoR.

cs.LG↗

arXiv2025

One Model for One Graph: A New Perspective for Pretraining with Cross-domain Graphs

Graph Neural Networks (GNNs) have emerged as a powerful tool to capture intricate network patterns, achieving success across different domains. However, existing GNNs require careful domain-specific architecture designs and training from scratch on each dataset, leading to an expertise-intensive process with difficulty in generalizing across graphs from different domains. Therefore, it can be hard for practitioners to infer which GNN model can generalize well to graphs from their domains. To address this challenge, we propose a novel cross-domain pretraining framework, "one model for one graph," which overcomes the limitations of previous approaches that failed to use a single GNN to capture diverse graph patterns across domains with significant gaps. Specifically, we pretrain a bank of expert models, with each one corresponding to a specific dataset. When inferring to a new graph, gating functions choose a subset of experts to effectively integrate prior model knowledge while avoiding negative transfer. Extensive experiments consistently demonstrate the superiority of our proposed method on both link prediction and node classification tasks.

cs.LG↗

arXiv2025

Higher-order Structure Boosts Link Prediction on Temporal Graphs

Temporal Graph Neural Networks (TGNNs) have gained growing attention for modeling and predicting structures in temporal graphs. However, existing TGNNs primarily focus on pairwise interactions while overlooking higher-order structures that are integral to link formation and evolution in real-world temporal graphs. Meanwhile, these models often suffer from efficiency bottlenecks, further limiting their expressive power. To tackle these challenges, we propose a Higher-order structure Temporal Graph Neural Network, which incorporates hypergraph representations into temporal graph learning. In particular, we develop an algorithm to identify the underlying higher-order structures, enhancing the model's ability to capture the group interactions. Furthermore, by aggregating multiple edge features into hyperedge representations, HTGN effectively reduces memory cost during training. We theoretically demonstrate the enhanced expressiveness of our approach and validate its effectiveness and efficiency through extensive experiments on various real-world temporal graphs. Experimental results show that HTGN achieves superior performance on dynamic link prediction while reducing memory costs by up to 50\% compared to existing methods.

cs.LG↗

arXiv2025

How Do Large Language Models Understand Graph Patterns? A Benchmark for Graph Pattern Comprehension

Benchmarking the capabilities and limitations of large language models (LLMs) in graph-related tasks is becoming an increasingly popular and crucial area of research. Recent studies have shown that LLMs exhibit a preliminary ability to understand graph structures and node features. However, the potential of LLMs in graph pattern mining remains largely unexplored. This is a key component in fields such as computational chemistry, biology, and social network analysis. To bridge this gap, this work introduces a comprehensive benchmark to assess LLMs' capabilities in graph pattern tasks. We have developed a benchmark that evaluates whether LLMs can understand graph patterns based on either terminological or topological descriptions. Additionally, our benchmark tests the LLMs' capacity to autonomously discover graph patterns from data. The benchmark encompasses both synthetic and real datasets, and a variety of models, with a total of 11 tasks and 7 models. Our experimental framework is designed for easy expansion to accommodate new models and datasets. Our findings reveal that: (1) LLMs have preliminary abilities to understand graph patterns, with O1-mini outperforming in the majority of tasks; (2) Formatting input data to align with the knowledge acquired during pretraining can enhance performance; (3) The strategies employed by LLMs may differ from those used in conventional algorithms.

cs.LG↗

arXiv2025

Learning with Less: Knowledge Distillation from Large Language Models via Unlabeled Data

In real-world NLP applications, Large Language Models (LLMs) offer promising solutions due to their extensive training on vast datasets. However, the large size and high computation demands of LLMs limit their practicality in many applications, especially when further fine-tuning is required. To address these limitations, smaller models are typically preferred for deployment. However, their training is hindered by the scarcity of labeled data. In contrast, unlabeled data is often readily which can be leveraged by using LLMs to generate pseudo-labels for training smaller models. This enables the smaller models (student) to acquire knowledge from LLMs(teacher) while reducing computational costs. This process introduces challenges, such as potential noisy pseudo-labels. Selecting high-quality and informative data is therefore critical to enhance model performance while improving the efficiency of data utilization. To address this, we propose LLKD that enables Learning with Less computational resources and less data for Knowledge Distillation from LLMs. LLKD is an adaptive sample selection method that incorporates signals from both the teacher and student. Specifically, it prioritizes samples where the teacher demonstrates high confidence in its labeling, indicating reliable labels, and where the student exhibits a high information need, identifying challenging samples that require further learning. Our comprehensive experiments show that LLKD achieves superior performance across various datasets with higher data efficiency.

cs.AI↗

arXiv2025

Empowering GraphRAG with Knowledge Filtering and Integration

In recent years, large language models (LLMs) have revolutionized the field of natural language processing. However, they often suffer from knowledge gaps and hallucinations. Graph retrieval-augmented generation (GraphRAG) enhances LLM reasoning by integrating structured knowledge from external graphs. However, we identify two key challenges that plague GraphRAG:(1) Retrieving noisy and irrelevant information can degrade performance and (2)Excessive reliance on external knowledge suppresses the model's intrinsic reasoning. To address these issues, we propose GraphRAG-FI (Filtering and Integration), consisting of GraphRAG-Filtering and GraphRAG-Integration. GraphRAG-Filtering employs a two-stage filtering mechanism to refine retrieved information. GraphRAG-Integration employs a logits-based selection strategy to balance external knowledge from GraphRAG with the LLM's intrinsic reasoning,reducing over-reliance on retrievals. Experiments on knowledge graph QA tasks demonstrate that GraphRAG-FI significantly improves reasoning performance across multiple backbone models, establishing a more reliable and effective GraphRAG framework.

cs.AI↗

arXiv2025

Aligning Large Language Models and Geometric Deep Models for Protein Representation

Latent representation alignment has become a foundational technique for constructing multimodal large language models (MLLM) by mapping embeddings from different modalities into a shared space, often aligned with the embedding space of large language models (LLMs) to enable effective cross-modal understanding. While preliminary protein-focused MLLMs have emerged, they have predominantly relied on heuristic approaches, lacking a fundamental understanding of optimal alignment practices across representations. In this study, we explore the alignment of multimodal representations between LLMs and Geometric Deep Models (GDMs) in the protein domain. We comprehensively evaluate three state-of-the-art LLMs (Gemma2-2B, LLaMa3.1-8B, and LLaMa3.1-70B) with four protein-specialized GDMs (GearNet, GVP, ScanNet, GAT). Our work examines alignment factors from both model and protein perspectives, identifying challenges in current alignment methodologies and proposing strategies to improve the alignment process. Our key findings reveal that GDMs incorporating both graph and 3D structural information align better with LLMs, larger LLMs demonstrate improved alignment capabilities, and protein rarity significantly impacts alignment performance. We also find that increasing GDM embedding dimensions, using two-layer projection heads, and fine-tuning LLMs on protein-specific data substantially enhance alignment quality. These strategies offer potential enhancements to the performance of protein-related multimodal models. Our code and data are available at https://github.com/Tizzzzy/LLM-GDM-alignment.

cs.LG↗

arXiv2025

Multi-Faceted Studies on Data Poisoning can Advance LLM Development

The lifecycle of large language models (LLMs) is far more complex than that of traditional machine learning models, involving multiple training stages, diverse data sources, and varied inference methods. While prior research on data poisoning attacks has primarily focused on the safety vulnerabilities of LLMs, these attacks face significant challenges in practice. Secure data collection, rigorous data cleaning, and the multistage nature of LLM training make it difficult to inject poisoned data or reliably influence LLM behavior as intended. Given these challenges, this position paper proposes rethinking the role of data poisoning and argue that multi-faceted studies on data poisoning can advance LLM development. From a threat perspective, practical strategies for data poisoning attacks can help evaluate and address real safety risks to LLMs. From a trustworthiness perspective, data poisoning can be leveraged to build more robust LLMs by uncovering and mitigating hidden biases, harmful outputs, and hallucinations. Moreover, from a mechanism perspective, data poisoning can provide valuable insights into LLMs, particularly the interplay between data and model behavior, driving a deeper understanding of their underlying mechanisms.

cs.CR↗

arXiv2025

Mitigating the Privacy Issues in Retrieval-Augmented Generation (RAG) via Pure Synthetic Data

Retrieval-augmented generation (RAG) enhances the outputs of language models by integrating relevant information retrieved from external knowledge sources. However, when the retrieval process involves private data, RAG systems may face severe privacy risks, potentially leading to the leakage of sensitive information. To address this issue, we propose using synthetic data as a privacy-preserving alternative for the retrieval data. We propose SAGE, a novel two-stage synthetic data generation paradigm. In the stage-1, we employ an attribute-based extraction and generation approach to preserve key contextual information from the original data. In the stage-2, we further enhance the privacy properties of the synthetic data through an agent-based iterative refinement process. Extensive experiments demonstrate that using our synthetic data as the retrieval context achieves comparable performance to using the original data while substantially reducing privacy risks. Our work takes the first step towards investigating the possibility of generating high-utility and privacy-preserving synthetic data for RAG, opening up new opportunities for the safe application of RAG systems in various domains.

cs.CR↗

arXiv2025

Unveiling Mode Connectivity in Graph Neural Networks

A fundamental challenge in understanding graph neural networks (GNNs) lies in characterizing their optimization dynamics and loss landscape geometry, critical for improving interpretability and robustness. While mode connectivity, a lens for analyzing geometric properties of loss landscapes has proven insightful for other deep learning architectures, its implications for GNNs remain unexplored. This work presents the first investigation of mode connectivity in GNNs. We uncover that GNNs exhibit distinct non-linear mode connectivity, diverging from patterns observed in fully-connected networks or CNNs. Crucially, we demonstrate that graph structure, rather than model architecture, dominates this behavior, with graph properties like homophily correlating with mode connectivity patterns. We further establish a link between mode connectivity and generalization, proposing a generalization bound based on loss barriers and revealing its utility as a diagnostic tool. Our findings further bridge theoretical insights with practical implications: they rationalize domain alignment strategies in graph learning and provide a foundation for refining GNN training paradigms.

cs.LG↗

arXiv2025

Stepwise Perplexity-Guided Refinement for Efficient Chain-of-Thought Reasoning in Large Language Models

Chain-of-Thought (CoT) reasoning, which breaks down complex tasks into intermediate reasoning steps, has significantly enhanced the performance of large language models (LLMs) on challenging tasks. However, the detailed reasoning process in CoT often incurs long generation times and high computational costs, partly due to the inclusion of unnecessary steps. To address this, we propose a method to identify critical reasoning steps using perplexity as a measure of their importance: a step is deemed critical if its removal causes a significant increase in perplexity. Our method enables models to focus solely on generating these critical steps. This can be achieved through two approaches: refining demonstration examples in few-shot CoT or fine-tuning the model using selected examples that include only critical steps. Comprehensive experiments validate the effectiveness of our method, which achieves a better balance between the reasoning accuracy and efficiency of CoT.

cs.CL↗

arXiv2025

A Survey to Recent Progress Towards Understanding In-Context Learning

In-Context Learning (ICL) empowers Large Language Models (LLMs) with the ability to learn from a few examples provided in the prompt, enabling downstream generalization without the requirement for gradient updates. Despite encouragingly empirical success, the underlying mechanism of ICL remains unclear. Existing research remains ambiguous with various viewpoints, utilizing intuition-driven and ad-hoc technical solutions to interpret ICL. In this paper, we leverage a data generation perspective to reinterpret recent efforts from a systematic angle, demonstrating the potential broader usage of these popular technical solutions. For a conceptual definition, we rigorously adopt the terms of skill recognition and skill learning. Skill recognition selects one learned data generation function previously seen during pre-training while skill learning can learn new data generation functions from in-context data. Furthermore, we provide insights into the strengths and weaknesses of both abilities, emphasizing their commonalities through the perspective of data generation. This analysis suggests potential directions for future research.

cs.CL↗

arXiv2025

Graph-level Representation Learning with Joint-Embedding Predictive Architectures

Joint-Embedding Predictive Architectures (JEPAs) have recently emerged as a novel and powerful technique for self-supervised representation learning. They aim to learn an energy-based model by predicting the latent representation of a target signal y from the latent representation of a context signal x. JEPAs bypass the need for negative and positive samples, traditionally required by contrastive learning while avoiding the overfitting issues associated with generative pretraining. In this paper, we show that graph-level representations can be effectively modeled using this paradigm by proposing a Graph Joint-Embedding Predictive Architecture (Graph-JEPA). In particular, we employ masked modeling and focus on predicting the latent representations of masked subgraphs starting from the latent representation of a context subgraph. To endow the representations with the implicit hierarchy that is often present in graph-level concepts, we devise an alternative prediction objective that consists of predicting the coordinates of the encoded subgraphs on the unit hyperbola in the 2D plane. Through multiple experimental evaluations, we show that Graph-JEPA can learn highly semantic and expressive representations, as shown by the downstream performance in graph classification, regression, and distinguishing non-isomorphic graphs. The code is available at https://github.com/geriskenderi/graph-jepa.

cs.LG↗

arXiv2025

Reasoning with Graphs: Structuring Implicit Knowledge to Enhance LLMs Reasoning

Large language models (LLMs) have demonstrated remarkable success across a wide range of tasks; however, they still encounter challenges in reasoning tasks that require understanding and inferring relationships between distinct pieces of information within text sequences. This challenge is particularly pronounced in tasks involving multi-step processes, such as logical reasoning and multi-hop question answering, where understanding implicit relationships between entities and leveraging multi-hop connections in the given context are crucial. Graphs, as fundamental data structures, explicitly represent pairwise relationships between entities, thereby offering the potential to enhance LLMs' reasoning capabilities. External graphs have proven effective in supporting LLMs across multiple tasks. However, in many reasoning tasks, no pre-existing graph structure is provided. Can we structure implicit knowledge derived from context into graphs to assist LLMs in reasoning? In this paper, we propose Reasoning with Graphs (RwG) by first constructing explicit graphs from the context and then leveraging these graphs to enhance LLM reasoning performance on reasoning tasks. Extensive experiments demonstrate the effectiveness of the proposed method in improving both logical reasoning and multi-hop question answering tasks.

cs.CL↗

arXiv2025

Retrieval-Augmented Generation with Graphs (GraphRAG)

Retrieval-augmented generation (RAG) is a powerful technique that enhances downstream task execution by retrieving additional information, such as knowledge, skills, and tools from external sources. Graph, by its intrinsic "nodes connected by edges" nature, encodes massive heterogeneous and relational information, making it a golden resource for RAG in tremendous real-world applications. As a result, we have recently witnessed increasing attention on equipping RAG with Graph, i.e., GraphRAG. However, unlike conventional RAG, where the retriever, generator, and external data sources can be uniformly designed in the neural-embedding space, the uniqueness of graph-structured data, such as diverse-formatted and domain-specific relational knowledge, poses unique and significant challenges when designing GraphRAG for different domains. Given the broad applicability, the associated design challenges, and the recent surge in GraphRAG, a systematic and up-to-date survey of its key concepts and techniques is urgently desired. Following this motivation, we present a comprehensive and up-to-date survey on GraphRAG. Our survey first proposes a holistic GraphRAG framework by defining its key components, including query processor, retriever, organizer, generator, and data source. Furthermore, recognizing that graphs in different domains exhibit distinct relational patterns and require dedicated designs, we review GraphRAG techniques uniquely tailored to each domain. Finally, we discuss research challenges and brainstorm directions to inspire cross-disciplinary opportunities. Our survey repository is publicly maintained at https://github.com/Graph-RAG/GraphRAG/.

cs.IR↗

arXiv2025

Revisiting the Graph Reasoning Ability of Large Language Models: Case Studies in Translation, Connectivity and Shortest Path

Large Language Models (LLMs) have achieved great success in various reasoning tasks. In this work, we focus on the graph reasoning ability of LLMs. Although theoretical studies proved that LLMs are capable of handling graph reasoning tasks, empirical evaluations reveal numerous failures. To deepen our understanding on this discrepancy, we revisit the ability of LLMs on three fundamental graph tasks: graph description translation, graph connectivity, and the shortest-path problem. Our findings suggest that LLMs can fail to understand graph structures through text descriptions and exhibit varying performance for all these three fundamental tasks. Meanwhile, we perform a real-world investigation on knowledge graphs and make consistent observations with our findings. The codes and datasets are available.

cs.CL↗

arXiv2024

Mixture of Link Predictors on Graphs

Link prediction, which aims to forecast unseen connections in graphs, is a fundamental task in graph machine learning. Heuristic methods, leveraging a range of different pairwise measures such as common neighbors and shortest paths, often rival the performance of vanilla Graph Neural Networks (GNNs). Therefore, recent advancements in GNNs for link prediction (GNN4LP) have primarily focused on integrating one or a few types of pairwise information. In this work, we reveal that different node pairs within the same dataset necessitate varied pairwise information for accurate prediction and models that only apply the same pairwise information uniformly could achieve suboptimal performance. As a result, we propose a simple mixture of experts model Link-MoE for link prediction. Link-MoE utilizes various GNNs as experts and strategically selects the appropriate expert for each node pair based on various types of pairwise information. Experimental results across diverse real-world datasets demonstrate substantial performance improvement from Link-MoE. Notably, Link-MoE achieves a relative improvement of 18.71\% on the MRR metric for the Pubmed dataset and 9.59\% on the Hits@100 metric for the ogbl-ppa dataset, compared to the best baselines.

cs.LG↗