Graph SSL

SSL: Self-Supervised Learning

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4 papers in the last four weeks, with none the four weeks before. 0.0% of all new papers.

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Latest papers 40

Oct 6, 2026cs.LG

Complementary Supervised and Self-Supervised Representations for Out-of-Distribution Graph Learning

Out-of-distribution (OOD) generalization remains challenging for graph neural networks (GNNs), as graph distributions can vary substantially across time and domains. Supervised and self-supervised graph representation learning are guided by distinct objectives and offer different perspectives on graph representations. In this work, we study whether self-supervised representations (SSL) can provide complementary signals to improve supervised OOD node classification. We develop two backbone-agnostic frameworks that exploit such information at different stages of learning and prediction. Co-Train jointly learns supervised and SSL representations and adaptively integrates them during training, while Dual-Space Retrieval performs non-parametric prediction in the two representation spaces and combines their predictions through confidence-aware fusion at inference time. The supervised and SSL encoders are separately parameterized and need not share the same GNN architecture. We evaluate multiple GNN backbones and two distinct SSL objectives, DGI and GRACE, on four graph benchmarks spanning temporal and cross-domain distribution shifts. Extensive experiments show that Co-Train consistently outperforms strong supervised OOD baselines, while Dual-Space Retrieval achieves competitive performance as a flexible non-parametric alternative. Results across different backbones and SSL objectives, together with representation analyses and ablations, demonstrate that SSL representations provide complementary information to supervised representations and can improve OOD node classification across diverse settings.

Qingying Hao, Zikang Chen, Chuxuan Hu +4

ShanghaiTech University Shanghai, China · University of Illinois Urbana-Champaign Urbana, Illinois, USA · The Pennsylvania State University University Park, Pennsylvania, USA

Graph Neural Networks Graph Representation Learning Graph SSL OOD Generalization

Oct 4, 2026cs.LG

LEON: Location Embeddings from OSM Neighborhoods via Hexagonal Graph Masked Autoencoders

Geographic information systems increasingly rely on sophisticated spatial representation learning techniques to extract meaningful patterns from complex geospatial data. This paper introduces LEON, a novel self-supervised framework that adapts Graph Masked Autoencoders (GraphMAE) for geospatial region representation learning. Our method leverages the inherent spatial structure of geographic data by constructing hexagonal grid graphs using H3 indexing and applying masked autoencoding techniques to learn robust spatial embeddings from OpenStreetMap (OSM) amenity distribution patterns. We evaluate LEON on multiple real-world datasets including EuroSAT satellite imagery classification and various geographic prediction tasks (housing prices, crime prediction, and urban analytics). Experimental results demonstrate that LEON achieves significant improvements in spatial understanding, with up to 1.87% accuracy improvement on EuroSAT classification and consistent performance gains across geographic prediction benchmarks. The learned embeddings exhibit highly structured and distinct properties, making them particularly suitable for downstream spatial analysis tasks. Our findings suggest that self-supervised learning provides an effective paradigm for geospatial region representation learning using widely available crowdsourced data.

Szymon Soltysiak, Radoslaw Malek, Jedrzej Kusnierz +3

Department of Artificial Intelligence, Wroclaw University of Science and Technology, Wroclaw, Poland

Masked Autoencoders Geospatial Representation Learning Graph SSL

Sep 28, 2026cs.LG

Temporal Heterogeneous Graph Pretraining for Relational Deep Learning

Relational deep learning models database rows and foreign-key links as a heterogeneous graph for prediction from record attributes and relational context. These graphs contain two distinct temporal signals: record age changes with the prediction cutoff, while intervals between observed records remain fixed. Prior work often treats time as a single signal or studies temporal representation and pretraining separately. We investigate how explicitly encoding both signals affects temporal pretraining for downstream tasks. Our framework combines Multi-scale Time Encoding, which captures record age using learnable time scales and type-specific projections, with Rotary Time Encoding, which represents signed inter-record intervals through rotary transformations during graph propagation. We pair these encodings with three self-supervised objectives: historical relation recovery, horizon-aware future relation activity prediction, and temporal subgraph contrast. All inputs respect their observation cutoffs. Pretraining proceeds in two stages: subgraph contrast first learns neighborhood representations, followed by refinement through either relation recovery or future activity prediction. We evaluate on five RelBench datasets across 11 classification and regression tasks using heterogeneous GNN and graph Transformer backbones. With both encodings, the best evaluated staged schedules improve over supervised training with the same encodings by 3.02% and 1.06% on the two backbones, respectively, and over controls without pretraining or either encoding by 3.24% and 2.37%.

Yixin Peng, Er Jin, Diego Collarana +1

RWTH Aachen University, Aachen, Germany · Fraunhofer FIT, Sankt Augustin, Germany

Temporal GNNs Heterogeneous GNNs Graph SSL Relational Deep Learning

Sep 15, 2026cond-mat.mtrl-sci

Robust and Efficient AI Frameworks for Scalable Material Design and Property Prediction

This thesis develops robust and efficient AI frameworks for accelerating crystalline materials discovery by addressing both major stages of the materials-design pipeline: crystal property prediction and crystal structure generation. Motivated by the high computational cost of Density Functional Theory (DFT) and the limited availability of labeled materials data, the thesis explores graph representation learning, pretraining, multimodal learning, and generative modeling for scalable materials design. For property prediction, the thesis first introduces CrysXPP, which learns transferable crystal representations through unsupervised graph autoencoding, reducing dependence on large property-labeled datasets. It then proposes CrysGNN, a large-scale self-supervised graph pretraining framework that captures atomic connectivity, chemical attributes, and global structural information and transfers this knowledge to downstream property predictors through knowledge distillation. CrysMMNet further enriches crystal representations by jointly modeling graph structure and textual descriptions, thereby incorporating both local chemical and global structural knowledge. For crystal generation, the thesis introduces TGDMat, a text-guided joint diffusion framework that jointly models lattice parameters, atomic types, and atomic coordinates while incorporating textual structural knowledge during denoising. This enables the generation of more valid and stable periodic materials while also supporting conditional generation from natural-language descriptions. Overall, the thesis establishes a unified AI-based framework for data-efficient property prediction and controllable crystal generation, demonstrating how graph learning, multimodal representations, and generative models can reduce computational cost and improve the scalability of materials

Kishalay Das

Graph SSL Materials Property Prediction Crystal Structure Generation Multimodal Graph Learning Conditional Generative Modeling

Sep 14, 2026cs.LG

Multi-View Molecular Representation Learning with Hierarchical Graphs and Contextualized Fingerprints

Molecular property prediction requires representations that generalize from limited labeled data to structurally novel compounds. Existing molecular pretraining methods often rely on a single view: graph-based approaches model atom-bond topology but provide limited fragment-level supervision, whereas fingerprint descriptors encode chemical patterns but are typically used as fixed auxiliary features. We propose HiFi-Mol, a multi-view framework that separately pretrains a hierarchical graph encoder and a contextualized fingerprint encoder before downstream integration. The graph branch uses fragment-aware masking with multi-resolution supervision to capture substructure-aware representations, while the fingerprint branch tokenizes active entries from seven fingerprint families and applies masked language modeling to learn contextualized embeddings. During fine-tuning, HiFi-Mol combines projected multi-resolution graph features with fingerprint embeddings for downstream prediction. Evaluated on MoleculeNet benchmarks under the scaffold split, HiFi-Mol achieves a 2.77% improvement in average ROC-AUC over the best baseline across eight classification tasks while maintaining competitive performance on three regression tasks. Further analyses reveal that fragment-aware masking improves graph representation quality, and classification results demonstrate dataset-dependent strengths of the individual graph and fingerprint variants, confirming that the two views provide complementary predictive signals.

Gwang-Hyeon Yun, Jong-Hoon Park, Bing Hu +3

Yonsei University · Wonju-si, Republic of Korea · University of Waterloo +1

Graph SSL Hierarchical Representation Learning Multi-View Learning Molecular Property Prediction Molecular Representation Learning

Aug 5, 2026cs.LG

NodeJEPA: Structure-Conditioned Latent Prediction for Node-Level Graph Self-Supervised Learning

Self-supervised learning on graphs is largely shaped by contrastive methods that depend on carefully designed augmentations, and by generative methods that reconstruct node attributes in the input space. Both paradigms can entangle representations with low-level input statistics rather than with relational structure. Joint-embedding predictive architectures (JEPA) instead learn by predicting latent targets rather than reconstructing inputs. Recent work has explored this idea for graph-level representation learning, but how to design JEPA-style objectives for node-level tasks, and which structural signals the predictor should condition on, remains less clear. We present NodeJEPA, a joint-embedding predictive architecture for node-level graph self-supervised learning. NodeJEPA masks structure-aware k-hop ego-subgraphs and trains a context encoder to predict the latent representations of the masked nodes. These targets come from an EMA-updated target encoder with stop-gradient. A structure-conditioned predictor integrates spectral and centrality descriptors through cross-attention. Variance, covariance, and Laplacian spectral regularizers help stabilize the embedding geometry, and an optional curriculum gradually increases masking difficulty during training. Because prediction occurs in latent space, NodeJEPA does not rely on input reconstruction or hand-crafted graph augmentations. We evaluate NodeJEPA on standard node classification benchmarks under linear probing and fine-tuning protocols, and conduct ablations on masking, prediction, and regularization design choices. Our study offers a practical recipe for node-level JEPA-style latent prediction on graphs, and clarifies when structural conditioning helps representation learning. Code, configurations, and evaluation scripts are publicly available at https://github.com/OliverZ-dot/Node-Jepa.

Tinghe Zhang, Jian Xu, Jiaheng Chen +3

1Northeastern University

Graph Representation Learning Graph SSL Joint-Embedding Predictive Architecture Predictive Representation Learning

Aug 1, 2026cs.LG

HP-JEPA: Hierarchical Partitioning for Multi-Resolution Graph Joint-Embedding Predictive Learning

Graph self-supervised learning aims to learn transferable representations from large-scale unlabeled graph data. Joint-embedding predictive architectures (JEPAs) avoid explicit negative-pair construction and raw-input reconstruction by predicting masked targets directly in latent space. However, existing graph JEPAs typically rely on a single predefined graph partition, biasing the learned representations toward one structural granularity and limiting their ability to capture complementary patterns at different graph scales. To address this limitation, we propose HP-JEPA, a hierarchical partitioning framework for multi-resolution graph joint-embedding prediction. HP-JEPA organizes each graph into an ordered bank of coarse-to-fine partition resolutions and performs context-target latent prediction separately at each resolution using an online encoder, an exponential-moving-average target encoder, and a latent predictor. The resulting resolution-specific graph representations are subsequently integrated through concatenation or task-specific resolution weighting, allowing downstream models to combine complementary local, regional, and global structural information. Experiments on seven graph classification benchmarks and one graph regression benchmark show that HP-JEPA outperforms the fixed-resolution Graph-JEPA baseline on 6 of 8 tasks, improving upon Graph-JEPA on most evaluated benchmarks. Size-stratified analyses further show that HP-JEPA achieves higher accuracy than Graph-JEPA in most evaluated graph-size quartiles on three representative datasets. These results highlight the effectiveness of hierarchical multi-resolution partitioning for transferable graph representation learning.

Ruichen Xu, Jingxiang Qu, Wenhan Gao +5

Department of Applied Mathematics and Statistics Stony Brook University Stony Brook, NY, USA · Department of Computer Science Stony Brook University Stony Brook, NY, USA · TikTok Bellevue, WA, USA +2

Graph Representation Learning Graph SSL Joint-Embedding Predictive Architecture Hierarchical Representation Learning Graph Classification

Jul 28, 2026cs.LG

CondPSE: A Polynomial-Filtered Structural Encoder with Conditional Modulation for Graphs

Message-passing graph neural networks are bounded by the 1-WL test and can miss topological structure that distinguishes non-isomorphic graphs. Positional and structural encodings (PSE) inject such topology-derived signals, and learned PSE encoders such as GPSE pretrain a single encoder to produce these signals from random node probes, which can then be frozen and reused as inputs across downstream graph models. We present CondPSE, a learned PSE encoder that applies a learnable polynomial graph filter bank to standard Gaussian node probes and refines the resulting structural-response branches through FiLM-style modulation conditioned on cross-filter, local message-passing, and graph-level signals. CondPSE is pretrained to reconstruct node-level positional/structural targets and graph-level invariants, and is then frozen for use as a downstream input encoding. On synthetic structural-discrimination benchmarks, CondPSE separates graph structures that 1-WL-bounded message passing cannot: it raises CSL accuracy from 42.9% to 97.3% and EXP accuracy from 68.3% to 99.9% relative to GPSE, and ablations show that the polynomial filter bank accounts for most of this gain. On real molecular property prediction, the picture is more limited. With a hybrid local-message-passing/global-attention backbone, CondPSE performs comparably to GPSE without surpassing it, and a ZINC backbone sweep shows no consistent ordering between the two encoders. We report these results and discuss why strong synthetic structural discrimination does not, on its own, yield a downstream advantage for frozen learned PSE encoders, including the role of downstream integration and possible mismatch between structural pretraining targets and molecular property labels.

Woohyun Lee, Hogun Park

Sungkyunkwan University Suwon, Republic of Korea

Graph Representation Learning Graph SSL GNN Expressivity

Jul 27, 2026cs.LG

Unsupervised Graph Representation Learning with Complementary View Alignment

Unsupervised graph representation learning aims to derive meaningful node embeddings by capturing both structural and attribute information without relying on labeled data. Existing methods, such as GAEs, have demonstrated effectiveness but typically rely on message-passing mechanisms that assume homophily, leading to performance degradation on heterophilous graphs, where connected nodes exhibit dissimilar features. This homophily bias results in the loss of critical high-frequency components that are essential for identifying heterophilous patterns. To address these challenges, we propose \textsc{AlignGAE}, a novel extension of \textit{MaskGAE} that preserves the full frequency spectrum through complementary view alignment. Our framework introduces a dual-encoder architecture that separately processes structural and attribute information, incorporates node positional encoding to approximate Neighborhood Identity Distribution (NID), and employs dual reconstruction tasks for both edges and node attributes. We further propose theoretically grounded NID alignment strategies that ensure semantic consistency across views while preserving their distinct characteristics. Through comprehensive spectral analysis, we demonstrate that \textsc{AlignGAE} achieves optimal representation properties when the alignment loss converges. Extensive experiments across 12 benchmark datasets validate our approach, showing that \textsc{AlignGAE} outperforms state-of-the-art methods by up to 18.7% on heterophilous graphs in node classification, while maintaining competitive performance on homophilous graphs. Our results establish a new paradigm for frequency-aware graph representation learning.

Zengyi Wo, Shiyu Zhang, Qiyao Peng +2

Nanjing University, Nanjing, China · Tianjin University, Tianjin, China

Graph Neural Networks Graph Representation Learning Graph SSL

Jul 27, 2026cs.LG

MEGA-CL: A Molecular Foundation Model for Generalizable ADMET Prediction through Graph External Attention and Contrastive Learning

Predicting the absorption, distribution, metabolism, excretion and toxicity (ADMET) properties of small molecules remains a major challenge in drug discovery. Here, we present MEGA-CL, a foundation graph neural network framework for universal molecular ADMET prediction. MEGA-CL integrates self-supervised contrastive learning with a multi-head external attention mechanism and an enhanced message-passing architecture, enabling simultaneous modeling of local chemical substructures and global inter-graph relationships while mitigating over-smoothing effects commonly observed in deep graph networks. Across 13 benchmark datasets and 21 downstream ADMET tasks, MEGA-CL consistently outperforms state-of-the-art baseline models. In particular, the framework demonstrates robust performance on challenging regression tasks, including clearance (CL) and steady-state volume of distribution (VDss), while maintaining strong generalization ability in independent external validation. Clinically relevant predictive accuracy was achieved, with more than 75% of predictions falling within a 3-fold error range. In an external evaluation on 18 novel compounds derived from recently approved FDA drugs, over 50% of human liver microsome clearance (HLMC) predictions were within a 2-fold error range. To further assess its practical applicability, MEGA-CL was prospectively evaluated on three preclinical drug candidates using in vitro hepatic microsomal metabolism assays and CYP450 inhibition assays guided by model predictions. The predicted HLMC values for all candidates were within 2.5-fold of the experimentally measured values, and 73.3% of CYP450 inhibition endpoints (11/15) were correctly classified. These results demonstrate the potential of MEGA-CL as a generalizable framework for accelerating in silico ADMET evaluation and early-stage drug candidate optimization.

Tinghui Jin, Kedu Jin, Ying Li +8

School of Science, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China · 2Sir Run Run Hospital, Nanjing Medical University, Nanjing, China · 3Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing, China

Graph SSL Graph Foundation Models Molecular Property Prediction

Jul 22, 2026cs.CV

Masked Topology Modeling for Self-Supervised Learning on Parametric CAD

Computer aided design (CAD) is ubiquitous: virtually any modern object was designed using editable CAD tools. However, with the shortage of available CAD datasets in its native editable and parametric format, boundary representation (B-Rep), it is ever more important to develop data-efficient methods for this domain. We present a new self-supervised pretraining task, Masked Topology Modeling (MTM), that leverages the face-adjacency graph, an induced structure unique to B-reps that the encoder can be asked to reconstruct. MTM masks a fraction of edges and trains a small head to predict each masked edge's convexity and curve type from the encoder's post-message-passing face features. We combine MTM with a MoCo-style momentum-queue contrastive learning over B-rep-aware augmentations, a BFS-connected face-region masked-reconstruction objective, and pretraining on the ABC dataset and our new procedurally generated dataset to show strong performance on a number of benchmarks.

Heinrich Jiang, Jennifer Jang

StoryGold AI

Graph SSL Parametric CAD Modeling Topological Representation Learning

Jul 20, 2026cs.LG

Scalable and Efficient Joint Spiking Embedding Predictive Architecture for Large-Scale Dynamic Graphs

Dynamic graph learning aims to capture evolving structural and semantic patterns in real-world systems, such as fraud detection and recommender systems. Due to the scarcity of labeled data in real-world dynamic graphs, recent studies have introduced generative or contrastive paradigms (e.g., masked graph autoencoders or graph contrastive learning) to generate task-agnostic graph embeddings. However, these methods typically rely on complex edge-level reconstruction objectives and tailored graph augmentation strategies. This incurs substantial computational overhead when scaling to large-scale dynamic graphs. In this paper, we propose SG-JEPA, a joint spiking embedding predictive architecture for large-scale dynamic graphs. In contrast to existing self-supervised methods, SG-JEPA partitions nodes into context and target sets along the temporal dimension to learn embeddings that are predictive of each other via additional spatial-temporal information. Furthermore, through encoding sequential inputs into coarse-to-fine spike count embeddings, spiking neurons enable SG-JEPA to adapt to the varying computational constraints of downstream tasks. Extensive experiments demonstrate that SG-JEPA achieves competitive or even superior performance over discriminative baselines on node classification, while effectively scaling to the dynamic graph with 13 million edges. SG-JEPA avoids the complex machinery (negative sampling, graph augmentations, edge-level reconstruction, etc.), resulting in superior training efficiency and memory scalability compared with prior self-supervised dynamic graph baselines.

Huizhe Zhang, Yuchang Zhu, Huazhen Zhong +2

Sun Yat-sen University Guangzhou, China · Sun Yat-sen University Zhuhai, China

Temporal GNNs Graph SSL Joint-Embedding Predictive Architecture Dynamic Graph Learning

Jul 19, 2026cs.LG

Node4All: Learning Node Representation Beyond Datasets

Node representation learning has advanced rapidly, yet most existing methods rely on per-dataset training and hyperparameter tuning. This dataset-specific optimization comes from the difficulty of designing reusable graph models that generalize across diverse graph datasets. In this work, we introduce Node4All, a node representation learner applicable to arbitrary graph datasets without any dataset-specific optimization. Node4All is built on two complementary ideas. At the architectural level, we introduce the Channel Graph Transformer (CGT), which enables a single fixed parameterization to process arbitrary graph datasets. At the learning level, we propose a self-supervised learning based on a series of synthetic graphs. Together, these components enable generalization beyond individual datasets, which is infeasible with existing architectures and learning frameworks. We extensively evaluate Node4All on node classification across 25 benchmarks against 21 baselines, covering both supervised and self-supervised methods. Despite all baselines being trained and optimized for each dataset, a single Node4All, applied uniformly across the datasets, achieves a competitive ranking of 5th among 21 baselines. Moreover, Node4All supports one-shot and in-context learning with an appropriate predictor and outperforms recent graph foundation models (GFMs) in these settings. These results demonstrate that Node4All not only achieves reusability across arbitrary graph datasets, but also remains an effective solution in practice. Code and model checkpoints are available in https://github.com/dooho00/node4all.

Dooho Lee, Jaemin Yoo

KAIST · Daejeon, Republic of Korea · Seoul National University +1

Graph Representation Learning Graph SSL Domain Generalization Graph Foundation Models Graph Transformer

Jul 19, 2026cs.LG

ChemHyperMag: Physics-informed magnetic hypergraph learning improves molecular ADMET prediction

Accurate prediction of ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) is important for drug discovery. Most predictors use undirected molecular graphs and pairwise edges. This choice misses asymmetric interactions, nonreversible dynamics, and motif level effects from functional groups and ring systems. We propose ChemHyperMag for multitask ADMET prediction under missing labels. ChemHyperMag builds a functional group hypergraph from rings, BRICS fragments, Bemis-Murcko scaffolds, and bonds. It also defines a potential driven nonreversible flow guided by electronegativity and Gasteiger partial charges. The resulting circulation is encoded by a Hermitian magnetic Laplacian and processed with a magnetic Chebyshev encoder. We perturb magnetic phases to form stochastic views and train with an InfoNCE objective. Experiments on multiple ADMET benchmarks show improvements over recent methods with fewer labeled samples and no conformers. ChemHyperMag is scalable and provides interpretable directional signals through its magnetic phases.

Hexiao Ding, Hongzhao Chen, Jing Lan +12

Department of Health Technology and Informatics, Hong Kong Polytechnic University, Hong Kong SAR, China · University of Liverpool, Liverpool, United Kingdom · Shanghai Jiao Tong University, Shanghai, China +1

Graph SSL Physics-Informed ML Molecular Property Prediction Hypergraph Learning

Jul 15, 2026cs.LG

LATTICE: Graph Self-Supervised Learning for Multimodal Spatial Omics Integration

Spatially resolved omics studies increasingly combine transcriptomic and epigenomic assays, yet downstream analysis is often still performed using single-modality pipelines. We present LATTICE (Latent Alignment of Tissue-level and Transcriptomic Information for Cross-modal Embedding), a graph-based self-supervised framework that learns spot-level representations from harmonized multimodal features. LATTICE integrates five aligned modality blocks per Visium spot: Visium RNA, scMultiome RNA, scMultiome ATAC, spatial ATAC, and spatial CUT&Tag. These modalities capture spatial transcriptomic measurements, single-cell inferred regulatory activity, and in situ chromatin and histone states within a unified lattice representation. LATTICE constructs a spatial neighborhood graph and trains a TransformerConv encoder using masked reconstruction, cross-modal alignment, and spatial smoothness objectives. On a private 11-sample melanoma cohort from an anonymized clinical collaborator comprising 54{,}912 total spots, LATTICE demonstrated stable optimization behavior, reproducible embeddings across analysis seeds, and complete multimodal integration across all samples. Adding scMultiome RNA to Visium RNA alone substantially improved concordance with Space Ranger clusters across 11 runs (adjusted Rand index [ARI] +0.157, normalized mutual information [NMI] +0.143, and spatial contiguity +0.174). Additional modalities further improved spatial contiguity and multimodal utility score (MUS), although they sometimes reduced agreement with RNA-derived reference labels, likely because the learned embeddings captured chromatin and regulatory structure beyond transcriptomic similarity alone. These results position LATTICE as a practical and empirically grounded framework for multimodal spatial omics integration, while also highlighting the need for stronger supervision and broader external benchmarking.

Jagan Mohan Reddy Dwarampudi, Veena Kochat, Suresh Satpati +2

University of Houston · MD Anderson Cancer Center

Spatial Transcriptomics Graph SSL Cross-Modal Alignment Multimodal Embedding Genomics

Jul 7, 2026cs.LG

Canopy: A Heterograph Foundation Model for Metabolic Engineering

Designing microbial strains that produce high-value chemicals at commercially viable titers remains a central challenge in metabolic engineering. Existing computational approaches either rely on stoichiometric constraint-based models that cannot learn from experimental data, or apply tabular machine learning to hand-crafted features that discard the relational structure of biological knowledge. We present Canopy, a heterogeneous graph foundation model that integrates ten public and proprietary data sources into a unified knowledge graph (KG) of 6.9M nodes across 13 types and 34 edge types, covering genes, proteins, metabolites, reactions, pathways, strains, and fermentation experiments. Node features are encoded through domain-specific foundation models (ESM-2 for protein sequences, MoLFormer for chemical SMILES, and PubMedBERT for biomedical text), yielding a multi-modal representation within a single graph. We pretrain a Heterogeneous Graph Transformer (HGT) augmented with SignNet positional encodings, Jumping Knowledge aggregation, and virtual nodes using four self-supervised objectives (link prediction, masked node modelling, distance prediction, and contrastive experiment clustering), balanced via learned homoscedastic uncertainty weighting. On the downstream task of fermentation titer prediction, frozen Canopy embeddings achieve

R^{2} = 0.41

with a lightweight probe, outperforming tabular baselines (best

R^{2} = 0.24

) and homogeneous GNN variants.

Jake Bowden, Laurence Legon, Satnam Surae

Twig Bio, London, United Kingdom

Heterogeneous GNNs Graph SSL Graph Foundation Models Multimodal Graph Learning Biomedical KGs

Jul 3, 2026cs.LG

MABLE: Masked Autoencoding with Bi-Lipschitz Decoding for Embeddings and Graph Metric Learning

We propose MABLE (Masked Autoencoding with Bi-Lipschitz Decoding for Embeddings and Graph Metric Learning), a self-supervised framework for learning node and graph embeddings from large, heterogeneous graphs, demonstrated here on geospatial mineral-exploration data. MABLE combines masked reconstruction with fixed cosine-similarity losses that align matched augmented views while keeping unpaired embeddings well spread. A bi-Lipschitz feature decoder ties a low-dimensional reconstruction component of each node embedding to feature similarity, while matched-node consistency shapes the remaining context used by graph pooling. Lipschitz-controlled pooling helps stabilize graph-level representations under perturbations of retained node embeddings, while augmentation alignment trains robustness to masking, node dropping, and sampling variation. Across local copper and regional Arabian Shield studies, MABLE embeddings provide complementary downstream signal and produce coherent embedding-derived layers for hypothesis generation without learned discriminators or hard-negative selection.

Yaniv Shulman, Shaghayegh Akbarpour, Jack B. Muir

Fleet Space Technologies, Adelaide, Australia · Research School of Earth Sciences, Australian National University, Acton, Australia

Masked Autoencoders Graph Representation Learning Geospatial Representation Learning Graph SSL Metric Learning

Jul 1, 2026cs.LG

SAOT: Self-Supervised Continual Graph Learning with Structure-Aware Optimal Transport

Self-supervised Continual Graph Learning (CGL) aims to successively learn from a graph sequence with different tasks without label supervision - a paradigm that has attracted widespread attention. Most existing self-supervised CGL methods rely on instance-level consistency objectives that enforce stability of individual node (or node-pair) embeddings. Due to optimizing nodes in isolation, these methods fail to maintain global relational structure, causing inter-node correspondences to progressively distort under continual learning. To this end, we propose a novel Structure-Aware Optimal Transport (SAOT) framework that explicitly captures and preserves relational structure within graph representations across sequential tasks. Specifically, SAOT leverages optimal transport theory to capture global inter-node correspondences, thereby facilitating and enhancing graph representation learning. Simultaneously, SAOT incorporates a cross-task knowledge distillation mechanism to preserve the previous structural knowledge. Extensive experiments on four CGL benchmark datasets demonstrate that SAOT outperforms existing self-supervised baselines. In particular, SAOT achieves significant performance gains, improving average accuracy by up to 5% on CoraFull-CL and over 15% on Products-CL compared with state-of-the-art methods in the Class-IL setting.

Yuting Zhang, Yanbei Liu, Zhitao Xiao +3

School of Electronics and Information Engineering, Tiangong University, Tianjin, China · School of Life Sciences, Tiangong University, Tianjin, China · School of Electrical and Infomation Engineering, Tianjin University, Tianjin, China +1

Graph Representation Learning Graph SSL

Jun 30, 2026cs.IR

AGE: Adaptive-masking for Graph Embedding in Graph Retrieval-Augmented Generation

GraphRAG is an extension of retrieval-augmented generation (RAG) that supports large language models (LLMs) by referring to graph-structured data as external knowledge. While this technique ideally captures intricate relationships, it often struggles with graph representations for LLMs, particularly for frozen LLMs, due to the misalignment between graph-based and text-based latent features. We tackle this issue by introducing the {\it Adaptive-masking for Graph Embedding (AGE)}. AGE employs a Transformer in a mask-based self-supervised learning (SSL) approach. We designed the architecture similar to text embedding encoders, addressing the latent feature misalignment. In contrast to natural language texts, graphs are concise representations, and there exist {\it key nodes} that hold dominant contextual information, which are challenging to predict from their surroundings. Masking such key nodes leads to inefficiency in the SSL process. Therefore, AGE focuses on predicting nodes apart from key nodes, utilizing a learnable node sampler. Our experimental results indicate that AGE significantly improves approaches using non-parametric search component in GraphQA tasks, achieving superior accuracy across four benchmark datasets with distinct characteristics.

Bao Long Nguyen Huu, Atsushi Hashimoto

OMRON Corporation · OMRON SINIC X Corporation

Graph Representation Learning Graph SSL Graph Retrieval-Augmented Generation Knowledge Graph Question Answering Graph Embedding

Jun 29, 2026cs.LG

GLIP: Graph and LLM Joint Pretraining for Graph-Level Tasks

Graphs are widely used to model relational systems, with applications in domains such as social networks, finance, and biomedicine. Graph neural networks (GNNs) have become a mainstream approach for learning graph representations. With the rise of large language models (LLMs), recent studies have attempted to combine GNNs with LLMs. However, most existing works concentrate on node-level and edge-level tasks, while graph-level tasks, which require capturing more complex structural and feature information, remain relatively underexplored. Moreover, graph pretraining is a widely adopted strategy to alleviate the challenge of label scarcity. Most existing approaches are designed solely for GNNs such as GraphCL, leaving LLMs uninvolved in the process. To address these limitations, we propose GLIP, a Graph-LLM JoInt Pretraining framework for graph-level tasks. GLIP first performs graph augmentation to construct positive and negative pairs and introduces a multi-token selection strategy to identify patches informative in both structure and features. It further leverages a diffusion-based projector to enrich them with contextual information, enabling GLIP to capture signals from both global and local perspectives. Finally, GLIP employs a joint objective that integrates the LLM's semantic judgments with a contrastive alignment loss, ensuring consistent supervision at both the semantic and structural levels. After pretraining, GLIP is fine-tuned with limited labeled data for downstream tasks, and extensive experiments show that it outperforms state-of-the-art methods on graph-level classification and reasoning tasks. Our source code is publicly available at https://anonymous.4open.science/r/GLIP.

Haoxin Sun, Yiqing Lin, Yajun Huang +3

Fudan University Shanghai, China · ByteDance Shanghai, China

Language Model Pretraining Graph SSL Graph Classification Graph Reasoning

Jun 29, 2026cs.CV

Progressive Self-Supervised Learning with Individualized Community Assignment for Brain Network Analysis

Brain networks exhibit a modular community structure that varies across individuals and neurological conditions. However, existing self-supervised learning (SSL) methods often overlook this heterogeneity, relying on generic masking strategies that fail to capture subject-specific functional organization. We propose BrainPICM, a self-supervised framework for brain network analysis via progressive individualized community aware masking. BrainPICM formulates ROI-to-community mapping as a progressive unbalanced optimal transport process, yielding soft assignments and per-ROI confidence scores. Guided by these confidence estimates, a curriculum-style masking strategy gradually incorporates low-confidence, potentially pathological regions into training, enabling the model to learn both stable modular structures and individual variations. Additionally, a deviation-aware aggregation module quantifies functional reorganization by measuring mass redistribution relative to a population template, enhancing interpretability and downstream prediction. Experiments on three fMRI datasets (ABIDE-I, ADHD-200, ADNI) show that BrainPICM consistently outperforms state-of-the-art supervised and SSL methods in diagnostic accuracy, indicating that explicitly injecting modular community structure into masked modeling yields more functionally consistent and generalizable representations. The source code for this approach will be released at https://github.com/Hrychen7/BrainPICM.

Hairui Chen, Yanwu Yang, Jianfeng Cao +3

Harbin Institute of Technology at Shenzhen, Shenzhen, China · Peng Cheng Laboratory, Shenzhen, China · University of Tübingen, Tübingen, Germany +1

Self-Supervised Learning Graph SSL Graph Clustering Neuroimaging Brain Network Analysis

Jun 27, 2026cs.LG

Towards Improved Anomaly Detection for Cloud Cybersecurity via Graph Neural Networks

Detecting security threats in an organization's cloud computing environment has become necessary due to the increased reliance on cloud infrastructure. Logging of all cloud computing events enables investigation into any incidents after they are detected. Automated detection of threats using the logs based on heuristics or anomaly detection could result in a high false positive rate due to its relatively static nature. In this article, we present an industrial case study of a self-supervised learning method using graph neural networks applied to AWS CloudTrail logs to surface suspicious events for analyst review. The model produces an anomaly score for each event and dynamically adapts to changes in the organization without requiring periodic retraining. Based on our experiments across five organizations, the proposed model produced substantially fewer alerts than a domain expert rule-based baseline in almost all cases, reducing alert volumes to approximately 1 per hour from thousands generated by traditional methods. We note that this evaluation covers only flagged events, and false negatives cannot be estimated from the current data; findings should therefore be interpreted as a practical deployment study offering insights into real-world constraints rather than a fully validated detection system. We discuss these limitations and the requirements for extending the approach to other cloud environments as future work.

Manu Nandan, TJ Jaymes, Michael Brautbar +1

CrowdStrike, Inc., USA · Univ. of Maryland, Baltimore County, USA

Graph SSL Cybersecurity Anomaly Detection

Jun 26, 2026cs.LG

Beyond Sparse Supervision: Diffusion-Guided Learning for Few-Shot Graph Fraud Detection

Graph-based fraud detection is essential for safeguarding large-scale transaction systems, where undetected anomalies may lead to substantial financial losses and security risks. Real-world fraud graphs pose two coupled challenges: sparse and imbalanced supervision, where verified fraudulent labels are scarce and heavily skewed toward benign accounts, and representation dilution, where spatial message passing may oversmooth camouflaged anomalies while spectral filters may suppress fraud-relevant mid- and high-frequency irregularities. To address these challenges, we propose ADC-GNN, short for Attention-guided Diffusion-Contrastive Graph Neural Network, a unified framework that combines diffusion-guided feature augmentation, contrastive representation learning, and multi-hop spectral attention for few-shot graph fraud detection. The diffusion component is formulated as a feature-space denoising augmentation mechanism rather than a full topology-generative graph diffusion model: it constructs noise-perturbed node-feature views under a cosine schedule and uses contrastive learning to stabilize node representations across perturbations. The spectral attention module further adaptively emphasizes fraud-relevant hop-level and relation-level cues. We evaluate ADC-GNN primarily on three public benchmarks and additionally report a proprietary real-world telecom transaction dataset with approximately 60,000 records as a private case study. Under the 1% training setting, ADC-GNN achieves consistent improvements over original graph fraud baselines and four protocol-consistent recent graph anomaly/fraud baselines on the public benchmarks. Additional analyses on split stability, training ratios, oversampling alternatives, module-level ablations, diffusion schedules, and runtime and memory-consumption comparisons further characterize the effective operating regime of ADC-GNN.

Liming Liu, Chao Hu, Mingfei Lu +3

Central South University, Changsha, China · University of Technology Sydney, Australian Artificial Intelligence Institute, Sydney, Australia

Graph Neural Networks Graph SSL Financial Fraud Detection Few-Shot Learning Spectral Graph Convolution Anomaly Detection

Jun 26, 2026cs.LG

scKDGM: KAN-guided Dynamic Graph Masked Learning for Single-Cell RNA-seq Clustering

Single-cell RNA sequencing (scRNA-seq) clustering is essential for identifying cell types, but high dimensionality, sparsity, dropout, and technical noise hinder robust expression representation and cell graph construction. Existing masked autoencoders mainly use expression recovery for feature reconstruction, while graph clustering methods usually depend on fixed KNN graphs and do not feed recovered expression back into graph optimization. We propose scKDGM, a KAN-guided dynamic graph masked learning framework for scRNA-seq clustering. scKDGM uses graph-aware distribution preserving gene masking (GDP-Mask) to perturb cell identity, a KAN-based TAKGCN encoder to learn masked-view representations, mask-guided expression recovery to construct a dynamic graph, and cross-view contrastive learning to transfer recovery signals into topology updates. A ZINB loss models overdispersion and zero inflation. Experiments on 12 real scRNA-seq datasets show that scKDGM outperforms 10 baselines in average NMI and ARI.

Jun Tang, Pengwei Hu, Sicong Gao +3

College of Computer and Information Science, Southwest University, Chongqing, China · Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi, China

Graph SSL Clustering Dynamic Graph Learning Graph Clustering Single-Cell RNA Sequencing

Jun 17, 2026cs.LG

scGTN: Deep Siamese Graph Transformer Network for Single-cell RNA Sequencing Clustering

Single-cell RNA sequencing (scRNA-seq) serves a pivotal role in characterizing gene expression at the cellular level, enabling the identification of cell types and advancing the understanding of cellular heterogeneity. Despite the significant progress in scRNA-seq data clustering, we argue that current methods always ignore the sparsity and noise, as well as the complex intercellular structural information inherent in scRNA-seq data. Toward this end, in this paper, we propose a novel single-cell RNA-seq clustering framework via deep Siamese Graph Transformer Network (termed scGTN), which explicitly integrates gene expression profile and intercellular structural dependencies for cell clustering. In particular, we formulate scRNA-seq data as a graph and construct two augmented graph views that serve as dual views to capture complementary intercellular information. Then, a Siamese graph transformer network is employed to explicitly incorporate shortest-path information and node-wise distances for capturing richer structural relationships between cells. Finally, we employ an optimal transport strategy to guide the cell clustering in a self-supervised manner. Extensive experiments on multiple benchmark scRNA-seq datasets demonstrate that our scGTN consistently outperforms existing methods. Our code is available at https://github.com/W-RMSL/scGTN.

Jinke Wu, Yifan Wang, Siyu Yi +5

Sichuan University · University of International Business and Economics · Great Bay University +1

Graph SSL Clustering Graph Clustering Graph Transformer Single-Cell RNA Sequencing

Jun 15, 2026cs.CR

Timestamp-Aware Spatio-Temporal Graph Contrastive Learning for Network Intrusion Detection

Given their effectiveness in modeling the relational structure among network traffic flows, graph neural networks (GNNs) have been widely adopted in network intrusion detection systems (NIDSs). However, most existing GNN-based NIDS approaches focus on the relational structure of traffic flows, and treat them as temporally independent, which limits their ability to cope with evolving attack behaviors. Moreover, their reliance on supervised or semi-supervised learning often restricts generalization to unseen attacks. To address these limitations, we propose a novel self-supervised GNN-based framework. To the best of our knowledge, the proposed model is among the first self-supervised GNN-based NIDS models to explicitly leverage real timestamps, which provides faithful temporal dependencies for representation learning. We first construct a series of temporal graphs from network traffic flows according to their timestamps, and then employ an E-GraphSAGE and LSTM based encoder to fully extract temporal information and spatial dependencies of network traffic, without introducing time-costly attention mechanisms. A multi-view graph contrastive learning (GCL) scheme is introduced, where temporal, spatial, and feature contrasts are jointly performed to capture temporal continuity, preserve structural consistency, and improve the generalization and robustness of the learned representations, respectively. In addition, a gradient-norm-based adaptive weighting strategy is designed to optimize the contrastive loss weights. Experimental results on four representative NIDS datasets with real timestamps demonstrate that our method significantly outperforms existing self-supervised approaches and achieves performance comparable to the supervised state-of-the-art GNN method, while maintaining high computational efficiency.

Jianli Dai, Guangwei Wu, Jiacheng Li +3

Central South University of Forestry and Technology, School of Computer Science and Mathematics, Changsha, 410004, Hunan, P.R. China · Central South University, School of Computer Science and Engineering, Changsha, 410083, Hunan, P.R. China

Temporal GNNs Graph SSL Network Intrusion Detection Graph Contrastive Learning Spatiotemporal GNNs

Jun 9, 2026cs.LG

Revisiting Positive Samples in Graph Contrastive Learning: From the Perspective of Message Passing

Graph Contrastive Learning (GCL), which trains graph encoders by maximizing similarity between positive samples and minimizing it between negative ones, has emerged as a mainstream graph pre-training paradigm. It is widely recognized that positive samples are essential in GCLs. Ideally, maximizing the similarity of positive samples enables graph encoders to capture intrinsic semantic and patterns of graph data. However, we discover an interesting phenomenon: GCLs can achieve competitive performance even without positive samples. This motivates us to revisit the fundamental mechanism of positive samples in GCLs. From the perspective of Dirichlet energy, we theoretically finds that message passing, a key mechanism in graph encoders, trivializes the maximization of positive samples, preventing GCLs from effectively learning from positive samples. To address this, we propose SPGCL to mitigate the trivialization caused by message passing and restore the learning efficacy of positive samples. Specifically, we find that high Dirichlet energy features help positive samples provide effective learning signals while low Dirichlet energy features contribute little to positive learning signal but is useful for positive sampling. Based on this, SPGCL propagates only high Dirichlet energy features and uses low energy features to construct a probability matrix for reliable positive sampling. Extensive experiments demonstrate the effectiveness of SPGCL.

Lianze Shan, Ningchong Wang, Jitao Zhao +2

School of Computer Science and Technology, Tianjin University, Tianjin, China · School of Future Technology, Tianjin University, Tianjin, China.

Graph SSL Message Passing Neural Networks Graph Contrastive Learning

Jun 2, 2026q-bio.MN

BRIDGE: Biological Evidence Refinement and Heterogeneous Dynamic Gating for Gene Regulatory Networks

Motivation: Gene regulatory network inference from single-cell RNA sequencing (scRNA-seq) data is important for uncovering cell-state-specific transcriptional programs. However, scRNA-seq measurements are sparse and noisy, and experimentally validated TF-target interactions remain limited, making reliable inference challenging. Although graph neural networks have advanced GRN prediction, existing methods often rely on biologically unconstrained graph augmentation, such as random edge perturbation, and insufficiently control information transfer between genes and cells. These limitations may distort regulatory structures and weaken robustness under noisy and weakly supervised settings. Results: To address these issues, we propose an innovative framework named Biological Evidence Refinement and Heterogeneous Dynamic Gating for Gene Regulatory Networks (BRIDGE). BRIDGE extracts gene and cell representations from the expression matrix and its matrix dual, and performs contrastive learning in the gene space and cell space between self and neighbors across the co-expression-refined regulatory view and the original graph. It then applies heterogeneous gated encoding to adaptively regulate information transfer between genes and cells, enabling robust transcription factor-to-target gene prediction. Experiments on benchmark datasets spanning three network types and seven cell types show that BRIDGE achieves state-of-the-art AUROC and AUPRC in most settings. In particular, on Specific networks, BRIDGE improves average AUPRC by 5% over the second-best baseline, GCLink. In cross-cell-type few-shot transfer, BRIDGE consistently outperforms GCLink and GENELink across all six target cell types. A case study on hESC further supports the biological relevance of the predictions, with 9 of the top 10 and 46 of the top 100 novel TF-target interactions validated by ChIPBase.

Ziyang Dong, Shanwen Tan, Hengchuang Yin +5

College of Computer Science, Sichuan University, Chengdu, 610065, China · Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi, 830011, China · School of Mathematics, Sichuan University, Chengdu, 610065, China +2

Heterogeneous GNNs Graph SSL Gene Regulatory Network Inference Single-Cell RNA Sequencing

May 27, 2026cs.CL

GraphLit: Learning Text-Enriched Dynamic Character Network Representations for Literary Study

Methods to represent literary texts as graphs or sequences of graphs mainly focus on representing character interactions, and often overlook another crucial aspect: the textual context in which characters interact. We introduce Dynamic Heterogeneous Character Networks (DHCNs), which organize long novels into temporally localized heterogeneous graphs that align characters with their textual contexts. We extract around 20,000 DHCNs from Project Gutenberg, and propose GraphLit, a self-supervised learning framework that learns rich literary representations through a masked graph autoencoder objective. Across a wide range of 12 character-related tasks, GraphLit improves over text-only, graph-only and prior hybrid baselines. Ablations over different kinds of dynamic graph structures and architectural elements show that grounding characters in their context is the main performance driver, while explicitly encoding narrative order and character relationships provide task-dependent improvements. Finally, we demonstrate the applicability of DHCNs and GraphLit for literary analysis by studying the link between narrative non-linearity and dynamic social features.

Gaspard Michel, Elena V. Epure, Romain Hennequin +2

Deezer Research, Paris, France · IDIAP, Martigny, Switzerland · Loria, Nancy, France +1

Computational Literary Studies Heterogeneous GNNs Graph SSL Text-Attributed Graph Learning Dynamic Graph Learning

May 26, 2026cs.LG

Learning Dynamic Graph Representations through Timespan View Contrasts

The rich information underlying graphs has inspired further investigation of unsupervised graph representation. Existing studies mainly depend on node features and topological properties within static graphs to create self-supervised signals, neglecting the temporal components carried by real-world graph data, such as timestamps of edges. To overcome this limitation, this paper explores how to model temporal evolution on dynamic graphs elegantly. Specifically, we introduce a new inductive bias, namely temporal translation invariance, which illustrates the tendency of the identical node to keep similar labels across different timespans. Based on this assumption, we develop a dynamic graph representation framework CLDG that encourages the node to maintain locally consistent temporal translation invariance through contrastive learning on different timespans. Except for standard CLDG which only considers explicit topological links, our further proposed CLDG++ additionally employs graph diffusion to uncover global contextual correlations between nodes, and designs a multi-scale contrastive learning objective composed of local-local, local-global, and global-global contrasts to enhance representation capabilities. Interestingly, by measuring the consistency between different timespans to shape anomaly indicators, CLDG and CLDG++ are seamlessly integrated with the task of spotting anomalies on dynamic graphs, which has broad applications in many high-impact domains, such as finance, cybersecurity, and healthcare. Experiments demonstrate that CLDG and CLDG++ both exhibit desirable performance in downstream tasks including node classification and dynamic graph anomaly detection. Moreover, CLDG significantly reduces time and space complexity by implicitly exploiting temporal cues instead of complicated sequence models.

Yiming Xu, Zhen Peng, Bin Shi +2

School of Computer Science and Technology, Xi’an Jiaotong University, P.R. China · School of Distance Education, Xi’an Jiaotong University, P.R. China

Graph SSL Dynamic Graph Learning Graph Contrastive Learning Anomaly Detection