Node Classification

Follow this topic Ask about this topic

Momentum

9 papers in the last four weeks, with none the four weeks before. 0.1% of all new papers.

Jul 13Week of Sep 28

Latest papers 52

Oct 7, 2026cs.LG

Node-level Graph Neural Architecture Search Framework

In recent years, Graph Neural Networks (GNNs) and architecture search frameworks have gained extensive application in non-Euclidean data processing, attributable to their superior capacity in managing unstructured data. Nevertheless, traditional approaches typically apply uniform convolution operations to all nodes, regardless of their varying structural and feature characteristics, which can undermine model performance and result in over-smoothing issues as the number of layers increases. To overcome this limitation, in this work, we propose a \textbf{N}ode-Level \textbf{G}raph \textbf{N}eural \textbf{A}rchitecture \textbf{S}earch (N-GNAS) algorithm. It can automatically choose an appropriate network architecture for each subset of nodes when updating node features. N-GNAS also introduces a contrastive learning loss to separate sample features from different categories and vice versa. In experiments conducted on eight datasets for node and graph classification, our methodology outperforms current leading GNAS techniques and traditional human-designed GNNs. For example, it achieves an accuracy rate of 78.26% on the CiteSeer dataset.

Lintao Yanga, Sirui Lia, Yaqing Wang +4

College of Information Science and Engineering, Ningbo University, Ningbo, 315211, China · Department of Computer Science and Technology, University of Cambridge, Cambridge, CB3 0FD, UK · School of Artificial Intelligence, Jilin University, Changchun, 130015, China

Graph Neural Networks Neural Architecture Search Node Classification

Oct 6, 2026cs.LG

Valid for Free: Homophily-Gated Conformal Prediction for Training-Free Node Classification with Tabular Foundation Models

Tabular foundation models (TFMs) can classify the nodes of a graph without training on it, by reading node and neighborhood features as table rows next to labeled context rows. Work in this line reports predictive performance, not conformal coverage or prediction-set size. To our knowledge, we give the first reliability study of the setting, with TabICL as the TFM and half of each graph as labeled context. As for any predictor fixed before calibration, a frozen in-context predictor makes split conformal prediction exactly valid in finite samples, with no training, validation fold, or tuning on the target graph. An audit across ten graphs then shows that the training-free TabICL posterior has lower expected calibration error (ECE) than GCN with temperature scaling (GCN+TS) on nine of them. Its mean ECE over the ten graphs is 0.019, about 35 percent below the 0.029 of GCN+TS. We also introduce HG-DAPS, a training-free diffusion score whose homophily gate reads only the in-context labels, so the guarantee still holds. Relative to adaptive prediction sets (APS), it reduces mean set size by 5.8 to 17.1 percent on six homophilous graphs and changes it by under 1 percent on four heterophilous ones. On two binary, class-imbalanced graphs, a pre-registered trap case shows that gating on raw rather than adjusted homophily lowers coverage among low-homophily nodes by 0.27 and 0.12. Marginal coverage stays at the nominal 0.90 and masks this drop.

Nguyen Duy Long, Phung Minh Hien, Nguyen Trong Viet +1

Faculty of Information Technology, Posts and Telecommunications Institute of Technology, Hanoi, Vietnam · Faculty of Engineering, School of Computer Science, The University of Sydney, Sydney, Australia · Faculty of Information Technology, Van Lang School of Technology, Van Lang University, Ho Chi Minh City, Vietnam

Tabular Foundation Models Conformal Prediction Node Classification

Sep 30, 2026cs.LG

NodeGround: A Node Classification Benchmark in the Graph Foundation Model Era

Can a pretrained graph model replace training and tuning a separate predictor for each dataset? Answering this requires evaluating prediction quality alongside computational cost. We present NodeGround, a node classification benchmark that puts graph foundation models (GFMs) and dataset-specific supervised learning under a common evaluation framework. The benchmark spans 51 datasets and evaluates six GFMs alongside 15 supervised methods under two label-availability regimes. Shared data partitions, validation-only model selection, controlled hyperparameter searches, and multiple predictive metrics make comparisons systematic, while workflow measurements account for adaptation, training, tuning, and inference. The results favor carefully tuned graph neural networks overall. GraphPFN reaches third place by Elo when more labels are available, yet its relative strengths vary substantially with dataset properties. Efficiency comparisons further qualify the benefits of pretrained reuse: GVT and GraphPFN appear on the Pareto frontiers when supervised methods are represented by their default and fully tuned configurations. Adding intermediate tuning budgets removes this advantage for GVT and leaves GraphPFN extending the estimated frontier in the label-rich setting alone. Thus, reusing pretrained parameters does not yet provide a broadly reliable route to either stronger predictions or cheaper workflows. We release the evaluation pipeline, run-level records, and an open leaderboard at https://github.com/nums-ai/nodeground.

Jinmo Lee, Dooho Lee, Minho Jeong +1

Nums AI

Graph Foundation Models Node Classification

Sep 28, 2026cs.LG

Propagate, Then Sharpen: Post-Hoc Refinement of Frozen Node Classifiers

We study post-hoc refinement of frozen node classifiers: given only the graph

G

and class distributions

Q

predicted by a frozen model, can we improve accuracy without access to node features, model parameters, or gradients? APPNP answers this by propagating logits with a restart towards the initial predictions, minimizing the anchored Dirichlet energy. Instead, we consider the Potts energy, and decompose it into a Dirichlet term, which penalizes disagreement between neighbouring nodes, and a Gini term, which penalizes indecision within each node. This decomposition motivates Propagate, Then Sharpen (PtS), which alternates between propagation of class probabilities and node-wise, mass-preserving sharpening, with only one additional hyperparameter selected using labelled validation nodes. Across nine homophilic graphs, with a frozen MLP backbone, PtS improves mean test accuracy over independently tuned APPNP by

1.71

percentage points on clean inputs and

3.90

under severe Gaussian feature corruption. Gains over APPNP become smaller, but remain positive with frozen GCN and GraphSAGE backbones. Sharpening also removes most of the accuracy loss of deep propagation: on clean inputs without restart, accuracy falls by

2.2

points between

2

and

100

propagation steps under PtS, compared with

33.8

for APPNP.

Preben Johnsen Bentdal, Nello Blaser, Xue-Cheng Tai

Department of Informatics, University of Bergen · Norwegian Research Centre (NORCE)

Graph-Based Semi-Supervised Learning Classification Node Classification Graph Diffusion

Sep 24, 2026cs.LG

ICE: Task-Aligned Clifford Latent Fields for Multimodal Graph Foundation Models

Multimodal attributed graphs connect entities, visual content, language, and observed relations. Learning one foundation across such graphs requires more than compressing each node into a fused Euclidean vector. The representation must preserve entity semantics, construct interaction state from graph neighborhoods, and expose that state to prediction units with different geometry. Our empirical study shows why these requirements are inseparable. Higher-grade channels recover pair relations across the foundation graphs, specialized queries reveal information hidden by a generic readout, and rigid blade isolation removes cross-grade capacity. We therefore introduce ICE (Interaction-aware Clifford Encoder), a multimodal graph foundation model built on a node-indexed Clifford latent field. Topology, text, and images enter explicit Cl(3) addresses. Edge-aware geometric products transform these directions into scalar, bivector, and trivector relations over observed neighborhoods. A protected Grade-1 route preserves entity semantics, while the full grade and depth bank remains available to fresh node and link heads. We establish exact cross-grade reachability, node-permutation equivariance, and a bound on the task residual around the semantic score. Experiments span one shared foundation over eleven graphs, six node-classification datasets, three link-prediction datasets, and matched few-shot tasks. ICE ranks first in all 30 reported supervised and few-shot comparisons. Core removals reduce every task summary, and mechanism controls connect the gains to higher-order transport, retained multidepth structure, semantic protection, and direct field access.

Xunkai Li, Xu Wang, Yinlin Zhu +4

Department of Computer Science, Beijing Institute of Technology, Beijing, China · School of Airspace Science and Engineering, Shandong University, WeiHai, China · School of Computer Science and Engineering, Sun Yat-sen University, GuangZhou, China

Graph Foundation Models Multimodal Graph Learning Node Classification

Sep 22, 2026cs.LG

Local Evidence and Geometric Readout Repair in Trained GNNs

Many node-classification GNNs apply a linear classifier to a nonnegative mixture of local messages. An error can reflect either poor mixture weights or a reachable logit set poorly positioned for the classifier. We separate these causes with an exact-mass linear program and two learned post-hoc repairs. Every reweighted prediction has an equivalent centered logit translation, but only translations in a message-induced displacement set are realizable by reweighting. Across eight datasets, eight GNN backbones, and ten splits, mean accuracy rises from 62.6% for the frozen models to 63.8% with reweighting and 65.3% with set-conditioned translation. A parameter-matched node-only translator reaches 64.6%, showing that translation explains most of the gain while the message set supplies a smaller additional benefit. Although oracle reweighting can correct many errors, label-free reweighting captures little of this potential: local evidence is often present but hard to select, and relaxing the evidence constraint is more effective than learning within it.

Nadi Tomeh, Hugo Attali

Université Sorbonne Paris Nord, CNRS, Laboratoire d’Informatique de Paris Nord, LIPN, F-93430 Villetaneuse, France

Graph Neural Networks Node Classification

Sep 22, 2026cs.LG

PreGS: A Parameter-Transfer-Based Multi-Expert Graph Neural Network for Node Classification

Graph neural networks have achieved strong performance in node classification by aggregating information from graph neighborhoods. However, a single aggregation mechanism may be insufficient to capture diverse structural patterns across graph datasets. Moreover, independently training multiple structural branches can introduce substantial overhead without necessarily producing stable node representations. To address these issues, this paper proposes PreGS, a parameter-transfer-based multi-expert graph neural network framework. PreGS first pretrains a multi-head graph attention network (GAT) and transfers the linear transformation weights of its first-layer attention heads to multiple GraphSAGE experts. The transferred experts are frozen and used as complementary structural branches. The fused raw node features, GAT head representations, and GraphSAGE expert representations are fed into a multilayer perceptron (MLP), whose output is further fused with the pretrained GAT logits. Based on PreGS, we further develop PreGSv2, which introduces source-level weighting and a structural gating mechanism for adaptive multi-source feature integration. Experiments on eight public graph datasets show that PreGS and PreGSv2 achieve competitive performance against representative graph neural network baselines. Ablation, parameter-transfer, sensitivity, aggregator, visualization, and training-time analyses further validate the effectiveness and stability of the proposed framework. The code and datasets are available at https://github.com/LH-Czc/PreGS.

Zhicong Cai, Yinglong Zhang, Xiaoying Hong +2

College of Physics and Information Engineering, Minnan Normal University, Zhangzhou 363000, China

Graph Neural Networks Mixture-of-Experts Models Node Classification

Sep 22, 2026cs.LG

Graph Domain Adaptation Does Not End with Representation Learning

Graph domain adaptation (GDA) transfers knowledge from a labeled source graph to an unlabeled target graph under shifts in both node attributes and graph structure. Existing methods primarily adapt graph representations through propagation redesign, distribution alignment, or source-to-target transition modeling, but still rely on a single graph-propagating path for target prediction. This leaves open whether an adapted graph representation exhausts the predictive evidence available in the target domain, since the graph-aware expert and graph-free local expert may exhibit different failure modes under topological shifts. To address this limitation, we propose EviGDA, an Evidence-Augmented Graph Domain Adaptation framework that complements graph representation adaptation with a graph-free local expert. The graph-aware expert performs message passing and entropy-aware marginal alignment, while the graph-free local expert learns solely from source node features and labels without graph propagation or target alignment. The two experts are optimized independently and combined only at inference through a task-level constant probability mixture, preserving complementary evidence without joint training, learned routing, or target pseudo-labels. Extensive experiments on ten datasets and 16 transfer tasks show that EviGDA outperforms state-of-the-art baselines.

Ziqian Liu, Yongxue Xu, Enze Zhang +3

Sun Yat-sen University, China · University of Wisconsin–Madison, USA · Jiangsu University, China +2

Unsupervised Domain Adaptation Graph Representation Learning Domain Adaptation Node Classification

Sep 16, 2026cs.LG

Provable Guarantees for Spectral Structured Prediction

Structured prediction is the simultaneous prediction of multiple labels, and is widely used in various fields, such as natural language processing and computer vision. In this paper, we study binary node label recovery on signed graphs with edge-flip noise, a model introduced by (Globerson et al., 2015), via a simple spectral method that decodes node labels from the signs of the principal eigenvector of the noisy signed adjacency matrix. We develop graph structure-agnostic theoretical guarantees for approximate inference of node labels as well as guarantees for maximum angle deviation with respect to the ground truth node labels. By leveraging tools from matrix concentration theory and eigenvector perturbation analysis, we derive new concentration inequalities that explicitly quantify the effect of the spectral gap of the adjacency matrix, number of nodes, degree distribution, and noise level. As a corollary, we relate our general results to the Cheeger constant and provide results for different classes of graphs. We perform several synthetic experiments to validate our theory. To the best of our knowledge, we are the first to provide theoretical guarantees for the spectral-based approach. As a byproduct of our analysis, we derive technical results that might be of independent interest and useful for other machine learning problems.

Violet Zheng, Jean Honorio

CIS, The University of Melbourne

Spectral Methods Node Classification Structured Prediction

Sep 16, 2026cs.SI

Not All Nodes Are Created Equal: Homophily-Aware Stratification for Stable GNN Evaluation

Graph neural networks are widely used for transductive node classification, with accuracy typically measured on randomly drawn train/validation/test splits. Reported accuracy has been shown to shift substantially across different random splits of the same dataset, making published comparisons between architectures unreliable. The classical remedy in non-graph settings is stratified

k

-fold cross-validation, which ensures each test fold reflects the full class distribution of the dataset. We argue that class stratification alone is insufficient for graphs: nodes are not isolated but connected, and folds that differ in their distribution of local neighbourhood homophily expose the model to systematically different relational conditions that directly affect message-passing behaviour. The resulting cross-fold variation reflects the homophily composition of each split, inflating reported variance beyond what model behaviour alone would produce. To address this, we propose \hp{}, a topology-aware stratification procedure that treats node homophily as the primary stratification axis, aligning folds with respect to local relational consistency alongside the class marginal that standard stratification already controls. Stratifying on homophily alone does not guarantee class balance, so \hp{} incorporates class label as a secondary axis, preserving class representativeness as a natural consequence of the procedure. We evaluate \hp{} on a broad benchmark suite comprising 15 node-classification datasets spanning the full homophily spectrum and 7 GNN architectures. \hp{} achieves a mean stability rank of 1.49 compared to 2.31 for random

k

-fold, achieving the lowest mean stability rank on 13 of 15 datasets while preserving class balance close to class-stratified splits and substantially better than random. We argue that homophily-aware split construction merits broader adoption for GNN evaluation.

Naga Venkata Sai Jitin Jami, Thomas Altstidl, Sebastian Hoefler +4

Chair for Machine Learning in Medicine, Universität Bayreuth · Department Artiﬁcial Intelligence in Biomedical Engineering, FAU Erlangen-Nürnberg · Chair of AI-supported Therapy Decisions, Ludwig-Maximilians-Universität München +1

Graph Neural Networks Node Classification

Sep 8, 2026cs.LG

HOPE: Heterophily-Aware Open-Set Node Classification with Pseudo-Extrapolation

Standard open-set node classification methods rely on the homophily assumption, where connected nodes share labels. However, real-world graphs are often heterophilic, exposing the limitations of current methods and posing new challenges to open-set node classification. On the one hand, cross-class connectivity causes representations from different known or unknown classes to become intertwined after aggregation, undermining their discriminative capacity. On the other hand, structural mixture invalidates threshold-based open-set methods and cross-class feature interpolation, leading to unreliable unknown-class rejection. To address these challenges, we propose HOPE, a Heterophily-aware Open-set node classification method with Pseudo-Extrapolation. To adapt open-set graph neural networks (GNNs) to heterophilic scenarios, HOPE uses a structure-augmented feature initialization layer to capture multi-hop structural patterns. Meanwhile, we design a trustworthy neighborhood aggregation mechanism for standard GNNs to dynamically filter noisy cross-class neighbors. To enhance unknown-class rejection, we introduce a heterophily-guided pseudo-extrapolation strategy. It dynamically maintains known-class centers and extrapolates along cross-class neighborhood displacement directions, synthesizing pseudo-unknown proxies near structurally ambiguous regions. Finally, we optimize the network with joint classification and logit margin regularization, routing synthetic proxies into a dedicated rejection slot without imposing geometric margin constraints in the representation space. Extensive experiments on multiple datasets show that HOPE consistently outperforms state-of-the-art models, validating its effectiveness, robustness, and efficiency.

Yumeng Dai, Yue Tan, Yixin Liu +3

Xi’an Jiaotong University, Xi’an, China · Griffith University, Brisbane, Australia

Graph Neural Networks Node Classification Graph Heterophily

Aug 5, 2026cs.SI

IMMENSE: Inductive Multi-perspective User Classification in Social Networks

Online social networks increasingly expose people to users who propagate discriminatory, hateful, and violent content. Young users, in particular, are vulnerable to exposure to such content, which can have harmful psychological and social repercussions. Given the massive scale of today's social networks, in terms of both published content and number of users, there is an urgent need for effective systems to aid Law Enforcement Agencies (LEAs) in identifying and addressing users that disseminate malicious content. In this work we introduce IMMENSE, a machine learning-based method for detecting malicious social network users. Our approach adopts a hybrid classification strategy that integrates three perspectives: the semantics of the users' published content, their social relationships and their spatial information. Such contextual perspectives potentially enhance classification performance beyond text-only analysis. Importantly, IMMENSE employs an inductive learning approach, enabling it to classify previously unseen users or entire new networks without the need for costly and time-consuming model retraining procedures. Experiments carried out on a real-world Twitter/X dataset showed the superiority of IMMENSE against five state of the art competitors, confirming the benefits of its hybrid approach for effective deployment in social network monitoring systems.

Francesco Benedetti, Antonio Pellicani, Gianvito Pio +1

Department of Computer Science, University of Bari, Via Orabona 4, Bari, 70125, Italy · Department of Computer Science, University of Pisa, Largo Bruno Pontecorvo 3, Pisa, 56127, Italy · Data Science Laboratory, National Interuniversity Consortium for Informatics (CINI), Via Volturno 58, Roma, 00185, Italy +1

Social Media Analysis Node Classification

Aug 3, 2026cs.SI

Network Information Enhances Unreliable News Domain Detection

Content-based detection of unreliable news is increasingly difficult, as low-reliability sources mimic credible journalism and generative AI makes fabricated content harder to flag. We ask whether network structure can improve news reliability classification, taking a domain-level approach that shifts the focus from individual articles to source reliability. From URL-sharing patterns in Telegram chats, we build a statistically validated domain co-sharing network and find assortative mixing by reliability: low-reliability domains group together, as do reliable ones. Exploiting this structure, we compare Graph Neural Networks against network-unaware baselines using both content-aware features (multilingual text embeddings) and content-agnostic features (spreading dynamics). GNNs consistently outperform Multi-Layer Perceptrons on identical features, with GraphSAGE best in both settings (accuracy 0.63 with content, 0.53 without), a 13-14% relative gain over the network-unaware baseline. Network topology thus systematically improves domain reliability assessment, and remains effective even when content analysis is infeasible.

Raphaela Keßler, Roman David Ventzke, Viola Priesemann +1

University of Konstanz, Germany · MPI for Dynamics and Self-Organization, Germany · University of Göttingen, Germany +2

Graph Neural Networks Fake News Detection Node Classification

Aug 3, 2026cs.LG

CoRe-GNN: Multilevel Message passing on Coarsened graphs

Training Graph Neural Networks on large graphs is challenged by the memory cost of storing all node representations across layers. We show that several existing scalable approaches can be written as structured modifications of the GNN propagation matrix, providing a unified perspective that exposes their respective limitations. In particular, graph coarsening replaces it by a low-rank approximation that enables spectral guarantees but assigns uniform representations to clustered nodes, while Cluster-GCN restricts the propagation matrix to intra-cluster connections that allow efficient batching but sever long-range information. These are complementary failures of the \emph{same} decomposition of the graph into groups of nodes. To obtain the best of both worlds, we propose \textbf{CoRe-GNN}, which performs both propagations in parallel at each layer: a coarsened inter-cluster term capturing long-range structure, and a local intra-cluster term preserving per-node discriminability. We prove that CoRe-GNN inherits analogous approximation guarantees to those of graph coarsening, and introduce a natural cluster-based \emph{batching scheme} that scales to graphs with millions of nodes. On node classification benchmarks spanning homophilic, heterophilic, large-scale, and long-range graphs, CoRe-GNN outperforms both graph coarsening and Cluster-GCN baselines. Notably, CoRe-GNN reaches competitive accuracy on \emph{long-range} tasks, while remaining memory-efficient through batching.

Antonin Joly, Nicolas Keriven, Aline Roumy

CNRS, IRISA, Rennes, FRANCE · INRIA, Rennes, FRANCE

Graph Neural Networks Graph Coarsening Message Passing Neural Networks Node Classification

Jul 31, 2026cs.AI

Towards Multi-Label Graph Foundation Models: from Single-Vector Representation Learning to Multi-Semantic Basis Learning

Multi-label node classification is an important yet challenging task in graph learning, where nodes exhibit multiple semantics simultaneously. Existing methods for multi-label node classification can effectively model multiple labels, while only considering in-domain scenarios where the model needs to be trained and tested within the same graph domain, resulting in limited cross-domain generalization. Recently, Graph Foundation Models (GFMs) have emerged as a promising paradigm for learning transferable graph representations across diverse graph domains and downstream tasks. However, existing GFMs are built upon single-label assumption, where all nodes are arbitrarily regarded as containing only one class of semantic and embedded into a single representation. For multi-label nodes, such a representation essentially approximates multiple semantics with a single point in the representation space, inevitably leading to semantic entanglement and making simultaneous discrimination of multiple labels difficult. To address these limitations, we propose a Multi-Semantic Basis Graph Foundation Model (MSB-GFM), a framework for cross-domain multi-label node classification. Specifically, we introduce a multi-semantic basis representation learning paradigm that models each multi-label node as an adaptive composition of semantic bases, thereby enabling flexible representational capacity for modeling multiple semantics. Furthermore, we develop a semantic-structure dual-channel architecture with domain adversarial training for effective cross-domain knowledge transfer. Extensive experiments demonstrate the effectiveness of our model.

Dongxiao He, Jiayu Zhang, Jitao Zhao +2

Tianjin University Tianjin, China

Domain-Adversarial Learning Representation Learning Cross-Domain Transfer Learning Graph Foundation Models Node Classification

Jul 30, 2026cs.LG

Same Graph Cross-Task Transfer in GNNs: Protocols and Predictors

Many real-world graphs support multiple predictive tasks over the same underlying structure, creating an opportunity to reuse supervision across node classification (NC) and link prediction (LP). However, existing evaluations often rely on incompatible splits, observed-graph assumptions, and negative sampling rules, making conclusions about same-graph cross-task transfer unreliable. We formalize same-graph NC-LP transfer and propose a leakage-free protocol that fixes node and edge splits, uses a shared message-passing graph that excludes evaluated edges, and employs fixed negatives for LP. Across three backbones (GCN, GraphSAGE, GPS), we find that transfer is strongly directional and predictable: NC

\to

LP is consistently beneficial on homophilic graphs, while LP

\to

NC is fragile and can even degrade accuracy under naive representation reuse. LP

\to

NC becomes reliably positive mainly in a structure-dominant regime where LP is easy but NC is unsaturated, suggesting that LP acts as structural pretraining. Finally, we introduce the CoTask Score (CTS) to summarize joint NC+LP utility when a shared encoder must serve both tasks, and show that simple dataset statistics, especially homophily, can guide mechanism choice and help avoid negative transfer.

Neelam Akula, Surbhi Kumar, Murat Kantarcioglu +1

Department of Mathematical Sciences, University of Texas at Dallas, Richardson, TX, USA · Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA

Graph Neural Networks Link Prediction Transfer Learning Node Classification

Jul 18, 2026math.ST

The Value of Depth in Message Passing on Sparse Graphs: A Kesten-Stigum Dichotomy

How deep does a graph neural network need to be on a sparse graph? We study its purest statistical form: node classification on the sparse contextual stochastic block model (CSBM) with average degree

Δ=O(1)

, whose local weak limit is a broadcast-labelled Poisson Galton-Watson tree. Prior work derived a message-passing classifier

h_\ell

that aggregates from each vertex at distance

k\le\ell

the attenuated evidence

2\operatorname{artanh}(γ^k t(X_v))

, with

γ

the edge signal and

t

a bounded likelihood-ratio transform of the feature. We prove that the value of depth is governed by a single number, the Kesten-Stigum ratio

κ=γ^2Δ

. Below the threshold (

κ<1

), the error sequence is Cauchy at a geometric rate,

|\mathcal{E}(\ell)-\mathcal{E}(\ell')|\le Cκ^{(\ell+1)/3}

for all

\ell'>\ell

, so all layers beyond depth

O(\log(1/ε))

change the error by less than

ε

; conversely, under mild regularity each sufficiently deep layer still flips the decision with probability at least

cκ^{\ell/2}

, the empirically sharp exponent. Above the threshold (

κ>1

), depth is geometrically productive:

\mathcal{E}(\ell)

is driven to a branching-process floor of order at most

1/(κ-1)

at any geometric rate

κ^{-s\ell}

,

s<1

(this bound has content only for

κ>17

). No local classifier of any depth beats the universal floor

e^{-Δ}Φ(-ζ)

set by isolated roots (

ζ

the feature signal-to-noise ratio), while the first layer provably helps by an explicit total-variation amount. Simulations with an exact belief-propagation baseline on the same trees show that the pairwise rule's error curve is mildly non-monotone in

\ell

, so an optimal finite depth exists (an exact instance is certified in the appendix), while BP saturates strictly faster, at an effective per-layer ratio below

κ

that we identify.

Aseem Raj Baranwal

Graph Neural Networks Message Passing Neural Networks Stochastic Block Model Node Classification

Jul 15, 2026cs.LG

NodeImport: Imbalanced Node Classification with Node Importance Assessment

In real-world applications, node classification on graphs often faces the challenge of class imbalance, where majority classes dominate training, resulting in biased model performance. Traditional GNNs often struggle in such scenarios, as they tend to overfit to majority classes while underrepresenting minority classes. Existing solutions, which either prioritize nodes based on class size or synthesize new nodes for minority classes, often fall short of effectively addressing this imbalance issue. This paper introduces an approach to class-imbalanced node classification by utilizing a balanced meta-set for importance measurement, where a training node is considered significant if it enhances model performance under an unbiased setting. Our method identifies important nodes that can counteract class imbalance and utilizes them for model training, allowing for fine-grained and dynamic node selection throughout the training process. We theoretically derive a formula to directly assess node importance, reducing computational overhead and providing an intuitive threshold for node selection. Guided by this metric, we develop a novel framework that filters valuable labeled, unlabeled, and synthetic nodes that enhance model performance in an unbiased context. A key advantage of this framework is its separation of the synthetic node generation process from the filtering process, ensuring compatibility with various node generation methods. Furthermore, we introduce a strategy to construct a high-quality meta-set that closely approximates the overall feature distribution, ensuring robust representation of each class. We evaluate our framework, NodeImport, across multiple datasets using popular GNN architectures, demonstrating its superiority over existing baselines. Our results highlight the flexibility and effectiveness of the framework in mitigating class imbalance, leading to improved outcomes.

Nan Chen, Zemin Liu, Bryan Hooi +3

Johns Hopkins University Baltimore, Maryland, USA · Zhejiang University Hangzhou, Zhejiang, China · National University of Singapore Singapore, Singapore +1

Class-Imbalanced Learning Graph Neural Networks Data Valuation Node Classification

Jul 13, 2026cs.LG

Structure-Feature Aligned Graph Learning via Alternating Constrained Optimization

We introduce a constrained two-view framework for node prediction that aligns structure-conditioned GNN embeddings with a structure-free feature prior learned by an anchor model. Conventional Graph Neural Networks (GNNs) couple feature transformation and neighborhood aggregation, which renders them vulnerable to topology noise and heterophilous connections. To decouple this dependency, our framework utilizes an independent anchor network to capture intrinsic attribute features via a self-supervised reconstruction objective. Furthermore, we propose a Channel-Split Adaptive Gated GNN (CSAG-GNN) that dynamically routes representations between global spectral smoothing and local spatial discrimination through a node-wise gating mechanism. We propose a stable cyclic alternating optimization strategy to solve the resulting coupled bi-level objective, preventing mutual representation drift during training. Empirical results on both homophilous and heterophilous benchmarks show balanced performance gains and structural robustness over competitive baselines.

Chengcheng Yan, Qingsong Wang

College of Artificial Intelligence, Shaoxing Institute of Technology, Shaoxing, 312000, China. · School of Mathematics and Computational Science, Xiangtan University, Xiangtan, 411105, China.

Graph Neural Networks Graph Representation Learning Node Classification

Jul 1, 2026cs.LG

Multi-Label Node Classification with Label Influence Propagation

Graphs are a complex and versatile data structure used across various domains, with possibly multi-label nodes playing a particularly crucial role. Examples include proteins in PPI networks with multiple functions and users in social or e-commerce networks exhibiting diverse interests. Tackling multi-label node classification (MLNC) on graphs has led to the development of various approaches. Some methods leverage graph neural networks (GNNs) to exploit label co-occurrence correlations, while others incorporate label embeddings to capture label proximity. However, these approaches fail to account for the intricate influences between labels in non-Euclidean graph data. To address this issue, we decompose the message passing process in GNNs into two operations: propagation and transformation. We then conduct a comprehensive analysis and quantification of the influence correlations between labels in each operation. Building on these insights, we propose a novel model, Label Influence Propagation (LIP). Specifically, we construct a label influence graph based on the integrated label correlations. Then, we propagate high-order influences through this graph, dynamically adjusting the learning process by amplifying labels with positive contributions and mitigating those with negative influence. Finally, our framework is evaluated on comprehensive benchmark datasets, consistently outperforming SOTA methods across various settings, demonstrating its effectiveness on MLNC tasks.

Yifei Sun, Zemin Liu, Bryan Hooi +4

Zhejiang University · National University of Singapore · Capital One +1

Multi-Label Classification Graph Neural Networks Node Classification

Jun 30, 2026cs.CL

TAG-DLM: Diffusion Language Models for Text-Attributed Graph Learning

Text-attributed graphs (TAGs), where each node carries a natural language description, require models to jointly reason over text and graph topology. Existing approaches often handle the two modalities separately: graph neural networks operate on shallow text features, while hybrids of LLMs and graphs use the language model mainly as a text encoder and delegate structure learning to a separate graph module. We propose method that unifies textual reasoning and graph message passing within a masked diffusion language model, a language model with bidirectional attention and generative decoding. For each graph instance, method linearises a sampled local neighbourhood into a token sequence and injects graph structure through a topology attention mask, which realises message passing over the graph. Because the diffusion language model can both interpret and generate text, the method adapts to different tasks simply by changing the prompt, supporting node classification, link prediction, and cross-dataset transfer with no target-specific fine-tuning. Experiments show that method outperforms graph neural networks, graph transformers, and LLM-based baselines on all three TAG benchmarks across two tasks, improving over the strongest baseline by up to 3.9 points.

Lingjie Chen, Yuanchen Bei, Haobo Xu +3

UIUC · VISA

Masked Diffusion Models Link Prediction LLM Reasoning with Graphs Text-Attributed Graph Learning Diffusion Language Models Node Classification+1

Jun 23, 2026cs.LG

A Fair Evaluation of Graph Foundation Models for Node Property Prediction

Due to the wide use of graph-structured data in different fields of industry and science, the development of Graph Foundation Models (GFMs) has recently attracted a lot of attention. While many different types of models are called GFMs, particular interest has been paid to GFMs designed for node property prediction tasks, which is one of the most popular settings in Graph ML with lots of real-world applications from fraud detection in financial and social networks to recommendation systems for e-commerce and user-generated content platforms. While a number of GFMs for this task have been recently proposed, the field has not converged to a unified evaluation setting, and different works evaluate their models in widely different ways, preventing reliable comparison of GFMs with each other and with other types of models. In this work, we conduct a fair and rigorous reevaluation of 9 recent GFMs for node property prediction, comparing them to strong Graph Neural Network (GNN) baselines. We find that, among these GFMs, only the most recent ones based on the Prior-data Fitted Networks paradigm outperform well-tuned GNNs in predictive performance, although at a higher inference cost.

Oleg Platonov, Gleb Bazhenov, Dmitry Eremeev +1

1HSE University · 2Yandex Research

Graph Neural Networks Graph Foundation Models Prior-Data Fitted Networks Node Classification

Jun 22, 2026cs.LG

A Spectral Theory of Normalized Corrected GNN Propagation

We develop a spectral theory for \emph{normalized corrected GNN propagation}. The object of study is the symmetric normalized adjacency with its degree-stationary component removed, matching the normalization used by standard GCN-style models while isolating the stationary direction most directly tied to oversmoothing. The central theoretical question is whether this corrected normalized operator preserves class-discriminative signal after many propagation layers. Our main result is a high-probability exact-recovery theorem for the binary Contextual Stochastic Block Model after

k=O(\log n)

propagation steps in the dense polylogarithmic regime

p\ge C\log^B n/n

, for any fixed

B>4

, under explicit graph-signal and feature-SNR conditions. We also establish a multi-class partial recovery theorem showing contraction toward class centers for most nodes. Synthetic and real node-classification experiments are included as empirical checks of the theory's predicted dependence on depth, graph signal, and feature noise.

Qihan Chen, Wei Li, Meng Qin +1

Center for Discrete Mathematics, Fuzhou University · School of Computer and Information Science, Fujian Agriculture and Forestry University · Department of Strategic & Advanced Interdisciplinary Research, Pengcheng Laboratory (PCL), Shenzhen, Guangdong, China

Graph Neural Networks Spectral Methods Node Classification

Jun 18, 2026cs.LG

Boundary Embedding Shaping with Adaptive Contrastive Learning for Graph Structural Disentanglement

Graph neural networks (GNNs) excel at aggregating neighbor information for classification, yet their performance is hindered by graph structural entanglement, where spurious correlations from semantically irrelevant neighbors contaminate node embeddings. This challenge is most acute for nodes near class boundaries in the embedding space, where amplified structural noise blurs decision boundaries and destabilizes predictions. Existing robust GNN methods largely treat all nodes uniformly, ignoring boundary vulnerabilities. In this paper, to improve classification performance, we tackle graph structural disentanglement by identifying boundary-region entanglement as the primary bottleneck and propose Boundary Embedding Shaping (BES), an adaptive contrastive learning GNN plug-in module that selectively suppresses spurious structural noise at decision boundaries with minimal model parameter perturbation. Extensive experiments demonstrate that BES consistently improves boundary discrimination and outperforms existing leading methods. Notably, BES boosts GCN performance by an average of 3.3% in node classification (up to 5.0% on WikiCS) and achieves superior accuracy in link prediction.

Jiaqing Chen, Zidu Yin, Yichao Cai +4

School of Information Science and Technology, Yunnan Normal University, Kunming, China · Australian Institute for Machine Learning, Adelaide University, Adelaide, Australia · School of Computer Science and Engineering, The University of New South Wales, Sydney, Australia.

Graph Representation Learning Graph Contrastive Learning Node Classification

Jun 17, 2026cs.LG

SEAGAN: domain-Specific and Edge-Aware Graph Attention Network for Dynamic Plant Processes

Graph neural networks (GNNs) offer a flexible framework for learning from scientific data with physical, biological, or functional associations. One promising domain is plant physiology, where observed responses result from several interacting processes that are difficult to isolate, even with human intervention. A key example is the A-Ci curve, which relates the net CO2 assimilation rate (Anet) to leaf intercellular CO2 concentration (Ci) and is also used to estimate photosynthetic parameters in biophysical models. However, accurate estimation requires accurate identification of the active biochemical limiting state at each curve point, which is a major source of uncertainty. Here, we express the limitation-state identification in A-Ci curves as a graph-based node classification problem. A graph representation of the A-Ci curve is created using distance-based k-nearest-neighbor (kNN) and auxiliary-signal-guided (ASG) connectivity. The methodology was evaluated against the conventional machine learning baselines, graph-based architectures, and an automated fitting-based benchmark. Results on a large synthetic dataset with known ground-truth limitation states show that graph-based models improve classification, especially near biochemical transition areas. The top-performing configuration, SEAGAN (domain-Specific and Edge-Aware Graph Attention Network for Dynamic Plant Processes), integrates process-aware node features, edge attributes, kNN connectivity, and graph attention with a weighted cross-entropy loss, obtaining an F1-score of 0.857 and accuracy of 0.882. The results suggest that using A-Ci curves as graphs enables better identification of the biochemical limiting condition and reduces the uncertainty associated with both human and automated methods.

Antriksh Srivastava, Soumyashree Kar

Center of Studies in Resources Engineering · Indian Institute of Technology Bombay · Mumbai, India 400076

Graph Attention Networks Graph Representation Learning Node Classification

Jun 16, 2026cs.LG

LLM Features Can Hurt GNNs: Concatenation Interference on Homophilous Graph Benchmarks

Adding LLM-generated node features to graph neural networks (GNNs) is widely reported to improve accuracy on standard benchmarks. We document a contrasting observation: when LLM features are introduced through pure input concatenation (rather than joint training, distillation, or prompt-conditioning), they can systematically degrade accuracy on the same homophilous benchmarks where end-to-end LLM pipelines succeed. With an MLP backbone on the Planetoid public split and bag-of-words original features, concatenating SBERT-encoded GPT-4o-mini TAPE features reduces PubMed test accuracy by -17.0 +/- 0.3 pp and Cora by -4.3 +/- 0.6 pp (CiteSeer -0.6 +/- 0.8 pp, within seed noise). The drop attenuates as we relax each condition (GCN / GCNII / GAT backbones, random splits, smaller encoders) and reverses on medium-homophily WikiCS (+4.4 pp) and ogbn-arxiv (+11.7 pp). To predict when concatenation helps versus hurts, we report a simple measure of LLM-alone discriminability, Delta_sig. Across 9 datasets Delta_sig correlates with the concatenation cost more strongly than homophily at point estimate (r^2 = 0.38 vs. 0.06; N=9, bootstrap CIs overlap). The bootstrap-best change-point is tau = 13.8 pp, and the rule "Delta_sig <= tau predicts non-positive concat cost" classifies 7/9 datasets correctly; since 60% of bootstrap samples place tau in [5, 30] pp, we treat Delta_sig as an interpretive lens rather than a precision filter. A dimension-controlled ablation on PubMed places the LLM-feature drop between same-source PCA (-2.3 pp) and same-dim Gaussian noise (-37.3 pp), ruling out dimensionality and weight-decay artifacts. Nine PubMed configurations fit a power law |Delta_concat| proportional to (sqrt(d_l/n))^1.31 with r^2 = 0.97; the low-Delta_sig, small-n corner is exactly where the headline -17 pp PubMed deficit appears.

Zhongyuan Wang, Pratyusha Vemuri

Graph Neural Networks Graph Representation Learning Text-Attributed Graph Learning Node Classification LLMs for Graph Learning

Jun 8, 2026cs.LG

When Design Rules Break: Benchmark Composition Determines Whether Label Informativeness Predicts GNN Aggregator Choice

We examine whether graph neural network (GNN) design rules generalize across benchmark families by studying aggregator selection (sum, mean, max) on 24 node-classification datasets spanning citation, heterophilic, LINKX Facebook-100, co-purchase, and co-authorship graphs. Edge homophily is only weakly predictive of the GIN-Sum versus GIN-Mean performance gap. Label informativeness predicts this gap well on legacy benchmarks but degrades substantially when Facebook-100 graphs are included. In these dense friendship networks, near-zero label informativeness coexists with a strong preference for sum aggregation, producing gains of 7-10% and up to 13% under extended training. Stochastic block model ablations, including degree-corrected variants matching Facebook-100 degree scales, fail to reproduce this behavior, indicating that mean degree alone does not explain the effect. Among several label-independent graph statistics, the spectral gap uniquely distinguishes these graphs from other low-informativeness datasets, with the effect localized to one-hop neighborhoods and replicated across architectures. We further identify training regimes that interact with aggregator choice and show that PNA can underperform the best single-aggregator GIN on standard citation benchmarks. Our results suggest that benchmark composition, rather than numerical insufficiency, determines whether design rules appear to generalize, and that the Facebook-100 regime provides a concrete target for future adaptive aggregation methods.

Neha Sharma, Ritesh Sharma

Department of Computer Science Virginia Commonwealth University · Department of Electrical and Computer Engineering Virginia Commonwealth University

Graph Neural Networks Node Classification

Jun 5, 2026cs.LG

Graph Neural Network leveraging Higher-order Class Label Connectivity for Heterophilous Graphs

Node classification in graph neural networks (GNNs) has been widely applied in various fields of graph analysis. GNNs achieve high-accuracy node classification in homophilous graphs, where nodes with the same class label tend to be connected. However, their performance remains limited in heterophilous graphs, where nodes with different class labels are more likely to be connected. In particular, current GNNs derived from graph convolutional networks cannot capture higher-order class label connectivity, which is frequently observed in real-world heterophilous graphs. To address this issue, we propose a novel classifier, Label Context Classifier (LCC), designed to capture higher-order class label connectivity in directed graphs. LCC estimates the class label of a target node by leveraging label context embeddings that are generated through four distinct types of walks. In addition, our approach allows the integration of LCC and any GNN by adaptively learning their importance. Experimental results demonstrate that GNNs integrated with LCC outperform SOTA methods and the label context embeddings improve the node classification performance in heterophilous directed graphs.

Takuto Takahashi, Itsuki Nakayama, Takahiro Mitani +3

The University of Osaka, 1-5 Yamadaoka, Suita, Osaka, Japan

Graph Neural Networks Node Classification Graph Heterophily

Jun 3, 2026cs.LG

ALINC: Active Learning for Inductive Node Classification via Graph Sampling

Active learning (AL) for node classification typically focuses on selecting the most informative nodes for annotation within one or a few large graphs (e.g., in social network analysis). However, in other domains, such as molecular chemistry or electronic design automation, datasets consist of thousands of independent graphs. In many of these inductive settings, annotating an individual node requires a full-graph analysis, which effectively yields the remaining node labels on-the-fly. Therefore, these scenarios require AL strategies that select entire graphs instead of single nodes, a problem which has not been tackled in the literature so far. Thus, we introduce ALINC, an AL framework for inductive node classification via graph sampling. It bridges the existing methodological gap by elevating node-level utility measures to graph-level selection criteria through various aggregation mechanisms. In an extensive benchmark including ten strategies, three aggregation methods, and four datasets, we identify CoreSet, TypiClust, and BADGE as the top-performing graph sampling strategies. Our detailed analysis further reveals that the choice of the aggregation method is pivotal, as it substantially affects model performance and annotation costs. Finally, we demonstrate the effectiveness of ALINC in two use case studies: site-of-metabolism prediction in molecules and design automation of printed circuit board schematics.

Pascal Plettenberg, Denis Huseljic, André Alcalde +2

Intelligent Embedded Systems, University of Kassel, 34121 Kassel, Germany · CELUS GmbH, 80339 Munich, Germany · GAIN Group, Institute of Data Science, University of Greifswald, 17489 Greifswald, Germany

Active Learning Node Classification

Jun 1, 2026cs.LG

GJDNet: Robust Graph Neural Networks via Joint Disentangled Learning Against Adversarial Attacks

Graph Neural Networks (GNNs) are vulnerable to adversarial attacks, which inherently invert connectivity patterns by introducing disassortative edges in assortative graphs and assortative edges in disassortative graphs. This structural inversion creates structure-feature mismatches that disrupt neighborhood aggregation across different graph types. However, we find that existing defenses are limited, as they either treat neighborhoods as monolithic under fixed assortativity assumptions or rely on standard softmax classifiers that fail to account for perturbation-induced representation shifts. To further exploit this observation, we adopt a robustness perspective that jointly disentangles node representations and decision spaces, isolating perturbation effects while enforcing well-separated decision regions. Based on this principle, we propose Graph Joint Disentanglement Network (GJDNet), a unified framework for robust node classification across diverse graph assortativity regimes. GJDNet enhances robustness at both representation and decision levels: it employs feature-driven soft structural disentanglement with skewness-aware neighbor filtering to suppress perturbation-induced structure-feature mismatches, and introduces a Spherical Decision Boundary (SDB) to promote intra-class compactness and inter-class separation in the embedding space, thereby stabilizing decision boundaries under perturbations. Theoretical analysis provides insights into the effectiveness of the proposed disentangled representation and decision mechanisms, while extensive experiments demonstrate that GJDNet consistently achieves strong robustness across graphs with different connectivity regimes.

Canyixing Cui, Tao Wu, Xingping Xian +3

School of Computer Science and Technology, Chongqing University of Posts and Telecommunications, Chongqing, China · School of Cyber Security and Information Law, Chongqing University of Posts and Telecommunications, Chongqing, China · Computational Communication Research Center, Beijing Normal University, Zhuhai, China +2

Disentangled Representation Learning Graph Neural Networks Adversarial Robustness Node Classification