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Philip S Yu

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18 papers

1 author row

NeurIPS Conference 2025 Conference Paper

AdmTree: Compressing Lengthy Context with Adaptive Semantic Trees

Yangning Li
Shaoshen Chen
Yinghui Li
Yankai Chen
Hai-Tao Zheng
Hui Wang
Wenhao Jiang
Philip S Yu

The quadratic complexity of self-attention limits Large Language Models (LLMs) in processing long contexts, a capability vital for many advanced applications. Context compression aims to mitigate this computational barrier while preserving essential semantic information. However, existing methods often falter: explicit methods can sacrifice local detail, while implicit ones may exhibit positional biases, struggle with information degradation, or fail to capture long-range semantic dependencies. We introduce AdmTree, a novel framework for adaptive, hierarchical context compression designed with a core focus on maintaining high semantic fidelity while keep efficiency. AdmTree dynamically segments input based on information density, employing gist tokens to summarize variable-length segments as leaves in a semantic binary tree. This structure, combined with a lightweight aggregation mechanism and a frozen backbone LLM (minimizing new trainable parameters), enables efficient hierarchical abstraction of the context. By effectively preserving fine-grained details alongside global semantic coherence, mitigating position bias, and adapting dynamically to content, AdmTree comprehensively preserves the semantic information of lengthy context.

NeurIPS Conference 2025 Conference Paper

Atomic Thinking of LLMs: Decoupling and Exploring Mathematical Reasoning Abilities

Jiayi Kuang
Haojing Huang
Yinghui Li
Xinnian Liang
Zhikun Xu
Yangning Li
Xiaoyu Tan
Chao Qu

Large Language Models (LLMs) have demonstrated outstanding performance in mathematical reasoning capabilities. However, we argue that current large-scale reasoning models primarily rely on scaling up training datasets with diverse mathematical problems and long thinking chains, which raises questions about whether LLMs genuinely acquire mathematical concepts and reasoning principles or merely remember the training data. In contrast, humans tend to break down complex problems into multiple fundamental atomic capabilities. Inspired by this, we propose a new paradigm for evaluating mathematical atomic capabilities. Our work categorizes atomic abilities into two dimensions: (1) field-specific abilities across four major mathematical fields, algebra, geometry, analysis, and topology, and (2) logical abilities at different levels, including conceptual understanding, forward multi-step reasoning with formal math language, and counterexample-driven backward reasoning. We propose corresponding training and evaluation datasets for each atomic capability unit, and conduct extensive experiments about how different atomic capabilities influence others, to explore the strategies to elicit the required specific atomic capability. Evaluation and experimental results on advanced models show many interesting discoveries and inspirations about the different performances of models on various atomic capabilities and the interactions between atomic capabilities. Our findings highlight the importance of decoupling mathematical intelligence into atomic components, providing new insights into model cognition and guiding the development of training strategies toward a more efficient, transferable, and cognitively grounded paradigm of "atomic thinking".

NeurIPS Conference 2025 Conference Paper

Deeper with Riemannian Geometry: Overcoming Oversmoothing and Oversquashing for Graph Foundation Models

Li Sun
Zhenhao Huang
Ming Zhang
Philip S Yu

Message Passing Neural Networks (MPNNs) are the building block of graph foundation models, but fundamentally suffer from oversmoothing and oversquashing. There has recently been a surge of interest in fixing both issues. Existing efforts primarily adopt global approaches, which may be beneficial in some regions but detrimental in others, ultimately leading to the suboptimal expressiveness. In this paper, we begin by revisiting oversquashing through a global measure -- spectral gap $\lambda$ -- and prove that the increase of $\lambda$ leads to gradient vanishing with respect to the input features, thereby undermining the effectiveness of message passing. Motivated by such theoretical insights, we propose a local approach that adaptively adjusts message passing based on local structures. To achieve this, we connect local Riemannian geometry with MPNNs, and establish a novel nonhomogeneous boundary condition to address both oversquashing and oversmoothing. Building on the Robin condition, we design a GBN network with local bottleneck adjustment, coupled with theoretical guarantees. Extensive experiments on homophilic and heterophilic graphs show the expressiveness of GBN. Furthermore, GBN does not exhibit performance degradation even when the network depth exceeds $256$ layers.

NeurIPS Conference 2025 Conference Paper

Dynamic Bundling with Large Language Models for Zero-Shot Inference on Text-Attributed Graphs

Yusheng Zhao
Qixin Zhang
Xiao Luo
Weizhi Zhang
Zhiping Xiao
Wei Ju
Philip S Yu
Ming Zhang

Large language models (LLMs) have been used in many zero-shot learning problems, with their strong generalization ability. Recently, adopting LLMs in text-attributed graphs (TAGs) has drawn increasing attention. However, the adoption of LLMs faces two major challenges: limited information on graph structure and unreliable responses. LLMs struggle with text attributes isolated from the graph topology. Worse still, they yield unreliable predictions due to both information insufficiency and the inherent weakness of LLMs (e. g. , hallucination). Towards this end, this paper proposes a novel method named Dynamic Text Bundling Supervision (DENSE) that queries LLMs with bundles of texts to obtain bundle-level labels and uses these labels to supervise graph neural networks. Specifically, we sample a set of bundles, each containing a set of nodes with corresponding texts of close proximity. We then query LLMs with the bundled texts to obtain the label of each bundle. Subsequently, the bundle labels are used to supervise the optimization of graph neural networks, and the bundles are further refined to exclude noisy items. To justify our design, we also provide theoretical analysis of the proposed method. Extensive experiments across ten datasets validate the effectiveness of the proposed method.

NeurIPS Conference 2025 Conference Paper

Embracing Trustworthy Brain-Agent Collaboration as Paradigm Extension for Intelligent Assistive Technologies

Yankai Chen
Xinni Zhang
Yifei Zhang
Yangning Li
Henry Zou
Chunyu Miao
Weizhi Zhang
Steve (Xue) Liu

Brain-Computer Interfaces (BCIs) offer a direct communication pathway between the human brain and external devices, holding significant promise for individuals with severe neurological impairments. However, their widespread adoption is hindered by critical limitations, such as low information transfer rates and extensive user-specific calibration. To overcome these challenges, recent research has explored the integration of Large Language Models (LLMs), extending the focus from simple command decoding to understanding complex cognitive states. Despite these advancements, deploying agentic AI faces technical hurdles and ethical concerns. Due to the lack of comprehensive discussion on this emerging direction, this position paper argues that the field is poised for a paradigm extension from BCI to Brain-Agent Collaboration (BAC). We emphasize reframing agents as active and collaborative partners for intelligent assistance rather than passive brain signal data processors, demanding a focus on ethical data handling, model reliability, and a robust human-agent collaboration framework to ensure these systems are safe, trustworthy, and effective.

NeurIPS Conference 2025 Conference Paper

Glocal Information Bottleneck for Time Series Imputation

Jie Yang
Kexin Zhang
Guibin Zhang
Philip S Yu
Kaize Ding

Time Series Imputation (TSI), which aims to recover missing values in temporal data, remains a fundamental challenge due to the complex and often high-rate missingness in real-world scenarios. Existing models typically optimize the point-wise reconstruction loss, focusing on recovering numerical values (local information). However, we observe that under high missing rates, these models still perform well in the training phase yet produce poor imputations and distorted latent representation distributions (global information) in the inference phase. This reveals a critical optimization dilemma: current objectives lack global guidance, leading models to overfit local noise and fail to capture global information of the data. To address this issue, we propose a new training paradigm, Glocal I nformation B ottleneck ( Glocal-IB ). Glocal-IB is model-agnostic and extends the standard IB framework by introducing a Global Alignment loss, derived from a tractable mutual information approximation. This loss aligns the latent representations of masked inputs with those of their originally observed counterparts. It helps the model retain global structure and local details while suppressing noise caused by missing values, giving rise to better generalization under high missingness. Extensive experiments on nine datasets confirm that Glocal-IB leads to consistently improved performance and aligned latent representations under missingness. Our code implementation is available in https: //github. com/Muyiiiii/NeurIPS-25-Glocal-IB.

NeurIPS Conference 2025 Conference Paper

GRAVER: Generative Graph Vocabularies for Robust Graph Foundation Models Fine-tuning

Haonan Yuan
Qingyun Sun
Junhua Shi
Xingcheng Fu
Bryan Hooi
Jianxin Li
Philip S Yu

Inspired by the remarkable success of foundation models in language and vision, Graph Foundation Models (GFMs) hold significant promise for broad applicability across diverse graph tasks and domains. However, existing GFMs struggle with unstable few-shot fine-tuning, where both performance and adaptation efficiency exhibit significant fluctuations caused by the randomness in the support sample selection and structural discrepancies between the pre-trained and target graphs. How to fine-tune GFMs robustly and efficiently to enable trustworthy knowledge transfer across domains and tasks is the major challenge. In this paper, we propose GRAVER, a novel G enerative g RA ph V ocabulari E s for R obust GFM fine-tuning framework that tackles the aforementioned instability via generative augmentations. Specifically, to identify transferable units, we analyze and extract key class-specific subgraph patterns by ego-graph disentanglement and validate their transferability both theoretically and empirically. To enable effective pre-training across diverse domains, we leverage a universal task template based on ego-graph similarity and construct graph vocabularies via graphon-based generative experts. To facilitate robust and efficient prompt fine-tuning, we grave the support samples with in-context vocabularies, where the lightweight MoE-CoE network attentively routes knowledge from source domains. Extensive experiments demonstrate the superiority of GRAVER over effectiveness, robustness, and efficiency on downstream few-shot node and graph classification tasks compared with 15 state-of-the-art baselines.

NeurIPS Conference 2025 Conference Paper

Robust Graph Condensation via Classification Complexity Mitigation

Jiayi Luo
Qingyun Sun
Beining Yang
Haonan Yuan
Xingcheng Fu
Yanbiao Ma
Jianxin Li
Philip S Yu

Graph condensation (GC) has gained significant attention for its ability to synthesize smaller yet informative graphs. However, existing studies often overlook the robustness of GC in scenarios where the original graph is corrupted. In such cases, we observe that the performance of GC deteriorates significantly, while existing robust graph learning technologies offer only limited effectiveness. Through both empirical investigation and theoretical analysis, we reveal that GC is inherently an intrinsic-dimension-reducing process, synthesizing a condensed graph with lower classification complexity. Although this property is critical for effective GC performance, it remains highly vulnerable to adversarial perturbations. To tackle this vulnerability and improve GC robustness, we adopt the geometry perspective of graph data manifold and propose a novel M anifold-constrained R obust G raph C ondensation framework named MRGC. Specifically, we introduce three graph data manifold learning modules that guide the condensed graph to lie within a smooth, low-dimensional manifold with minimal class ambiguity, thereby preserving the classification complexity reduction capability of GC and ensuring robust performance under universal adversarial attacks. Extensive experiments demonstrate the robustness of MRGC across diverse attack scenarios.

NeurIPS Conference 2025 Conference Paper

Seeking and Updating with Live Visual Knowledge

Mingyang Fu
Yuyang Peng
Dongping Chen
Zetong Zhou
Benlin Liu
Yao Wan
Zhou Zhao
Philip S Yu

The visual world around us constantly evolves, from real-time news and social media trends to global infrastructure changes visible through satellite imagery and augmented reality enhancements. However, Multimodal Large Language Models (MLLMs), which automate many tasks, struggle to stay current, limited by the cutoff dates in their fixed training datasets. To quantify this stagnation, we introduce LiveVQA, the first-of-its-kind dataset featuring 107, 143 samples and 12 categories data specifically designed to support research in both seeking and updating with live visual knowledge. Drawing from recent news articles, video platforms, and academic publications in April 2024-May 2025, LiveVQA enables evaluation of how models handle latest visual information beyond their knowledge boundaries and how current methods help to update them. Our comprehensive benchmarking of 17 state-of-the-art MLLMs reveals significant performance gaps on content beyond knowledge cutoff, and tool-use or agentic visual seeking framework drastically gain an average of 327% improvement. Furthermore, we explore parameter-efficient fine-tuning methods to update MLLMs with new visual knowledge. We dive deeply to the critical balance between adapter capacity and model capability when updating MLLMs with new visual knowledge. All the experimental dataset and source code are publicly available at: https: //livevqa. github. io.

NeurIPS Conference 2025 Conference Paper

SSRB: Direct Natural Language Querying to Massive Heterogeneous Semi-Structured Data

Xin Zhang
Mingxin Li
Yanzhao Zhang
Dingkun Long
Yongqi Li
Yinghui Li
Pengjun Xie
Meishan Zhang

Searching over semi-structured data with natural language (NL) queries has attracted sustained attention, enabling broader audiences to access information easily. As more applications, such as LLM agents and RAG systems, emerge to search and interact with semi-structured data, two major challenges have become evident: (1) the increasing diversity of domains and schema variations, making domain-customized solutions prohibitively costly; (2) the growing complexity of NL queries, which combine both exact field matching conditions and fuzzy semantic requirements, often involving multiple fields and implicit reasoning. These challenges make formal language querying or keyword-based search insufficient. In this work, we explore neural retrievers as a unified non-formal querying solution by directly index semi-structured collections and understand NL queries. We employ LLM-based automatic evaluation and build a large-scale semi-structured retrieval benchmark (SSRB) using LLM generation and filtering, containing 14M semi-structured objects from 99 different schemas across 6 domains, along with 8, 485 test queries that combine both exact and fuzzy matching conditions. Our systematic evaluation of popular retrievers shows that current state-of-the-art models could achieve acceptable performance, yet they still lack precise understanding of matching constraints. While by in-domain training of dense retrievers, the performance can be significantly improved. We believe that our SSRB could serve as a valuable resource for future research in this area, and we hope to inspire further exploration of semi-structured retrieval with complex queries.

NeurIPS Conference 2025 Conference Paper

Topology-Aware Conformal Prediction for Stream Networks

Jifan Zhang
Fangxin Wang
Zihe Song
Philip S Yu
Kaize Ding
Shixiang Zhu

Stream networks, a unique class of spatiotemporal graphs, exhibit complex directional flow constraints and evolving dependencies, making uncertainty quantification a critical yet challenging task. Traditional conformal prediction methods struggle in this setting due to the need for joint predictions across multiple interdependent locations and the intricate spatio-temporal dependencies inherent in stream networks. Existing approaches either neglect dependencies, leading to overly conservative predictions, or rely solely on data-driven estimations, failing to capture the rich topological structure of the network. To address these challenges, we propose Spatio-Temporal Adaptive Conformal Inference (STACI), a novel framework that integrates network topology and temporal dynamics into the conformal prediction framework. STACI introduces a topology-aware nonconformity score that respects directional flow constraints and dynamically adjusts prediction sets to account for temporal distributional shifts. We provide theoretical guarantees on the validity of our approach and demonstrate its superior performance on both synthetic and real-world datasets. Our results show that STACI effectively balances prediction efficiency and coverage, outperforming existing conformal prediction methods for stream networks.

NeurIPS Conference 2023 Conference Paper

Equal Opportunity of Coverage in Fair Regression

Fangxin Wang
Lu Cheng
Ruocheng Guo
Kay Liu
Philip S Yu

We study fair machine learning (ML) under predictive uncertainty to enable reliable and trustworthy decision-making. The seminal work of 'equalized coverage' proposed an uncertainty-aware fairness notion. However, it does not guarantee equal coverage rates across more fine-grained groups (e. g. , low-income females) conditioning on the true label and is biased in the assessment of uncertainty. To tackle these limitations, we propose a new uncertainty-aware fairness -- Equal Opportunity of Coverage (EOC) -- that aims to achieve two properties: (1) coverage rates for different groups with similar outcomes are close, and (2) the coverage rate for the entire population remains at a predetermined level. Further, the prediction intervals should be narrow to be informative. We propose Binned Fair Quantile Regression (BFQR), a distribution-free post-processing method to improve EOC with reasonable width for any trained ML models. It first calibrates a hold-out set to bound deviation from EOC, then leverages conformal prediction to maintain EOC on a test set, meanwhile optimizing prediction interval width. Experimental results demonstrate the effectiveness of our method in improving EOC.

AAAI Conference 2022 Conference Paper

A Self-Supervised Mixed-Curvature Graph Neural Network

Li Sun
Zhongbao Zhang
Junda Ye
Hao Peng
Jiawei Zhang
Sen Su
Philip S Yu

Graph representation learning received increasing attentions in recent years. Most of the existing methods ignore the complexity of the graph structures and restrict graphs in a single constant-curvature representation space, which is only suitable to particular kinds of graph structure indeed. Additionally, these methods follow the supervised or semi-supervised learning paradigm, and thereby notably limit their deployment on the unlabeled graphs in real applications. To address these aforementioned limitations, we take the first attempt to study the self-supervised graph representation learning in the mixed-curvature spaces. In this paper, we present a novel Self-Supervised Mixed-Curvature Graph Neural Network (SELFMGNN). To capture the complex graph structures, we construct a mixed-curvature space via the Cartesian product of multiple Riemannian component spaces, and design hierarchical attention mechanisms for learning and fusing graph representations across these component spaces. To enable the self-supervised learning, we propose a novel dual contrastive approach. The constructed mixed-curvature space actually provides multiple Riemannian views for the contrastive learning. We introduce a Riemannian projector to reveal these views, and utilize a well-designed Riemannian discriminator for the single-view and cross-view contrastive learning within and across the Riemannian views. Finally, extensive experiments show that SELFMGNN captures the complex graph structures and outperforms state-of-the-art baselines.

NeurIPS Conference 2022 Conference Paper

BOND: Benchmarking Unsupervised Outlier Node Detection on Static Attributed Graphs

Kay Liu
Yingtong Dou
Yue Zhao
Xueying Ding
Xiyang Hu
Ruitong Zhang
Kaize Ding
Canyu Chen

Detecting which nodes in graphs are outliers is a relatively new machine learning task with numerous applications. Despite the proliferation of algorithms developed in recent years for this task, there has been no standard comprehensive setting for performance evaluation. Consequently, it has been difficult to understand which methods work well and when under a broad range of settings. To bridge this gap, we present—to the best of our knowledge—the first comprehensive benchmark for unsupervised outlier node detection on static attributed graphs called BOND, with the following highlights. (1) We benchmark the outlier detection performance of 14 methods ranging from classical matrix factorization to the latest graph neural networks. (2) Using nine real datasets, our benchmark assesses how the different detection methods respond to two major types of synthetic outliers and separately to “organic” (real non-synthetic) outliers. (3) Using an existing random graph generation technique, we produce a family of synthetically generated datasets of different graph sizes that enable us to compare the running time and memory usage of the different outlier detection algorithms. Based on our experimental results, we discuss the pros and cons of existing graph outlier detection algorithms, and we highlight opportunities for future research. Importantly, our code is freely available and meant to be easily extendable: https: //github. com/pygod-team/pygod/tree/main/benchmark

AAAI Conference 2022 Conference Paper

Graph Structure Learning with Variational Information Bottleneck

Qingyun Sun
Jianxin Li
Hao Peng
Jia Wu
Xingcheng Fu
Cheng Ji
Philip S Yu

Graph Neural Networks (GNNs) have shown promising results on a broad spectrum of applications. Most empirical studies of GNNs directly take the observed graph as input, assuming the observed structure perfectly depicts the accurate and complete relations between nodes. However, graphs in the real-world are inevitably noisy or incomplete, which could even exacerbate the quality of graph representations. In this work, we propose a novel Variational Information Bottleneck guided Graph Structure Learning framework, namely VIB-GSL, in the perspective of information theory. VIB-GSL is the first attempt to advance the Information Bottleneck (IB) principle for graph structure learning, providing a more elegant and universal framework for mining underlying task-relevant relations. VIB-GSL learns an informative and compressive graph structure to distill the actionable information for specific downstream tasks. VIB-GSL deduces a variational approximation for irregular graph data to form a tractable IB objective function, which facilitates training stability. Extensive experimental results demonstrate that the superior effectiveness and robustness of VIB-GSL.

NeurIPS Conference 2022 Conference Paper

Rethinking and Scaling Up Graph Contrastive Learning: An Extremely Efficient Approach with Group Discrimination

Yizhen Zheng
Shirui Pan
Vincent CS Lee
Yu Zheng
Philip S Yu

Graph contrastive learning (GCL) alleviates the heavy reliance on label information for graph representation learning (GRL) via self-supervised learning schemes. The core idea is to learn by maximising mutual information for similar instances, which requires similarity computation between two node instances. However, GCL is inefficient in both time and memory consumption. In addition, GCL normally requires a large number of training epochs to be well-trained on large-scale datasets. Inspired by an observation of a technical defect (i. e. , inappropriate usage of Sigmoid function) commonly used in two representative GCL works, DGI and MVGRL, we revisit GCL and introduce a new learning paradigm for self-supervised graph representation learning, namely, Group Discrimination (GD), and propose a novel GD-based method called Graph Group Discrimination (GGD). Instead of similarity computation, GGD directly discriminates two groups of node samples with a very simple binary cross-entropy loss. In addition, GGD requires much fewer training epochs to obtain competitive performance compared with GCL methods on large-scale datasets. These two advantages endow GGD with very efficient property. Extensive experiments show that GGD outperforms state-of-the-art self-supervised methods on eight datasets. In particular, GGD can be trained in 0. 18 seconds (6. 44 seconds including data preprocessing) on ogbn-arxiv, which is orders of magnitude (10, 000+) faster than GCL baselines while consuming much less memory. Trained with 9 hours on ogbn-papers100M with billion edges, GGD outperforms its GCL counterparts in both accuracy and efficiency.

NeurIPS Conference 2021 Conference Paper

From Canonical Correlation Analysis to Self-supervised Graph Neural Networks

Hengrui Zhang
Qitian Wu
Junchi Yan
David Wipf
Philip S Yu

We introduce a conceptually simple yet effective model for self-supervised representation learning with graph data. It follows the previous methods that generate two views of an input graph through data augmentation. However, unlike contrastive methods that focus on instance-level discrimination, we optimize an innovative feature-level objective inspired by classical Canonical Correlation Analysis. Compared with other works, our approach requires none of the parameterized mutual information estimator, additional projector, asymmetric structures, and most importantly, negative samples which can be costly. We show that the new objective essentially 1) aims at discarding augmentation-variant information by learning invariant representations, and 2) can prevent degenerated solutions by decorrelating features in different dimensions. Our theoretical analysis further provides an understanding for the new objective which can be equivalently seen as an instantiation of the Information Bottleneck Principle under the self-supervised setting. Despite its simplicity, our method performs competitively on seven public graph datasets.

IJCAI Conference 2020 Conference Paper

Deep Learning for Community Detection: Progress, Challenges and Opportunities

Fanzhen Liu
Shan Xue
Jia Wu
Chuan Zhou
Wenbin Hu
Cecile Paris
Surya Nepal
Jian Yang

As communities represent similar opinions, similar functions, similar purposes, etc. , community detection is an important and extremely useful tool in both scientific inquiry and data analytics. However, the classic methods of community detection, such as spectral clustering and statistical inference, are falling by the wayside as deep learning techniques demonstrate an increasing capacity to handle high-dimensional graph data with impressive performance. Thus, a survey of current progress in community detection through deep learning is timely. Structured into three broad research streams in this domain – deep neural networks, deep graph embedding, and graph neural networks, this article summarizes the contributions of the various frameworks, models, and algorithms in each stream along with the current challenges that remain unsolved and the future research opportunities yet to be explored.

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