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Yingxu Wang

Publications and source records attributed to Yingxu Wang.

At least 19 recordsLinked to original sources
arXiv2026

Data-Efficient Agentic Graph Domain Adaptation via Reliability-Aware Prototype Learning

Agentic learning systems are often required to adapt after deployment by observing new data and reusing prior knowledge under limited supervision or feedback. For graph-structured prediction, Graph Domain Adaptation (GDA) naturally instantiates this setting by transferring knowledge from labeled source graphs to unlabeled target graphs under distribution shifts. However, most GDA methods assume sufficient labeled source graphs, which becomes restrictive in data-efficient agentic settings where only limited source evidence can be retained. Under such constraints, source semantics become unreliable, leading to unstable source anchoring, uncertain target association, and fragile targetmarginal calibration. To address these challenges, we propose DEAG, a reliability-aware prototype learning framework for data-efficient agentic GDA. DEAG estimates class reliability from retained source support and embedding compactness, and constructs stable reusable source anchors by blending empirical prototypes with classifier directions. Guided by these anchors, DEAG performs prototype-aware soft target association and aligns confidence-weighted target centers with source semantics. A source-prior regularizer further sharpens target predictions while keeping the target marginal consistent with retained source evidence. Experiments on graph benchmarks with diverse domain shifts show that DEAG improves average adaptation performance over competitive GDA baselines under the same source-data budget.

cs.LG↗
arXiv2026

Cross-Resolution Semantic Learning for Graph Domain Adaptation

Graph Domain Adaptation (GDA) transfers predictive knowledge from labeled source graphs to unlabeled target graphs under distribution shift. Existing methods align representations or regularize graph structures, but do not explicitly model how class-discriminative knowledge learned at different source neighborhood ranges should be routed across target ranges. We call the neighborhood range encoded by a graph representation its propagation resolution and define semantic resolution shift as a cross-domain change in the propagation resolutions at which class-discriminative evidence is strongest. Such shifts can make fixed same-resolution pairing suboptimal and increase the risk of negative transfer. To address this issue, we propose Cross-Resolution Semantic Learning (CReSL), a GDA method that learns soft sourceto-target resolution correspondence from cross-domain class structure. First, CReSL constructs a multi-resolution representation bank using a shared Graph Neural Network and learnable resolution embeddings, with a resolution-indexed expert for each source resolution. Second, CReSL introduces Cross-Resolution Prototype Transport, which constructs class-resolution prototypes from source labels and soft target posteriors and converts cross-domain prototype discrepancies into expert-specific routing over target resolutions. Third, CReSL introduces Cross-Resolution Target Grafting, which constructs posterior-weighted target-to-source prototype displacements and enforces correspondence-weighted prediction consistency for instance-level adaptation under class uncertainty. Extensive experiments on graph benchmarks under diverse domain shifts show that CReSL outperforms strong representative baselines across most settings.

cs.LG↗
arXiv2026

MOLAR: Learning Multimodal Molecular Representations from Noisy Labels

Motivation: Noisy labels are a common challenge in molecular property prediction because molecular annotations are often obtained from assays, curated databases, or weak annotation pipelines rather than directly observed clean biological states. Treating recorded labels as reliable supervision can cause models to memorize corrupted observations and learn misleading molecular evidence. In multimodal molecular representation learning, this issue can be amplified by graph-text fusion or alignment, which may propagate label-induced errors across modalities. Results: We propose MOLAR, a noise-aware framework for learning multimodal molecular representations from noisy labels. MOLAR separates latent clean-property inference from recorded-label observation: graph and text views contribute residual evidence to a clean-property distribution, and a categorical label-observation channel maps this distribution to recorded labels for training. This formulation derives posterior label reliability and modality-specific molecular evidence from the model. Experiments on naturally noisy molecular benchmarks and controlled label-flipping benchmarks show that MOLAR consistently outperforms representative baselines. Visualization analyses further show that MOLAR provides interpretable reliability and modality-evidence diagnostics.

cs.LG↗
arXiv2026

REFLECT: Intervention-Supported Error Attribution for Silent Failures in LLM Agent Traces

Large language model (LLM) agents now solve complex tasks through long plan-and-execution traces, yet the ability to locate errors in a completed traces still lags far behind, especially in the \emph{silent failure} regime. Existing approaches predict suspect steps via classifiers or LLM judges, or recover correct answers via retry, but none feed the intervention outcome back to \emph{refine the attribution itself}. We propose \methodname, a method that closes this gap by diagnosing a candidate error step, testing it through controlled replay with a diagnosis-specific patch, and using the verified outcome flip as contrastive evidence to refine the final attribution. Across four localization benchmarks spanning multi-hop reasoning across domains, \methodname achieves the highest localization accuracy among same-auditor methods across all four benchmarks, with the largest gains on structured tool-use traces, while providing actionable localization even when ground-truth answers are unavailable.

cs.AI↗
arXiv2026

Safe-Subspace Pseudo-Label Refinement for Source-Free Graph Domain Adaptation

Source-free graph domain adaptation (SF-GDA) aims to adapt source-trained graph models to unlabeled target graphs when source graphs are no longer accessible. A central obstacle is pseudo-label reliability: under feature and topological shifts, source-induced predictions may become confidently wrong, and indiscriminate self-training can amplify systematic errors through graph message passing. This paper studies SF-GDA from a selective pseudo-labeling perspective. Instead of assuming globally bounded pseudo-label noise over the entire target domain, we identify a confidence-consistent safe subspace on which pseudo-label noise can be controlled under restricted posterior discrepancy, and derive a target-risk decomposition that separates safe-subspace fitting error, selected-label noise, and uncertain-set risk. Guided by this analysis, we propose SafeSubspace Pseudo-Label Refinement (S$^2$PLR), a source-free graph adaptation framework that applies hard pseudo-label supervision only to target graphs supported by both semantic and structural evidence. Specifically, S$^2$PLR estimates semantic reliability using source-committee confidence and disagreement, learns a targetintrinsic structural representation via graph contrastive learning, verifies pseudo-labels through neighborhood consistency, and exploits the remaining uncertain samples with noise-tolerant soft regularization rather than unreliable hard labels. Experiments on image and real-world graph benchmarks under different domain shifts demonstrate that S$^2$PLR achieves robust and competitive performance across diverse source-free transfer settings.

cs.LG↗
arXiv2026

DisRFM: Polar Riemannian Flow Matching for Structure-Preserving Graph Domain Adaptation

Graph Domain Adaptation (GDA) aims to transfer graph classifiers across domains with both semantic and topological shifts. Existing Euclidean adversarial methods face two challenges: Structural Degeneration, where domain confusion entangles and suppresses label-relevant topology, and Optimization Instability, where minimax training induces oscillatory gradients under large structural shifts. We propose DisRFM, a geometry-aware GDA framework that addresses these challenges with Riemannian representation learning and flow-based transport. DisRFM embeds graph representations on a constant-curvature manifold and expresses them in geodesic polar coordinates. Polar endpoint regularization calibrates topologysensitive radial scales via univariate Wasserstein alignment and preserves scalenormalized class semantics through confidence-filtered angular alignment, with radial magnitude modulating pseudo-label reliability. DisRFM introduces topologyconditioned polar flow matching, which couples class-compatible source and target samples by a normalized polar transport cost and learns a metric-corrected vector field along geodesic interpolants. Theoretical analysis characterizes the structural risk of unconditional domain confusion and relates polar discrepancies and flow error to target risk. Extensive experiments under diverse domain shifts demonstrate that DisRFM consistently outperforms state-of-the-art methods.

cs.LG↗
arXiv2026

When Brain Networks Travel: Learning Beyond Site

Graph-based learning on functional magnetic resonance imaging (fMRI) has shown strong potential for brain network analysis. However, existing methods degrade under cross-site out-of-distribution (OOD) settings because site-conditioned confounders induce non-pathological shortcuts, while functional connectivity constructed by temporal averaging obscures transient neurodynamics, limiting generalization to unseen sites. In this paper, we propose Cross-site OOD Robust brain nEtwork (CORE), a unified framework for brain network learning across unseen sites. CORE first performs site-aware confounder decoupling to mitigate site-conditioned bias and extract a cross-site population scaffold of reproducible diagnostic connectivity edges. It then profiles transient pathway dynamics over this scaffold using lightweight temporal descriptors and organizes scaffold edges into a line graph for transferable pathway-level modeling. Finally, CORE introduces a prior-guided subject-adaptive gating mechanism that leverages scaffold-derived population priors while preserving subject-specific connectivity variability. Extensive experiments under leave-one-site-out evaluation on real-world datasets (ABIDE, REST-meta-MDD, SRPBS, and ABCD) show that CORE consistently outperforms state-of-the-art baselines, with up to 6.7% relative gain. Furthermore, CORE remains robust to atlas variations, maintaining performance gains across different brain parcellation schemes.

cs.LG↗
arXiv2026

SEW: Self-Evolving Agentic Workflows for Automated Code Generation

Large Language Models (LLMs) have demonstrated effectiveness in code generation tasks. To enable LLMs to address more complex coding challenges, existing research has focused on crafting multi-agent systems with agentic workflows, where complex coding tasks are decomposed into sub-tasks, assigned to specialized agents. Despite their effectiveness, current approaches heavily rely on hand-crafted agentic workflows, with both agent topologies and prompts manually designed, which limits their ability to automatically adapt to different types of coding problems. To address these limitations and enable automated workflow design, we propose \textbf{S}elf-\textbf{E}volving \textbf{W}orkflow (\textbf{SEW}), a novel self-evolving framework that automatically generates and optimises multi-agent workflows. Extensive experiments on three coding benchmark datasets, including the challenging LiveCodeBench, demonstrate that our SEW can automatically design agentic workflows and optimise them through self-evolution, bringing up to 12\% improvement on LiveCodeBench compared to using the backbone LLM only. Furthermore, by investigating different representation schemes of workflow, we provide insights into the optimal way to encode workflow information with text.

cs.SE↗
arXiv2026

TRACE: An Experiential Framework for Coherent Multi-hop Knowledge Graph Question Answering

Multi-hop Knowledge Graph Question Answering (KGQA) requires coherent reasoning across relational paths, yet existing methods often treat each reasoning step independently and fail to effectively leverage experience from prior explorations, leading to fragmented reasoning and redundant exploration. To address these challenges, we propose Trajectoryaware Reasoning with Adaptive Context and Exploration priors (TRACE), an experiential framework that unifies LLM-driven contextual reasoning with exploration prior integration to enhance the coherence and robustness of multihop KGQA. Specifically, TRACE dynamically translates evolving reasoning paths into natural language narratives to maintain semantic continuity, while abstracting prior exploration trajectories into reusable experiential priors that capture recurring exploration patterns. A dualfeedback re-ranking mechanism further integrates contextual narratives with exploration priors to guide relation selection during reasoning. Extensive experiments on multiple KGQA benchmarks demonstrate that TRACE consistently outperforms state-of-the-art baselines.

cs.CL↗
arXiv2026

DSBD: Dual-Aligned Structural Basis Distillation for Graph Domain Adaptation

Graph domain adaptation (GDA) aims to transfer knowledge from a labeled source graph to an unlabeled target graph under distribution shifts. However, existing methods are largely feature-centric and overlook structural discrepancies, which become particularly detrimental under significant topology shifts. Such discrepancies alter both geometric relationships and spectral properties, leading to unreliable transfer of graph neural networks (GNNs). To address this limitation, we propose Dual-Aligned Structural Basis Distillation (DSBD) for GDA, a novel framework that explicitly models and adapts cross-domain structural variation. DSBD constructs a differentiable structural basis by synthesizing continuous probabilistic prototype graphs, enabling gradient-based optimization over graph topology. The basis is learned under source-domain supervision to preserve semantic discriminability, while being explicitly aligned to the target domain through a dual-alignment objective. Specifically, geometric consistency is enforced via permutation-invariant topological moment matching, and spectral consistency is achieved through Dirichlet energy calibration, jointly capturing structural characteristics across domains. Furthermore, we introduce a decoupled inference paradigm that mitigates source-specific structural bias by training a new GNN on the distilled structural basis. Extensive experiments on graph and image benchmarks demonstrate that DSBD consistently outperforms state-of-the-art methods.

cs.LG↗
arXiv2026

USBD: Universal Structural Basis Distillation for Source-Free Graph Domain Adaptation

SF-GDA is pivotal for privacy-preserving knowledge transfer across graph datasets. Although recent works incorporate structural information, they implicitly condition adaptation on the smoothness priors of sourcetrained GNNs, thereby limiting their generalization to structurally distinct targets. This dependency becomes a critical bottleneck under significant topological shifts, where the source model misinterprets distinct topological patterns unseen in the source domain as noise, rendering pseudo-label-based adaptation unreliable. To overcome this limitation, we propose the Universal Structural Basis Distillation, a framework that shifts the paradigm from adapting a biased model to learning a universal structural basis for SF-GDA. Instead of adapting a biased source model to a specific target, our core idea is to construct a structure-agnostic basis that proactively covers the full spectrum of potential topological patterns. Specifically, USBD employs a bi-level optimization framework to distill the source dataset into a compact structural basis. By enforcing the prototypes to span the full Dirichlet energy spectrum, the learned basis explicitly captures diverse topological motifs, ranging from low-frequency clusters to high-frequency chains, beyond those present in the source. This ensures that the learned basis creates a comprehensive structural covering capable of handling targets with disparate structures. For inference, we introduce a spectral-aware ensemble mechanism that dynamically activates the optimal prototype combination based on the spectral fingerprint of the target graph. Extensive experiments on benchmarks demonstrate that USBD significantly outperforms state-of-the-art methods, particularly in scenarios with severe structural shifts, while achieving superior computational efficiency by decoupling the adaptation cost from the target data scale.

cs.LG↗
arXiv2026

DiEC: Diffusion Embedded Clustering

Deep clustering methods typically rely on a single, well-defined representation for clustering. In contrast, pretrained diffusion models provide abundant and diverse multi-scale representations across network layers and noise timesteps. However, a key challenge is how to efficiently identify the most clustering-friendly representation in the layer*timestep space. To address this issue, we propose Diffusion Embedded Clustering (DiEC), an unsupervised framework that performs clustering by leveraging optimal intermediate representations from pretrained diffusion models. DiEC systematically evaluates the clusterability of representations along the trajectory of network depth and noise timesteps. Meanwhile, an unsupervised search strategy is designed for recognizing the Clustering-optimal Layer (COL) and Clustering-optimal Timestep (COT) in the layer*timestep space of pretrained diffusion models, aiming to promote clustering performance and reduce computational overhead. DiEC is fine-tuned primarily with a structure-preserving DEC-style KL-divergence objective at the fixed COL + COT, together with a random-timestep diffusion denoising objective to maintain the generative capability of the pretrained model. Without relying on augmentation-based consistency constraints or contrastive learning, DiEC achieves excellent clustering performance across multiple benchmark datasets.

cs.LG↗
arXiv2026

SGAC: A Graph Neural Network Framework for Imbalanced and Structure-Aware AMP Classification

Classifying Antimicrobial Peptides (AMPs) from the vast collection of peptides derived from metagenomic sequencing offers a promising avenue for combating antibiotic resistance. However, most existing AMP classification methods rely primarily on sequence-based representations and fail to capture the spatial structural information critical for accurate identification. Although recent graph-based approaches attempt to incorporate structural information, they typically construct residue- or atom-level graphs that introduce redundant atomic details and increase structural complexity. Furthermore, the class imbalance between the small number of known AMPs and the abundant non-AMPs significantly hinders predictive performance. To address these challenges, we employ lightweight OmegaFold to predict the three-dimensional structures of peptides and construct peptide graphs using C α atoms to capture their backbone geometry and spatial topology. Building on this representation, we propose the Spatial GNN-based AMP Classifier (SGAC), a novel framework that leverages Graph Neural Networks (GNNs) to extract structural features and generate discriminative graph representations. To handle class imbalance, SGAC incorporates Weight-enhanced Contrastive Learning to cluster structurally similar peptides and separate dissimilar ones through adaptive weighting, and applies Weight-enhanced Pseudo-label Distillation to generate high-confidence pseudo labels for unlabeled samples, achieving balanced and consistent representation learning. Experiments on publicly available AMP and non-AMP datasets demonstrate that SGAC significantly achieves state-of-the-art performance compared to baselines.

q-bio.QM↗
arXiv2025

DuSEGO: Dual Second-order Equivariant Graph Ordinary Differential Equation

Graph Neural Networks (GNNs) with equivariant properties have achieved significant success in modeling complex dynamic systems and molecular properties. However, their expressiveness ability is limited by: (1) Existing methods often overlook the over-smoothing issue caused by traditional GNN models, as well as the gradient explosion or vanishing problems in deep GNNs. (2) Most models operate on first-order information, neglecting that the real world often consists of second-order systems, which further limits the model's representation capabilities. To address these issues, we propose the \textbf{Du}al \textbf{S}econd-order \textbf{E}quivariant \textbf{G}raph \textbf{O}rdinary Differential Equation (\method{}) for equivariant representation. Specifically, \method{} apply the dual second-order equivariant graph ordinary differential equations (Graph ODEs) on graph embeddings and node coordinates, simultaneously. Theoretically, we first prove that \method{} maintains the equivariant property. Furthermore, we provide theoretical insights showing that \method{} effectively alleviates the over-smoothing problem in both feature representation and coordinate update. Additionally, we demonstrate that the proposed \method{} mitigates the exploding and vanishing gradients problem, facilitating the training of deep multi-layer GNNs. Extensive experiments on benchmark datasets validate the superiority of the proposed \method{} compared to baselines.

cs.LG↗
arXiv2025

ProtoMol: Enhancing Molecular Property Prediction via Prototype-Guided Multimodal Learning

Multimodal molecular representation learning, which jointly models molecular graphs and their textual descriptions, enhances predictive accuracy and interpretability by enabling more robust and reliable predictions of drug toxicity, bioactivity, and physicochemical properties through the integration of structural and semantic information. However, existing multimodal methods suffer from two key limitations: (1) they typically perform cross-modal interaction only at the final encoder layer, thus overlooking hierarchical semantic dependencies; (2) they lack a unified prototype space for robust alignment between modalities. To address these limitations, we propose ProtoMol, a prototype-guided multimodal framework that enables fine-grained integration and consistent semantic alignment between molecular graphs and textual descriptions. ProtoMol incorporates dual-branch hierarchical encoders, utilizing Graph Neural Networks to process structured molecular graphs and Transformers to encode unstructured texts, resulting in comprehensive layer-wise representations. Then, ProtoMol introduces a layer-wise bidirectional cross-modal attention mechanism that progressively aligns semantic features across layers. Furthermore, a shared prototype space with learnable, class-specific anchors is constructed to guide both modalities toward coherent and discriminative representations. Extensive experiments on multiple benchmark datasets demonstrate that ProtoMol consistently outperforms state-of-the-art baselines across a variety of molecular property prediction tasks.

cs.LG↗
arXiv2025

Degree-Conscious Spiking Graph for Cross-Domain Adaptation

Spiking Graph Networks (SGNs) have demonstrated significant potential in graph classification by emulating brain-inspired neural dynamics to achieve energy-efficient computation. However, existing SGNs are generally constrained to in-distribution scenarios and struggle with distribution shifts. In this paper, we first propose the domain adaptation problem in SGNs, and introduce a novel framework named Degree-Consicious Spiking Graph for Cross-Domain Adaptation (DeSGraDA). DeSGraDA enhances generalization across domains with three key components. First, we introduce the degree-conscious spiking representation module by adapting spike thresholds based on node degrees, enabling more expressive and structure-aware signal encoding. Then, we perform temporal distribution alignment by adversarially matching membrane potentials between domains, ensuring effective performance under domain shift while preserving energy efficiency. Additionally, we extract consistent predictions across two spaces to create reliable pseudo-labels, effectively leveraging unlabeled data to enhance graph classification performance. Furthermore, we establish the first generalization bound for SGDA, providing theoretical insights into its adaptation performance. Extensive experiments on benchmark datasets validate that DeSGraDA consistently outperforms state-of-the-art methods in both classification accuracy and energy efficiency.

cs.LG↗
arXiv2025

DAMR: Efficient and Adaptive Context-Aware Knowledge Graph Question Answering with LLM-Guided MCTS

Knowledge Graph Question Answering (KGQA) aims to interpret natural language queries and perform structured reasoning over knowledge graphs by leveraging their relational and semantic structures to retrieve accurate answers. Existing methods primarily follow either the retrieve-then-reason paradigm, which relies on Graph Neural Networks or heuristic rules to extract static candidate paths, or dynamic path generation strategies that employ LLMs with prompting to jointly perform retrieval and reasoning. However, the former lacks adaptability due to static path extraction and the absence of contextual refinement, while the latter suffers from high computational costs and limited evaluation accuracy because of their dependence on fixed scoring functions and repeated LLM calls. To address these issues, this paper proposes Dynamically Adaptive MCTS-based Reasoning (DAMR), a novel framework that integrates LLM-guided Monte Carlo Tree Search (MCTS) with adaptive path evaluation to enable efficient and context-aware KGQA. DAMR leverages MCTS as a backbone, where an LLM-based planner selects the top-$k$ semantically relevant relations at each expansion step to effectively reduce the search space. To enhance evaluation accuracy, we introduce a lightweight Transformer-based scorer that performs context-aware plausibility estimation by jointly encoding the question and relation sequence through cross-attention, thereby capturing fine-grained semantic shifts during multi-hop reasoning. Furthermore, to mitigate the scarcity of high-quality supervision, DAMR incorporates a dynamic pseudo-path refinement mechanism that periodically generates training signals from partial paths explored during search, enabling the scorer to continually adapt to the evolving distribution of reasoning trajectories. Extensive experiments on multiple KGQA benchmarks show that DAMR significantly outperforms SOTA methods.

cs.CL↗
arXiv2025

EvoAgentX: An Automated Framework for Evolving Agentic Workflows

Multi-agent systems (MAS) have emerged as a powerful paradigm for orchestrating large language models (LLMs) and specialized tools to collaboratively address complex tasks. However, existing MAS frameworks often require manual workflow configuration and lack native support for dynamic evolution and performance optimization. In addition, many MAS optimization algorithms are not integrated into a unified framework. In this paper, we present EvoAgentX, an open-source platform that automates the generation, execution, and evolutionary optimization of multi-agent workflows. EvoAgentX employs a modular architecture consisting of five core layers: the basic components, agent, workflow, evolving, and evaluation layers. Specifically, within the evolving layer, EvoAgentX integrates three MAS optimization algorithms, TextGrad, AFlow, and MIPRO, to iteratively refine agent prompts, tool configurations, and workflow topologies. We evaluate EvoAgentX on HotPotQA, MBPP, and MATH for multi-hop reasoning, code generation, and mathematical problem solving, respectively, and further assess it on real-world tasks using GAIA. Experimental results show that EvoAgentX consistently achieves significant performance improvements, including a 7.44% increase in HotPotQA F1, a 10.00% improvement in MBPP pass@1, a 10.00% gain in MATH solve accuracy, and an overall accuracy improvement of up to 20.00% on GAIA. The source code is available at: https://github.com/EvoAgentX/EvoAgentX

cs.AI↗