Beyond Node Attention: Multi-Scale Harmonic Encoding for Feature-Wise Graph Message Passing

Conventional Graph Neural Networks (GNNs) aggregate neighbor embeddings as holistic vectors, lacking the ability to identify fine-grained, direction-specific feature relevance. We propose MSH-GNN (Multi-Scale Harmonic Graph Neural Network), a novel architecture that performs feature-wise adaptive message passing through node-specific harmonic projections. For each node, MSH-GNN dynamically projects neighbor features onto frequency-sensitive directions determined by the target node's own representation. These projections are further modulated using learnable sinusoidal encodings at multiple frequencies, enabling the model to capture both smooth and oscillatory structural patterns across scales. A frequency-aware attention pooling mechanism is introduced to emphasize spectrally and structurally salient nodes during readout. Theoretically, we prove that MSH-GNN approximates shift-invariant kernels and matches the expressive power of the 1-Weisfeiler-Lehman (1-WL) test. Empirically, MSH-GNN consistently outperforms state-of-the-art models on a wide range of graph and node classification tasks. Furthermore, in challenging classification settings involving joint variations in graph topology and spectral frequency, MSH-GNN excels at capturing structural asymmetries and high-frequency modulations, enabling more accurate graph discrimination.

Partition-wise Graph Filtering: A Unified Perspective Through the Lens of Graph Coarsening

Filtering-based graph neural networks (GNNs) constitute a distinct class of GNNs that employ graph filters to handle graph-structured data, achieving notable success in various graph-related tasks. Conventional methods adopt a graph-wise filtering paradigm, imposing a uniform filter across all nodes, yet recent findings suggest that this rigid paradigm struggles with heterophilic graphs. To overcome this, recent works have introduced node-wise filtering, which assigns distinct filters to individual nodes, offering enhanced adaptability. However, a fundamental gap remains: a comprehensive framework unifying these two strategies is still absent, limiting theoretical insights into the filtering paradigms. Moreover, through the lens of Contextual Stochastic Block Model, we reveal that a synthesis of graph-wise and node-wise filtering provides a sufficient solution for classification on graphs exhibiting both homophily and heterophily, suggesting the risk of excessive parameterization and potential overfitting with node-wise filtering. To address the limitations, this paper introduces Coarsening-guided Partition-wise Filtering (CPF). CPF innovates by performing filtering on node partitions. The method begins with structure-aware partition-wise filtering, which filters node partitions obtained via graph coarsening algorithms, and then performs feature-aware partition-wise filtering, refining node embeddings via filtering on clusters produced by $k$-means clustering over features. In-depth analysis is conducted for each phase of CPF, showing its superiority over other paradigms. Finally, benchmark node classification experiments, along with a real-world graph anomaly detection application, validate CPF's efficacy and practical utility.

LOBSTUR: A Local Bootstrap Framework for Tuning Unsupervised Representations in Graph Neural Networks

Graph Neural Networks (GNNs) are increasingly used in conjunction with unsupervised learning techniques to learn powerful node representations, but their deployment is hindered by their high sensitivity to hyperparameter tuning and the absence of established methodologies for selecting the optimal models. To address these challenges, we propose LOBSTUR-GNN ({\bf Lo}cal {\bf B}oot{\bf s}trap for {\bf T}uning {\bf U}nsupervised {\bf R}epresentations in GNNs) i), a novel framework designed to adapt bootstrapping techniques for unsupervised graph representation learning. LOBSTUR-GNN tackles two main challenges: (a) adapting the bootstrap edge and feature resampling process to account for local graph dependencies in creating alternative versions of the same graph, and (b) establishing robust metrics for evaluating learned representations without ground-truth labels. Using locally bootstrapped resampling and leveraging Canonical Correlation Analysis (CCA) to assess embedding consistency, LOBSTUR provides a principled approach for hyperparameter tuning in unsupervised GNNs. We validate the effectiveness and efficiency of our proposed method through extensive experiments on established academic datasets, showing an 65.9\% improvement in the classification accuracy compared to an uninformed selection of hyperparameters. Finally, we deploy our framework on a real-world application, thereby demonstrating its validity and practical utility in various settings. \footnote{The code is available at \href{https://github.com/sowonjeong/lobstur-graph-bootstrap}{github.com/sowonjeong/lobstur-graph-bootstrap}.}

scSiameseClu: A Siamese Clustering Framework for Interpreting single-cell RNA Sequencing Data

Single-cell RNA sequencing (scRNA-seq) reveals cell heterogeneity, with cell clustering playing a key role in identifying cell types and marker genes. Recent advances, especially graph neural networks (GNNs)-based methods, have significantly improved clustering performance. However, the analysis of scRNA-seq data remains challenging due to noise, sparsity, and high dimensionality. Compounding these challenges, GNNs often suffer from over-smoothing, limiting their ability to capture complex biological information. In response, we propose scSiameseClu, a novel Siamese Clustering framework for interpreting single-cell RNA-seq data, comprising of 3 key steps: (1) Dual Augmentation Module, which applies biologically informed perturbations to the gene expression matrix and cell graph relationships to enhance representation robustness; (2) Siamese Fusion Module, which combines cross-correlation refinement and adaptive information fusion to capture complex cellular relationships while mitigating over-smoothing; and (3) Optimal Transport Clustering, which utilizes Sinkhorn distance to efficiently align cluster assignments with predefined proportions while maintaining balance. Comprehensive evaluations on seven real-world datasets demonstrate that~\methodname~outperforms state-of-the-art methods in single-cell clustering, cell type annotation, and cell type classification, providing a powerful tool for scRNA-seq data interpretation.

Pave Your Own Path: Graph Gradual Domain Adaptation on Fused Gromov-Wasserstein Geodesics

Graph neural networks, despite their impressive performance, are highly vulnerable to distribution shifts on graphs. Existing graph domain adaptation (graph DA) methods often implicitly assume a \textit{mild} shift between source and target graphs, limiting their applicability to real-world scenarios with \textit{large} shifts. Gradual domain adaptation (GDA) has emerged as a promising approach for addressing large shifts by gradually adapting the source model to the target domain via a path of unlabeled intermediate domains. Existing GDA methods exclusively focus on independent and identically distributed (IID) data with a predefined path, leaving their extension to \textit{non-IID graphs without a given path} an open challenge. To bridge this gap, we present Gadget, the first GDA framework for non-IID graph data. First (\textit{theoretical foundation}), the Fused Gromov-Wasserstein (FGW) distance is adopted as the domain discrepancy for non-IID graphs, based on which, we derive an error bound revealing that the target domain error is proportional to the length of the path. Second (\textit{optimal path}), guided by the error bound, we identify the FGW geodesic as the optimal path, which can be efficiently generated by our proposed algorithm. The generated path can be seamlessly integrated with existing graph DA methods to handle large shifts on graphs, improving state-of-the-art graph DA methods by up to 6.8\% in node classification accuracy on real-world datasets.

SpecSphere: Dual-Pass Spectral-Spatial Graph Neural Networks with Certified Robustness

We introduce SpecSphere, the first dual-pass spectral-spatial GNN that certifies every prediction against both $\ell\_{0}$ edge flips and $\ell\_{\infty}$ feature perturbations, adapts to the full homophily-heterophily spectrum, and surpasses the expressive power of 1-Weisfeiler-Lehman while retaining linear-time complexity. Our model couples a Chebyshev-polynomial spectral branch with an attention-gated spatial branch and fuses their representations through a lightweight MLP trained in a cooperative-adversarial min-max game. We further establish (i) a uniform Chebyshev approximation theorem, (ii) minimax-optimal risk across the homophily-heterophily spectrum, (iii) closed-form robustness certificates, and (iv) universal approximation strictly beyond 1-WL. SpecSphere achieves state-of-the-art node-classification accuracy and delivers tighter certified robustness guarantees on real-world benchmarks. These results demonstrate that high expressivity, heterophily adaptation, and provable robustness can coexist within a single, scalable architecture.

Few-Shot Learning of Visual Compositional Concepts through Probabilistic Schema Induction

The ability to learn new visual concepts from limited examples is a hallmark of human cognition. While traditional category learning models represent each example as an unstructured feature vector, compositional concept learning is thought to depend on (1) structured representations of examples (e.g., directed graphs consisting of objects and their relations) and (2) the identification of shared relational structure across examples through analogical mapping. Here, we introduce Probabilistic Schema Induction (PSI), a prototype model that employs deep learning to perform analogical mapping over structured representations of only a handful of examples, forming a compositional concept called a schema. In doing so, PSI relies on a novel conception of similarity that weighs object-level similarity and relational similarity, as well as a mechanism for amplifying relations relevant to classification, analogous to selective attention parameters in traditional models. We show that PSI produces human-like learning performance and outperforms two controls: a prototype model that uses unstructured feature vectors extracted from a deep learning model, and a variant of PSI with weaker structured representations. Notably, we find that PSI's human-like performance is driven by an adaptive strategy that increases relational similarity over object-level similarity and upweights the contribution of relations that distinguish classes. These findings suggest that structured representations and analogical mapping are critical to modeling rapid human-like learning of compositional visual concepts, and demonstrate how deep learning can be leveraged to create psychological models.

Representation Learning with Mutual Influence of Modalities for Node Classification in Multi-Modal Heterogeneous Networks

Nowadays, numerous online platforms can be described as multi-modal heterogeneous networks (MMHNs), such as Douban's movie networks and Amazon's product review networks. Accurately categorizing nodes within these networks is crucial for analyzing the corresponding entities, which requires effective representation learning on nodes. However, existing multi-modal fusion methods often adopt either early fusion strategies which may lose the unique characteristics of individual modalities, or late fusion approaches overlooking the cross-modal guidance in GNN-based information propagation. In this paper, we propose a novel model for node classification in MMHNs, named Heterogeneous Graph Neural Network with Inter-Modal Attention (HGNN-IMA). It learns node representations by capturing the mutual influence of multiple modalities during the information propagation process, within the framework of heterogeneous graph transformer. Specifically, a nested inter-modal attention mechanism is integrated into the inter-node attention to achieve adaptive multi-modal fusion, and modality alignment is also taken into account to encourage the propagation among nodes with consistent similarities across all modalities. Moreover, an attention loss is augmented to mitigate the impact of missing modalities. Extensive experiments validate the superiority of the model in the node classification task, providing an innovative view to handle multi-modal data, especially when accompanied with network structures.

DPQ-HD: Post-Training Compression for Ultra-Low Power Hyperdimensional Computing

Hyperdimensional Computing (HDC) is emerging as a promising approach for edge AI, offering a balance between accuracy and efficiency. However, current HDC-based applications often rely on high-precision models and/or encoding matrices to achieve competitive performance, which imposes significant computational and memory demands, especially for ultra-low power devices. While recent efforts use techniques like precision reduction and pruning to increase the efficiency, most require retraining to maintain performance, making them expensive and impractical. To address this issue, we propose a novel Post Training Compression algorithm, Decomposition-Pruning-Quantization (DPQ-HD), which aims at compressing the end-to-end HDC system, achieving near floating point performance without the need of retraining. DPQ-HD reduces computational and memory overhead by uniquely combining the above three compression techniques and efficiently adapts to hardware constraints. Additionally, we introduce an energy-efficient inference approach that progressively evaluates similarity scores such as cosine similarity and performs early exit to reduce the computation, accelerating prediction inference while maintaining accuracy. We demonstrate that DPQ-HD achieves up to 20-100x reduction in memory for image and graph classification tasks with only a 1-2% drop in accuracy compared to uncompressed workloads. Lastly, we show that DPQ-HD outperforms the existing post-training compression methods and performs better or at par with retraining-based state-of-the-art techniques, requiring significantly less overall optimization time (up to 100x) and faster inference (up to 56x) on a microcontroller

Graffe: Graph Representation Learning via Diffusion Probabilistic Models

Diffusion probabilistic models (DPMs), widely recognized for their potential to generate high-quality samples, tend to go unnoticed in representation learning. While recent progress has highlighted their potential for capturing visual semantics, adapting DPMs to graph representation learning remains in its infancy. In this paper, we introduce Graffe, a self-supervised diffusion model proposed for graph representation learning. It features a graph encoder that distills a source graph into a compact representation, which, in turn, serves as the condition to guide the denoising process of the diffusion decoder. To evaluate the effectiveness of our model, we first explore the theoretical foundations of applying diffusion models to representation learning, proving that the denoising objective implicitly maximizes the conditional mutual information between data and its representation. Specifically, we prove that the negative logarithm of the denoising score matching loss is a tractable lower bound for the conditional mutual information. Empirically, we conduct a series of case studies to validate our theoretical insights. In addition, Graffe delivers competitive results under the linear probing setting on node and graph classification tasks, achieving state-of-the-art performance on 9 of the 11 real-world datasets. These findings indicate that powerful generative models, especially diffusion models, serve as an effective tool for graph representation learning.