arXiv subjects

Pan Li

Publications and source records attributed to Pan Li.

At least 91 records · Page 5Linked to original sources

arXiv2025

STRIDE: Structure and Embedding Distillation with Attention for Graph Neural Networks

Recent advancements in Graph Neural Networks (GNNs) have led to increased model sizes to enhance their capacity and accuracy. Such large models incur high memory usage, latency, and computational costs, thereby restricting their inference deployment. GNN compression techniques compress large GNNs into smaller ones with negligible accuracy loss. One of the most promising compression techniques is knowledge distillation (KD). However, most KD approaches for GNNs only consider the outputs of the last layers and do not consider the outputs of the intermediate layers of the GNNs. The intermediate layers may contain important inductive biases indicated by the graph structure and embeddings. Ignoring these layers may lead to a high accuracy drop, especially when the compression ratio is high. To address these shortcomings, we propose a novel KD approach for GNN compression that we call Structure and Embedding Distillation with Attention (STRIDE). STRIDE utilizes attention to identify important intermediate teacher-student layer pairs and focuses on using those pairs to align graph structure and node embeddings. We evaluate STRIDE on several datasets, such as OGBN-Mag and OGBN-Arxiv, using different model architectures, including GCNIIs, RGCNs, and GraphSAGE. On average, STRIDE achieves a 2.13% increase in accuracy with a 32.3X compression ratio on OGBN-Mag, a large graph dataset, compared to state-of-the-art approaches. On smaller datasets (e.g., Pubmed), STRIDE achieves up to a 141X compression ratio with the same accuracy as state-of-the-art approaches. These results highlight the effectiveness of focusing on intermediate-layer knowledge to obtain compact, accurate, and practical GNN models.

cs.LG↗

arXiv2025

FAEDKV: Infinite-Window Fourier Transform for Unbiased KV Cache Compression

The efficacy of Large Language Models (LLMs) in long-context tasks is often hampered by the substantial memory footprint and computational demands of the Key-Value (KV) cache. Current compression strategies, including token eviction and learned projections, frequently lead to biased representations -- either by overemphasizing recent/high-attention tokens or by repeatedly degrading information from earlier context -- and may require costly model retraining. We present FAEDKV (Frequency-Adaptive Infinite-Window for KV cache), a novel, training-free KV cache compression framework that ensures unbiased information retention. FAEDKV operates by transforming the KV cache into the frequency domain using a proposed Infinite-Window Fourier Transform (IWDFT). This approach allows for the equalized contribution of all tokens to the compressed representation, effectively preserving both early and recent contextual information. A preliminary frequency ablation study identifies critical spectral components for layer-wise, targeted compression. Experiments on LongBench benchmark demonstrate FAEDKV's superiority over existing methods by up to 22\%. In addition, our method shows superior, position-agnostic retrieval accuracy on the Needle-In-A-Haystack task compared to compression based approaches.

cs.CL↗

arXiv2025

Weak-to-Strong GraphRAG: Aligning Weak Retrievers with Large Language Models for Graph-based Retrieval Augmented Generation

Graph-based retrieval-augmented generation (RAG) enables large language models (LLMs) to ground responses with structured external knowledge from up-to-date knowledge graphs (KGs) and reduce hallucinations. However, LLMs often rely on a weak retriever in graph-based RAG: I) Due to the lack of ground truth, the retriever is often trained on weak supervision, which often introduces spurious signals to the LLMs. II) Due to the abstraction of graph data, the retrieved knowledge is often presented in unorganized forms. To mitigate the issue, we present Refined Graph-based RAG (ReG) to align weak retrievers to LLMs for graph-based RAG. Specifically, ReG incorporates LLM feedback to get rid of spurious signals and improve the quality of the supervision. Meanwhile, ReG introduces a structure-aware reorganization module to refactor the retrieval results into logically coherent evidence chains. Experiments on prominent benchmarks demonstrate that ReG significantly and consistently brings improvements across different LLM backbones by up to 10%. The improved supervision quality enables ReG to match the state-of-the-art performance with 5% training data and to transfer to out-of-distribution KGs. Notably, when adopted to reasoning-based LLMs, ReG reduces the reasoning token cost by up to 30% and improves the performance by up to 4%.

cs.CL↗

arXiv2025

Learning Efficient and Generalizable Graph Retriever for Knowledge-Graph Question Answering

Large Language Models (LLMs) have shown strong inductive reasoning ability across various domains, but their reliability is hindered by the outdated knowledge and hallucinations. Retrieval-Augmented Generation mitigates these issues by grounding LLMs with external knowledge; however, most existing RAG pipelines rely on unstructured text, limiting interpretability and structured reasoning. Knowledge graphs, which represent facts as relational triples, offer a more structured and compact alternative. Recent studies have explored integrating knowledge graphs with LLMs for knowledge graph question answering (KGQA), with a significant proportion adopting the retrieve-then-reasoning paradigm. In this framework, graph-based retrievers have demonstrated strong empirical performance, yet they still face challenges in generalization ability. In this work, we propose RAPL, a novel framework for efficient and effective graph retrieval in KGQA. RAPL addresses these limitations through three aspects: (1) a two-stage labeling strategy that combines heuristic signals with parametric models to provide causally grounded supervision; (2) a model-agnostic graph transformation approach to capture both intra- and inter-triple interactions, thereby enhancing representational capacity; and (3) a path-based reasoning strategy that facilitates learning from the injected rational knowledge, and supports downstream reasoner through structured inputs. Empirically, RAPL outperforms state-of-the-art methods by $2.66\%-20.34\%$, and significantly reduces the performance gap between smaller and more powerful LLM-based reasoners, as well as the gap under cross-dataset settings, highlighting its superior retrieval capability and generalizability. Codes are available at: https://github.com/tianyao-aka/RAPL.

cs.CL↗

arXiv2025

NAM: A Normalization Attention Model for Personalized Product Search In Fliggy

Personalized product search provides significant benefits to e-commerce platforms by extracting more accurate user preferences from historical behaviors. Previous studies largely focused on the user factors when personalizing the search query, while ignoring the item perspective, which leads to the following two challenges that we summarize in this paper: First, previous approaches relying only on co-occurrence frequency tend to overestimate the conversion rates for popular items and underestimate those for long-tail items, resulting in inaccurate item similarities; Second, user purchasing propensity is highly heterogeneous according to the popularity of the target item: it is less correlated with the user's historical behavior for a popular item and more correlated for a long-tail item. To address these challenges, in this paper we propose NAM, a Normalization Attention Model, which optimizes ''when to personalize'' by utilizing Inverse Item Frequency (IIF) and employing a gating mechanism, as well as optimizes ''how to personalize'' by normalizing the attention mechanism from a global perspective. Through comprehensive experiments, we demonstrate that our proposed NAM model significantly outperforms state-of-the-art baseline models. Furthermore, we conducted an online A/B test at Fliggy, and obtained a significant improvement of 0.8% over the latest production system in conversion rate.

cs.IR↗

arXiv2025

Model Generalization on Text Attribute Graphs: Principles with Large Language Models

Large language models (LLMs) have recently been introduced to graph learning, aiming to extend their zero-shot generalization success to tasks where labeled graph data is scarce. Among these applications, inference over text-attributed graphs (TAGs) presents unique challenges: existing methods struggle with LLMs' limited context length for processing large node neighborhoods and the misalignment between node embeddings and the LLM token space. To address these issues, we establish two key principles for ensuring generalization and derive the framework LLM-BP accordingly: (1) Unifying the attribute space with task-adaptive embeddings, where we leverage LLM-based encoders and task-aware prompting to enhance generalization of the text attribute embeddings; (2) Developing a generalizable graph information aggregation mechanism, for which we adopt belief propagation with LLM-estimated parameters that adapt across graphs. Evaluations on 11 real-world TAG benchmarks demonstrate that LLM-BP significantly outperforms existing approaches, achieving 8.10% improvement with task-conditional embeddings and an additional 1.71% gain from adaptive aggregation. The code and task-adaptive embeddings are publicly available.

cs.LG↗

arXiv2025

Powers of Magnetic Graph Matrix: Fourier Spectrum, Walk Compression, and Applications

Magnetic graphs, originally developed to model quantum systems under magnetic fields, have recently emerged as a powerful framework for analyzing complex directed networks. Existing research has primarily used the spectral properties of the magnetic graph matrix to study global and stationary network features. However, their capacity to model local, non-equilibrium behaviors, often described by matrix powers, remains largely unexplored. We present a novel combinatorial interpretation of the magnetic graph matrix powers through directed walk profiles -- counts of graph walks indexed by the number of edge reversals. Crucially, we establish that walk profiles correspond to a Fourier transform of magnetic matrix powers. The connection allows exact reconstruction of walk profiles from magnetic matrix powers at multiple discrete potentials, and more importantly, an even smaller number of potentials often suffices for accurate approximate reconstruction in real networks. This shows the empirical compressibility of the information captured by the magnetic matrix. This fresh perspective suggests new applications; for example, we illustrate how powers of the magnetic matrix can identify frustrated directed cycles (e.g., feedforward loops) and can be effectively employed for link prediction by encoding local structural details in directed graphs.

physics.soc-ph↗

arXiv2025

Underestimated Privacy Risks for Minority Populations in Large Language Model Unlearning

Large Language Models (LLMs) embed sensitive, human-generated data, prompting the need for unlearning methods. Although certified unlearning offers strong privacy guarantees, its restrictive assumptions make it unsuitable for LLMs, giving rise to various heuristic approaches typically assessed through empirical evaluations. These standard evaluations randomly select data for removal, apply unlearning techniques, and use membership inference attacks (MIAs) to compare unlearned models against models retrained without the removed data. However, to ensure robust privacy protections for every data point, it is essential to account for scenarios in which certain data subsets face elevated risks. Prior research suggests that outliers, particularly including data tied to minority groups, often exhibit higher memorization propensity which indicates they may be more difficult to unlearn. Building on these insights, we introduce a complementary, minority-aware evaluation framework to highlight blind spots in existing frameworks. We substantiate our findings with carefully designed experiments, using canaries with personally identifiable information (PII) to represent these minority subsets and demonstrate that they suffer at least 20% higher privacy leakage across various unlearning methods, MIAs, datasets, and LLM scales. Our proposed minority-aware evaluation framework marks an essential step toward more equitable and comprehensive assessments of LLM unlearning efficacy.

cs.LG↗

arXiv2025

MatterTune: An Integrated, User-Friendly Platform for Fine-Tuning Atomistic Foundation Models to Accelerate Materials Simulation and Discovery

Geometric machine learning models such as graph neural networks have achieved remarkable success in recent years in chemical and materials science research for applications such as high-throughput virtual screening and atomistic simulations. The success of these models can be attributed to their ability to effectively learn latent representations of atomic structures directly from the training data. Conversely, this also results in high data requirements for these models, hindering their application to problems which are data sparse which are common in this domain. To address this limitation, there is a growing development in the area of pre-trained machine learning models which have learned general, fundamental, geometric relationships in atomistic data, and which can then be fine-tuned to much smaller application-specific datasets. In particular, models which are pre-trained on diverse, large-scale atomistic datasets have shown impressive generalizability and flexibility to downstream applications, and are increasingly referred to as atomistic foundation models. To leverage the untapped potential of these foundation models, we introduce MatterTune, a modular and extensible framework that provides advanced fine-tuning capabilities and seamless integration of atomistic foundation models into downstream materials informatics and simulation workflows, thereby lowering the barriers to adoption and facilitating diverse applications in materials science. In its current state, MatterTune supports a number of state-of-the-art foundation models such as ORB, MatterSim, JMP, and EquformerV2, and hosts a wide range of features including a modular and flexible design, distributed and customizable fine-tuning, broad support for downstream informatics tasks, and more.

cond-mat.mtrl-sci↗

arXiv2025

Automating Personalization: Prompt Optimization for Recommendation Reranking

Modern recommender systems increasingly leverage large language models (LLMs) for reranking to improve personalization. However, existing approaches face two key limitations: (1) heavy reliance on manually crafted prompts that are difficult to scale, and (2) inadequate handling of unstructured item metadata that complicates preference inference. We present AGP (Auto-Guided Prompt Refinement), a novel framework that automatically optimizes user profile generation prompts for personalized reranking. AGP introduces two key innovations: (1) position-aware feedback mechanisms for precise ranking correction, and (2) batched training with aggregated feedback to enhance generalization.

cs.IR↗

arXiv2025

A Survey of Deep Graph Learning under Distribution Shifts: from Graph Out-of-Distribution Generalization to Adaptation

Distribution shifts on graphs -- the discrepancies in data distribution between training and employing a graph machine learning model -- are ubiquitous and often unavoidable in real-world scenarios. These shifts may severely deteriorate model performance, posing significant challenges for reliable graph machine learning. Consequently, there has been a surge in research on graph machine learning under distribution shifts, aiming to train models to achieve satisfactory performance on out-of-distribution (OOD) test data. In our survey, we provide an up-to-date and forward-looking review of deep graph learning under distribution shifts. Specifically, we cover three primary scenarios: graph OOD generalization, training-time graph OOD adaptation, and test-time graph OOD adaptation. We begin by formally formulating the problems and discussing various types of distribution shifts that can affect graph learning, such as covariate shifts and concept shifts. To provide a better understanding of the literature, we introduce a systematic taxonomy that classifies existing methods into model-centric and data-centric approaches, investigating the techniques used in each category. We also summarize commonly used datasets in this research area to facilitate further investigation. Finally, we point out promising research directions and the corresponding challenges to encourage further study in this vital domain. We also provide a continuously updated reading list at https://github.com/kaize0409/Awesome-Graph-OOD.

cs.LG↗

arXiv2025

Understanding and Mitigating Bottlenecks of State Space Models through the Lens of Recency and Over-smoothing

Structured State Space Models (SSMs) have emerged as alternatives to transformers. While SSMs are often regarded as effective in capturing long-sequence dependencies, we rigorously demonstrate that they are inherently limited by strong recency bias. Our empirical studies also reveal that this bias impairs the models' ability to recall distant information and introduces robustness issues. Our scaling experiments then discovered that deeper structures in SSMs can facilitate the learning of long contexts. However, subsequent theoretical analysis reveals that as SSMs increase in depth, they exhibit another inevitable tendency toward over-smoothing, e.g., token representations becoming increasingly indistinguishable. This fundamental dilemma between recency and over-smoothing hinders the scalability of existing SSMs. Inspired by our theoretical findings, we propose to polarize two channels of the state transition matrices in SSMs, setting them to zero and one, respectively, simultaneously addressing recency bias and over-smoothing. Experiments demonstrate that our polarization technique consistently enhances the associative recall accuracy of long-range tokens and unlocks SSMs to benefit further from deeper architectures. All source codes are released at https://github.com/VITA-Group/SSM-Bottleneck.

cs.LG↗

arXiv2025

Improving Graph Neural Networks on Multi-node Tasks with the Labeling Trick

In this paper, we study using graph neural networks (GNNs) for \textit{multi-node representation learning}, where a representation for a set of more than one node (such as a link) is to be learned. Existing GNNs are mainly designed to learn single-node representations. When used for multi-node representation learning, a common practice is to directly aggregate the single-node representations obtained by a GNN. In this paper, we show a fundamental limitation of such an approach, namely the inability to capture the dependence among multiple nodes in the node set. A straightforward solution is to distinguish target nodes from others. Formalizing this idea, we propose \text{labeling trick}, which first labels nodes in the graph according to their relationships with the target node set before applying a GNN and then aggregates node representations obtained in the labeled graph for multi-node representations. Besides node sets in graphs, we also extend labeling tricks to posets, subsets and hypergraphs. Experiments verify that the labeling trick technique can boost GNNs on various tasks, including undirected link prediction, directed link prediction, hyperedge prediction, and subgraph prediction. Our work explains the superior performance of previous node-labeling-based methods and establishes a theoretical foundation for using GNNs for multi-node representation learning.

cs.LG↗

arXiv2025

LayerDAG: A Layerwise Autoregressive Diffusion Model for Directed Acyclic Graph Generation

Directed acyclic graphs (DAGs) serve as crucial data representations in domains such as hardware synthesis and compiler/program optimization for computing systems. DAG generative models facilitate the creation of synthetic DAGs, which can be used for benchmarking computing systems while preserving intellectual property. However, generating realistic DAGs is challenging due to their inherent directional and logical dependencies. This paper introduces LayerDAG, an autoregressive diffusion model, to address these challenges. LayerDAG decouples the strong node dependencies into manageable units that can be processed sequentially. By interpreting the partial order of nodes as a sequence of bipartite graphs, LayerDAG leverages autoregressive generation to model directional dependencies and employs diffusion models to capture logical dependencies within each bipartite graph. Comparative analyses demonstrate that LayerDAG outperforms existing DAG generative models in both expressiveness and generalization, particularly for generating large-scale DAGs with up to 400 nodes-a critical scenario for system benchmarking. Extensive experiments on both synthetic and real-world flow graphs from various computing platforms show that LayerDAG generates valid DAGs with superior statistical properties and benchmarking performance. The synthetic DAGs generated by LayerDAG enhance the training of ML-based surrogate models, resulting in improved accuracy in predicting performance metrics of real-world DAGs across diverse computing platforms.

cs.LG↗

arXiv2025

Differentially Private Graph Diffusion with Applications in Personalized PageRanks

Graph diffusion, which iteratively propagates real-valued substances among the graph, is used in numerous graph/network-involved applications. However, releasing diffusion vectors may reveal sensitive linking information in the data such as transaction information in financial network data. However, protecting the privacy of graph data is challenging due to its interconnected nature. This work proposes a novel graph diffusion framework with edge-level differential privacy guarantees by using noisy diffusion iterates. The algorithm injects Laplace noise per diffusion iteration and adopts a degree-based thresholding function to mitigate the high sensitivity induced by low-degree nodes. Our privacy loss analysis is based on Privacy Amplification by Iteration (PABI), which to our best knowledge, is the first effort that analyzes PABI with Laplace noise and provides relevant applications. We also introduce a novel Infinity-Wasserstein distance tracking method, which tightens the analysis of privacy leakage and makes PABI more applicable in practice. We evaluate this framework by applying it to Personalized Pagerank computation for ranking tasks. Experiments on real-world network data demonstrate the superiority of our method under stringent privacy conditions.

cs.IR↗

arXiv2025

Convergent Privacy Loss of Noisy-SGD without Convexity and Smoothness

We study the Differential Privacy (DP) guarantee of hidden-state Noisy-SGD algorithms over a bounded domain. Standard privacy analysis for Noisy-SGD assumes all internal states are revealed, which leads to a divergent R'enyi DP bound with respect to the number of iterations. Ye & Shokri (2022) and Altschuler & Talwar (2022) proved convergent bounds for smooth (strongly) convex losses, and raise open questions about whether these assumptions can be relaxed. We provide positive answers by proving convergent R'enyi DP bound for non-convex non-smooth losses, where we show that requiring losses to have Hölder continuous gradient is sufficient. We also provide a strictly better privacy bound compared to state-of-the-art results for smooth strongly convex losses. Our analysis relies on the improvement of shifted divergence analysis in multiple aspects, including forward Wasserstein distance tracking, identifying the optimal shifts allocation, and the H"older reduction lemma. Our results further elucidate the benefit of hidden-state analysis for DP and its applicability.

cs.LG↗

arXiv2025

Simple Is Effective: The Roles of Graphs and Large Language Models in Knowledge-Graph-Based Retrieval-Augmented Generation

Large Language Models (LLMs) demonstrate strong reasoning abilities but face limitations such as hallucinations and outdated knowledge. Knowledge Graph (KG)-based Retrieval-Augmented Generation (RAG) addresses these issues by grounding LLM outputs in structured external knowledge from KGs. However, current KG-based RAG frameworks still struggle to optimize the trade-off between retrieval effectiveness and efficiency in identifying a suitable amount of relevant graph information for the LLM to digest. We introduce SubgraphRAG, extending the KG-based RAG framework that retrieves subgraphs and leverages LLMs for reasoning and answer prediction. Our approach innovatively integrates a lightweight multilayer perceptron with a parallel triple-scoring mechanism for efficient and flexible subgraph retrieval while encoding directional structural distances to enhance retrieval effectiveness. The size of retrieved subgraphs can be flexibly adjusted to match the query's need and the downstream LLM's capabilities. This design strikes a balance between model complexity and reasoning power, enabling scalable and generalizable retrieval processes. Notably, based on our retrieved subgraphs, smaller LLMs like Llama3.1-8B-Instruct deliver competitive results with explainable reasoning, while larger models like GPT-4o achieve state-of-the-art accuracy compared with previous baselines -- all without fine-tuning. Extensive evaluations on the WebQSP and CWQ benchmarks highlight SubgraphRAG's strengths in efficiency, accuracy, and reliability by reducing hallucinations and improving response grounding.

cs.CL↗

arXiv2025

Certified Machine Unlearning via Noisy Stochastic Gradient Descent

``The right to be forgotten'' ensured by laws for user data privacy becomes increasingly important. Machine unlearning aims to efficiently remove the effect of certain data points on the trained model parameters so that it can be approximately the same as if one retrains the model from scratch. We propose to leverage projected noisy stochastic gradient descent for unlearning and establish its first approximate unlearning guarantee under the convexity assumption. Our approach exhibits several benefits, including provable complexity saving compared to retraining, and supporting sequential and batch unlearning. Both of these benefits are closely related to our new results on the infinite Wasserstein distance tracking of the adjacent (un)learning processes. Extensive experiments show that our approach achieves a similar utility under the same privacy constraint while using $2\%$ and $10\%$ of the gradient computations compared with the state-of-the-art gradient-based approximate unlearning methods for mini-batch and full-batch settings, respectively.

cs.LG↗