arXiv subjects

Yili Wang

Publications and source records attributed to Yili Wang.

At least 37 records · Page 2Linked to original sources

arXiv2026

Mamba-Based Graph Convolutional Networks: Tackling Over-smoothing with Selective State Space

Graph Neural Networks (GNNs) have shown great success in various graph-based learning tasks. However, it often faces the issue of over-smoothing as the model depth increases, which causes all node representations to converge to a single value and become indistinguishable. This issue stems from the inherent limitations of GNNs, which struggle to distinguish the importance of information from different neighborhoods. In this paper, we introduce MbaGCN, a novel graph convolutional architecture that draws inspiration from the Mamba paradigm-originally designed for sequence modeling. MbaGCN presents a new backbone for GNNs, consisting of three key components: the Message Aggregation Layer, the Selective State Space Transition Layer, and the Node State Prediction Layer. These components work in tandem to adaptively aggregate neighborhood information, providing greater flexibility and scalability for deep GNN models. While MbaGCN may not consistently outperform all existing methods on each dataset, it provides a foundational framework that demonstrates the effective integration of the Mamba paradigm into graph representation learning. Through extensive experiments on benchmark datasets, we demonstrate that MbaGCN paves the way for future advancements in graph neural network research.

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arXiv2026

PRBench: End-to-end Paper Reproduction in Physics Research

AI agents powered by large language models exhibit strong reasoning and problem-solving capabilities, enabling them to assist scientific research tasks such as formula derivation and code generation. However, whether these agents can reliably perform end-to-end reproduction from real scientific papers remains an open question. We introduce PRBench, a benchmark of 30 expert-curated tasks spanning 11 subfields of physics. Each task requires an agent to comprehend the methodology of a published paper, implement the corresponding algorithms from scratch, and produce quantitative results matching the original publication. Agents are provided only with the task instruction and paper content, and operate in a sandboxed execution environment. All tasks are contributed by domain experts from over 20 research groups at the School of Physics, Peking University, each grounded in a real published paper and validated through end-to-end reproduction with verified ground-truth results and detailed scoring rubrics. Using an agentified assessment pipeline, we evaluate a set of coding agents on PRBench and analyze their capabilities across key dimensions of scientific reasoning and execution. The best-performing agent, OpenAI Codex powered by GPT-5.3-Codex, achieves a mean overall score of 34%. All agents exhibit a zero end-to-end callback success rate, with particularly poor performance in data accuracy and code correctness. We further identify systematic failure modes, including errors in formula implementation, inability to debug numerical simulations, and fabrication of output data. Overall, PRBench provides a rigorous benchmark for evaluating progress toward autonomous scientific research.

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arXiv2025

HyperD: Hybrid Periodicity Decoupling Framework for Traffic Forecasting

Accurate traffic forecasting plays a vital role in intelligent transportation systems, enabling applications such as congestion control, route planning, and urban mobility optimization. However, traffic forecasting remains challenging due to two key factors: (1) complex spatial dependencies arising from dynamic interactions between road segments and traffic sensors across the network, and (2) the coexistence of multi-scale periodic patterns (e.g., daily and weekly periodic patterns driven by human routines) with irregular fluctuations caused by unpredictable events (e.g., accidents, weather, or construction). To tackle these challenges, we propose HyperD (Hybrid Periodic Decoupling), a novel framework that decouples traffic data into periodic and residual components. The periodic component is handled by the Hybrid Periodic Representation Module, which extracts fine-grained daily and weekly patterns using learnable periodic embeddings and spatial-temporal attention. The residual component, which captures non-periodic, high-frequency fluctuations, is modeled by the Frequency-Aware Residual Representation Module, leveraging complex-valued MLP in frequency domain. To enforce semantic separation between the two components, we further introduce a Dual-View Alignment Loss, which aligns low-frequency information with the periodic branch and high-frequency information with the residual branch. Extensive experiments on four real-world traffic datasets demonstrate that HyperD achieves state-of-the-art prediction accuracy, while offering superior robustness under disturbances and improved computational efficiency compared to existing methods.

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arXiv2025

Violation of the elliptic flow scaling of $f_0(980)$ in p-Pb collisions at the LHC

We investigate the production and elliptic flow of the $f_0(980)$ in high-multiplicity p-Pb collisions at $\sqrt{s_{NN}}=5.02$ TeV using a hadronic coalescence model with the $K$ and $\bar K$ phase-space distributions provided by the Hydro-Coal-Frag hybrid model. Our results, which agree with the ALICE and CMS measurements, support the $K\bar K$ molecular interpretation of the $f_0(980)$ structure and show, however, a breakdown of the simple number-of-constituent (NC) scaling of its elliptic flow. The latter is in contrast to the deuteron elliptic flow, which exhibits a significantly better NC scaling when the same coalescence width parameter is used.

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arXiv2025

Probing the structure of $f_{0}(980)$ from the elliptic flow in p-Pb collisions at the LHC

The $f_{0}(980)$ is a light scalar meson whose internal structure remains under debate and investigation. Assuming that the $f_0(980)$ is a $K\bar K$ molecule that can only survive at the kinetic freeze-out of the evolving bulk matter, we implement the coalescence model to study its transverse momentum ($p_T$) spectra and elliptic flow ($v_2$) in high-multiplicity p-Pb collisions at $\sqrt{s_{NN}}=5.02$ TeV. Using the well-tuned kaon phase-space distributions from the Hydro-Coal-Frag model, our $K\bar{K}$ coalescence calculations with reasonable values for the $f_0(980)$ radius successfully reproduce the elliptic flow measured by CMS over the range $0 < p_{T} < 12$ GeV and also agree with the $p_T$-spectra from ALICE. These results in heavy ion collisions are consistent with the $K\bar K$ molecular picture of the $f_0(980)$. We also find that the number-of-constituent scaling of $v_2$ for the $f_0(980)$ is violated in p-Pb collisions at the LHC because most $f_0(980)$ are produced from the coalescence of kaons that have different momenta. Our study demonstrates the necessity of realistic coalescence model calculations and also explains why the CMS interpretation of the $f_0(980)$ as an ordinary $q\bar q$ meson is no longer valid by interpreting the measured $v_2$ with a simple scaling formula based on the assumption of equal momentum coalescence. The investigation also provides a novel way to explore the internal structure of light exotic hadrons that can be abundantly produced in relativistic heavy and/or light ion collisions.

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arXiv2025

Simple and Efficient Heterogeneous Temporal Graph Neural Network

Heterogeneous temporal graphs (HTGs) are ubiquitous data structures in the real world. Recently, to enhance representation learning on HTGs, numerous attention-based neural networks have been proposed. Despite these successes, existing methods rely on a decoupled temporal and spatial learning paradigm, which weakens interactions of spatio-temporal information and leads to a high model complexity. To bridge this gap, we propose a novel learning paradigm for HTGs called Simple and Efficient Heterogeneous Temporal Graph N}eural Network (SE-HTGNN). Specifically, we innovatively integrate temporal modeling into spatial learning via a novel dynamic attention mechanism, which retains attention information from historical graph snapshots to guide subsequent attention computation, thereby improving the overall discriminative representations learning of HTGs. Additionally, to comprehensively and adaptively understand HTGs, we leverage large language models to prompt SE-HTGNN, enabling the model to capture the implicit properties of node types as prior knowledge. Extensive experiments demonstrate that SE-HTGNN achieves up to 10x speed-up over the state-of-the-art and latest baseline while maintaining the best forecasting accuracy.

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arXiv2025

Can LLMs Find Fraudsters? Multi-level LLM Enhanced Graph Fraud Detection

Graph fraud detection has garnered significant attention as Graph Neural Networks (GNNs) have proven effective in modeling complex relationships within multimodal data. However, existing graph fraud detection methods typically use preprocessed node embeddings and predefined graph structures to reveal fraudsters, which ignore the rich semantic cues contained in raw textual information. Although Large Language Models (LLMs) exhibit powerful capabilities in processing textual information, it remains a significant challenge to perform multimodal fusion of processed textual embeddings with graph structures. In this paper, we propose a \textbf{M}ulti-level \textbf{L}LM \textbf{E}nhanced Graph Fraud \textbf{D}etection framework called MLED. In MLED, we utilize LLMs to extract external knowledge from textual information to enhance graph fraud detection methods. To integrate LLMs with graph structure information and enhance the ability to distinguish fraudsters, we design a multi-level LLM enhanced framework including type-level enhancer and relation-level enhancer. One is to enhance the difference between the fraudsters and the benign entities, the other is to enhance the importance of the fraudsters in different relations. The experiments on four real-world datasets show that MLED achieves state-of-the-art performance in graph fraud detection as a generalized framework that can be applied to existing methods.

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arXiv2025

CrystalICL: Enabling In-Context Learning for Crystal Generation

Designing crystal materials with desired physicochemical properties remains a fundamental challenge in materials science. While large language models (LLMs) have demonstrated strong in-context learning (ICL) capabilities, existing LLM-based crystal generation approaches are limited to zero-shot scenarios and are unable to benefit from few-shot scenarios. In contrast, human experts typically design new materials by modifying relevant known structures which aligns closely with the few-shot ICL paradigm. Motivated by this, we propose CrystalICL, a novel model designed for few-shot crystal generation. Specifically, we introduce a space-group based crystal tokenization method, which effectively reduces the complexity of modeling crystal symmetry in LLMs. We further introduce a condition-structure aware hybrid instruction tuning framework and a multi-task instruction tuning strategy, enabling the model to better exploit ICL by capturing structure-property relationships from limited data. Extensive experiments on four crystal generation benchmarks demonstrate the superiority of CrystalICL over the leading baseline methods on conditional and unconditional generation tasks.

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arXiv2025

Raising the Bar in Graph OOD Generalization: Invariant Learning Beyond Explicit Environment Modeling

Out-of-distribution (OOD) generalization has emerged as a critical challenge in graph learning, as real-world graph data often exhibit diverse and shifting environments that traditional models fail to generalize across. A promising solution to address this issue is graph invariant learning (GIL), which aims to learn invariant representations by disentangling label-correlated invariant subgraphs from environment-specific subgraphs. However, existing GIL methods face two major challenges: (1) the difficulty of capturing and modeling diverse environments in graph data, and (2) the semantic cliff, where invariant subgraphs from different classes are difficult to distinguish, leading to poor class separability and increased misclassifications. To tackle these challenges, we propose a novel method termed Multi-Prototype Hyperspherical Invariant Learning (MPHIL), which introduces two key innovations: (1) hyperspherical invariant representation extraction, enabling robust and highly discriminative hyperspherical invariant feature extraction, and (2) multi-prototype hyperspherical classification, which employs class prototypes as intermediate variables to eliminate the need for explicit environment modeling in GIL and mitigate the semantic cliff issue. Derived from the theoretical framework of GIL, we introduce two novel objective functions: the invariant prototype matching loss to ensure samples are matched to the correct class prototypes, and the prototype separation loss to increase the distinction between prototypes of different classes in the hyperspherical space. Extensive experiments on 11 OOD generalization benchmark datasets demonstrate that MPHIL achieves state-of-the-art performance, significantly outperforming existing methods across graph data from various domains and with different distribution shifts.

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arXiv2025

A Comprehensive Survey of Synthetic Tabular Data Generation

Tabular data is one of the most prevalent and important data formats in real-world applications such as healthcare, finance, and education. However, its effective use in machine learning is often constrained by data scarcity, privacy concerns, and class imbalance. Synthetic tabular data generation has emerged as a powerful solution, leveraging generative models to learn underlying data distributions and produce realistic, privacy-preserving samples. Although this area has seen growing attention, most existing surveys focus narrowly on specific methods (e.g., GANs or privacy-enhancing techniques), lacking a unified and comprehensive view that integrates recent advances such as diffusion models and large language models (LLMs). In this survey, we present a structured and in-depth review of synthetic tabular data generation methods. Specifically, the survey is organized into three core components: (1) Background, which covers the overall generation pipeline, including problem definitions, synthetic tabular data generation methods, post processing, and evaluation; (2) Generation Methods, where we categorize existing approaches into traditional generation methods, diffusion model methods, and LLM-based methods, and compare them in terms of architecture, generation quality, and applicability; and (3) Applications and Challenges, which summarizes practical use cases, highlights common datasets, and discusses open challenges such as heterogeneity, data fidelity, and privacy protection. This survey aims to provide researchers and practitioners with a holistic understanding of the field and to highlight key directions for future work in synthetic tabular data generation.

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arXiv2025

Understanding the Information Propagation Effects of Communication Topologies in LLM-based Multi-Agent Systems

The communication topology in large language model-based multi-agent systems fundamentally governs inter-agent collaboration patterns, critically shaping both the efficiency and effectiveness of collective decision-making. While recent studies for communication topology automated design tend to construct sparse structures for efficiency, they often overlook why and when sparse and dense topologies help or hinder collaboration. In this paper, we present a causal framework to analyze how agent outputs, whether correct or erroneous, propagate under topologies with varying sparsity. Our empirical studies reveal that moderately sparse topologies, which effectively suppress error propagation while preserving beneficial information diffusion, typically achieve optimal task performance. Guided by this insight, we propose a novel topology design approach, EIB-leanrner, that balances error suppression and beneficial information propagation by fusing connectivity patterns from both dense and sparse graphs. Extensive experiments show the superior effectiveness, communication cost, and robustness of EIB-leanrner.

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arXiv2025

Unifying Unsupervised Graph-Level Anomaly Detection and Out-of-Distribution Detection: A Benchmark

To build safe and reliable graph machine learning systems, unsupervised graph-level anomaly detection (GLAD) and unsupervised graph-level out-of-distribution (OOD) detection (GLOD) have received significant attention in recent years. Though those two lines of research indeed share the same objective, they have been studied independently in the community due to distinct evaluation setups, creating a gap that hinders the application and evaluation of methods from one to the other. To bridge the gap, in this work, we present a \underline{\textbf{U}}nified \underline{\textbf{B}}enchmark for unsupervised \underline{\textbf{G}}raph-level \underline{\textbf{O}}OD and anoma\underline{\textbf{L}}y \underline{\textbf{D}}etection (\ourmethod), a comprehensive evaluation framework that unifies GLAD and GLOD under the concept of generalized graph-level OOD detection. Our benchmark encompasses 35 datasets spanning four practical anomaly and OOD detection scenarios, facilitating the comparison of 18 representative GLAD/GLOD methods. We conduct multi-dimensional analyses to explore the effectiveness, OOD sensitivity spectrum, robustness, and efficiency of existing methods, shedding light on their strengths and limitations. Furthermore, we provide an open-source codebase (https://github.com/UB-GOLD/UB-GOLD) of \ourmethod to foster reproducible research and outline potential directions for future investigations based on our insights.

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arXiv2024

Pioneering Reliable Assessment in Text-to-Image Knowledge Editing: Leveraging a Fine-Grained Dataset and an Innovative Criterion

During pre-training, the Text-to-Image (T2I) diffusion models encode factual knowledge into their parameters. These parameterized facts enable realistic image generation, but they may become obsolete over time, thereby misrepresenting the current state of the world. Knowledge editing techniques aim to update model knowledge in a targeted way. However, facing the dual challenges posed by inadequate editing datasets and unreliable evaluation criterion, the development of T2I knowledge editing encounter difficulties in effectively generalizing injected knowledge. In this work, we design a T2I knowledge editing framework by comprehensively spanning on three phases: First, we curate a dataset \textbf{CAKE}, comprising paraphrase and multi-object test, to enable more fine-grained assessment on knowledge generalization. Second, we propose a novel criterion, \textbf{adaptive CLIP threshold}, to effectively filter out false successful images under the current criterion and achieve reliable editing evaluation. Finally, we introduce \textbf{MPE}, a simple but effective approach for T2I knowledge editing. Instead of tuning parameters, MPE precisely recognizes and edits the outdated part of the conditioning text-prompt to accommodate the up-to-date knowledge. A straightforward implementation of MPE (Based on in-context learning) exhibits better overall performance than previous model editors. We hope these efforts can further promote faithful evaluation of T2I knowledge editing methods.

cs.CL↗

arXiv2024

Efficient Sharpness-Aware Minimization for Molecular Graph Transformer Models

Sharpness-aware minimization (SAM) has received increasing attention in computer vision since it can effectively eliminate the sharp local minima from the training trajectory and mitigate generalization degradation. However, SAM requires two sequential gradient computations during the optimization of each step: one to obtain the perturbation gradient and the other to obtain the updating gradient. Compared with the base optimizer (e.g., Adam), SAM doubles the time overhead due to the additional perturbation gradient. By dissecting the theory of SAM and observing the training gradient of the molecular graph transformer, we propose a new algorithm named GraphSAM, which reduces the training cost of SAM and improves the generalization performance of graph transformer models. There are two key factors that contribute to this result: (i) \textit{gradient approximation}: we use the updating gradient of the previous step to approximate the perturbation gradient at the intermediate steps smoothly (\textbf{increases efficiency}); (ii) \textit{loss landscape approximation}: we theoretically prove that the loss landscape of GraphSAM is limited to a small range centered on the expected loss of SAM (\textbf{guarantees generalization performance}). The extensive experiments on six datasets with different tasks demonstrate the superiority of GraphSAM, especially in optimizing the model update process. The code is in:https://github.com/YL-wang/GraphSAM/tree/graphsam

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arXiv2024

Rethinking Independent Cross-Entropy Loss For Graph-Structured Data

Graph neural networks (GNNs) have exhibited prominent performance in learning graph-structured data. Considering node classification task, based on the i.i.d assumption among node labels, the traditional supervised learning simply sums up cross-entropy losses of the independent training nodes and applies the average loss to optimize GNNs' weights. But different from other data formats, the nodes are naturally connected. It is found that the independent distribution modeling of node labels restricts GNNs' capability to generalize over the entire graph and defend adversarial attacks. In this work, we propose a new framework, termed joint-cluster supervised learning, to model the joint distribution of each node with its corresponding cluster. We learn the joint distribution of node and cluster labels conditioned on their representations, and train GNNs with the obtained joint loss. In this way, the data-label reference signals extracted from the local cluster explicitly strengthen the discrimination ability on the target node. The extensive experiments demonstrate that our joint-cluster supervised learning can effectively bolster GNNs' node classification accuracy. Furthermore, being benefited from the reference signals which may be free from spiteful interference, our learning paradigm significantly protects the node classification from being affected by the adversarial attack.

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arXiv2024

Heterogeneous Graph Neural Networks with Loss-decrease-aware Curriculum Learning

In recent years, heterogeneous graph neural networks (HGNNs) have achieved excellent performance in handling heterogeneous information networks (HINs). Curriculum learning is a machine learning strategy where training examples are presented to a model in a structured order, starting with easy examples and gradually increasing difficulty, aiming to improve learning efficiency and generalization. To better exploit the rich information in HINs, previous methods have started to explore the use of curriculum learning strategy to train HGNNs. Specifically, these works utilize the absolute value of the loss at each training epoch to evaluate the learning difficulty of each training sample. However, the relative loss, rather than the absolute value of loss, reveals the learning difficulty. Therefore, we propose a novel loss-decrease-aware training schedule (LDTS). LDTS uses the trend of loss decrease between each training epoch to better evaluating the difficulty of training samples, thereby enhancing the curriculum learning of HGNNs for downstream tasks. Additionally, we propose a sampling strategy to alleviate training imbalance issues. Our method further demonstrate the efficacy of curriculum learning in enhancing HGNNs capabilities. We call our method Loss-decrease-aware Heterogeneous Graph Neural Networks (LDHGNN). The code is public at https://github.com/wangyili00/LDHGNN.

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arXiv2024

Optimizing OOD Detection in Molecular Graphs: A Novel Approach with Diffusion Models

The open-world test dataset is often mixed with out-of-distribution (OOD) samples, where the deployed models will struggle to make accurate predictions. Traditional detection methods need to trade off OOD detection and in-distribution (ID) classification performance since they share the same representation learning model. In this work, we propose to detect OOD molecules by adopting an auxiliary diffusion model-based framework, which compares similarities between input molecules and reconstructed graphs. Due to the generative bias towards reconstructing ID training samples, the similarity scores of OOD molecules will be much lower to facilitate detection. Although it is conceptually simple, extending this vanilla framework to practical detection applications is still limited by two significant challenges. First, the popular similarity metrics based on Euclidian distance fail to consider the complex graph structure. Second, the generative model involving iterative denoising steps is time-consuming especially when it runs on the enormous pool of drugs. To address these challenges, our research pioneers an approach of Prototypical Graph Reconstruction for Molecular OOD Detection, dubbed as PGR-MOOD and hinges on three innovations: i) An effective metric to comprehensively quantify the matching degree of input and reconstructed molecules; ii) A creative graph generator to construct prototypical graphs that are in line with ID but away from OOD; iii) An efficient and scalable OOD detector to compare the similarity between test samples and pre-constructed prototypical graphs and omit the generative process on every new molecule. Extensive experiments on ten benchmark datasets and six baselines are conducted to demonstrate our superiority.

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arXiv2023

What is the Best Automated Metric for Text to Motion Generation?

There is growing interest in generating skeleton-based human motions from natural language descriptions. While most efforts have focused on developing better neural architectures for this task, there has been no significant work on determining the proper evaluation metric. Human evaluation is the ultimate accuracy measure for this task, and automated metrics should correlate well with human quality judgments. Since descriptions are compatible with many motions, determining the right metric is critical for evaluating and designing effective generative models. This paper systematically studies which metrics best align with human evaluations and proposes new metrics that align even better. Our findings indicate that none of the metrics currently used for this task show even a moderate correlation with human judgments on a sample level. However, for assessing average model performance, commonly used metrics such as R-Precision and less-used coordinate errors show strong correlations. Additionally, several recently developed metrics are not recommended due to their low correlation compared to alternatives. We also introduce a novel metric based on a multimodal BERT-like model, MoBERT, which offers strongly human-correlated sample-level evaluations while maintaining near-perfect model-level correlation. Our results demonstrate that this new metric exhibits extensive benefits over all current alternatives.

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