Leveraging Manifold Embeddings for Enhanced Graph Transformer Representations and Learning

Graph transformers typically embed every node in a single Euclidean space, blurring heterogeneous topologies. We prepend a lightweight Riemannian mixture-of-experts layer that routes each node to various kinds of manifold, mixture of spherical, flat, hyperbolic - best matching its local structure. These projections provide intrinsic geometric explanations to the latent space. Inserted into a state-of-the-art ensemble graph transformer, this projector lifts accuracy by up to 3% on four node-classification benchmarks. The ensemble makes sure that both euclidean and non-euclidean features are captured. Explicit, geometry-aware projection thus sharpens predictive power while making graph representations more interpretable.

ST-GRIT: Spatio-Temporal Graph Transformer For Internal Ice Layer Thickness Prediction

Understanding the thickness and variability of internal ice layers in radar imagery is crucial for monitoring snow accumulation, assessing ice dynamics, and reducing uncertainties in climate models. Radar sensors, capable of penetrating ice, provide detailed radargram images of these internal layers. In this work, we present ST-GRIT, a spatio-temporal graph transformer for ice layer thickness, designed to process these radargrams and capture the spatiotemporal relationships between shallow and deep ice layers. ST-GRIT leverages an inductive geometric graph learning framework to extract local spatial features as feature embeddings and employs a series of temporal and spatial attention blocks separately to model long-range dependencies effectively in both dimensions. Experimental evaluation on radargram data from the Greenland ice sheet demonstrates that ST-GRIT consistently outperforms current state-of-the-art methods and other baseline graph neural networks by achieving lower root mean-squared error. These results highlight the advantages of self-attention mechanisms on graphs over pure graph neural networks, including the ability to handle noise, avoid oversmoothing, and capture long-range dependencies. Moreover, the use of separate spatial and temporal attention blocks allows for distinct and robust learning of spatial relationships and temporal patterns, providing a more comprehensive and effective approach.

GNN-CNN: An Efficient Hybrid Model of Convolutional and Graph Neural Networks for Text Representation

Time, cost, and energy efficiency are critical considerations in Deep-Learning (DL), particularly when processing long texts. Transformers, which represent the current state of the art, exhibit quadratic computational complexity relative to input length, making them inefficient for extended documents. This study introduces a novel model architecture that combines Graph Neural Networks (GNNs) and Convolutional Neural Networks (CNNs), integrated with a real-time, end-to-end graph generation mechanism. The model processes compact batches of character-level inputs without requiring padding or truncation. To enhance performance while maintaining high speed and efficiency, the model incorporates information from Large Language Models (LLMs), such as token embeddings and sentiment polarities, through efficient dictionary lookups. It captures local contextual patterns using CNNs, expands local receptive fields via lattice-based graph structures, and employs small-world graphs to aggregate document-level information. The generated graphs exhibit structural properties indicative of meaningful semantic organization, with an average clustering coefficient of approximately 0.45 and an average shortest path length ranging between 4 and 5. The model is evaluated across multiple text classification tasks, including sentiment analysis and news-categorization, and is compared against state-of-the-art models. Experimental results confirm the proposed model's efficiency and competitive performance.

Platform for Representation and Integration of multimodal Molecular Embeddings

Existing machine learning methods for molecular (e.g., gene) embeddings are restricted to specific tasks or data modalities, limiting their effectiveness within narrow domains. As a result, they fail to capture the full breadth of gene functions and interactions across diverse biological contexts. In this study, we have systematically evaluated knowledge representations of biomolecules across multiple dimensions representing a task-agnostic manner spanning three major data sources, including omics experimental data, literature-derived text data, and knowledge graph-based representations. To distinguish between meaningful biological signals from chance correlations, we devised an adjusted variant of Singular Vector Canonical Correlation Analysis (SVCCA) that quantifies signal redundancy and complementarity across different data modalities and sources. These analyses reveal that existing embeddings capture largely non-overlapping molecular signals, highlighting the value of embedding integration. Building on this insight, we propose Platform for Representation and Integration of multimodal Molecular Embeddings (PRISME), a machine learning based workflow using an autoencoder to integrate these heterogeneous embeddings into a unified multimodal representation. We validated this approach across various benchmark tasks, where PRISME demonstrated consistent performance, and outperformed individual embedding methods in missing value imputations. This new framework supports comprehensive modeling of biomolecules, advancing the development of robust, broadly applicable multimodal embeddings optimized for downstream biomedical machine learning applications.

Few-shot Learning on AMS Circuits and Its Application to Parasitic Capacitance Prediction

Graph representation learning is a powerful method to extract features from graph-structured data, such as analog/mixed-signal (AMS) circuits. However, training deep learning models for AMS designs is severely limited by the scarcity of integrated circuit design data. In this work, we present CircuitGPS, a few-shot learning method for parasitic effect prediction in AMS circuits. The circuit netlist is represented as a heterogeneous graph, with the coupling capacitance modeled as a link. CircuitGPS is pre-trained on link prediction and fine-tuned on edge regression. The proposed method starts with a small-hop sampling technique that converts a link or a node into a subgraph. Then, the subgraph embeddings are learned with a hybrid graph Transformer. Additionally, CircuitGPS integrates a low-cost positional encoding that summarizes the positional and structural information of the sampled subgraph. CircuitGPS improves the accuracy of coupling existence by at least 20\% and reduces the MAE of capacitance estimation by at least 0.067 compared to existing methods. Our method demonstrates strong inherent scalability, enabling direct application to diverse AMS circuit designs through zero-shot learning. Furthermore, the ablation studies provide valuable insights into graph models for representation learning.

GNN-ViTCap: GNN-Enhanced Multiple Instance Learning with Vision Transformers for Whole Slide Image Classification and Captioning

Microscopic assessment of histopathology images is vital for accurate cancer diagnosis and treatment. Whole Slide Image (WSI) classification and captioning have become crucial tasks in computer-aided pathology. However, microscopic WSI face challenges such as redundant patches and unknown patch positions due to subjective pathologist captures. Moreover, generating automatic pathology captions remains a significant challenge. To address these issues, we introduce a novel GNN-ViTCap framework for classification and caption generation from histopathological microscopic images. First, a visual feature extractor generates patch embeddings. Redundant patches are then removed by dynamically clustering these embeddings using deep embedded clustering and selecting representative patches via a scalar dot attention mechanism. We build a graph by connecting each node to its nearest neighbors in the similarity matrix and apply a graph neural network to capture both local and global context. The aggregated image embeddings are projected into the language model's input space through a linear layer and combined with caption tokens to fine-tune a large language model. We validate our method on the BreakHis and PatchGastric datasets. GNN-ViTCap achieves an F1 score of 0.934 and an AUC of 0.963 for classification, along with a BLEU-4 score of 0.811 and a METEOR score of 0.569 for captioning. Experimental results demonstrate that GNN-ViTCap outperforms state of the art approaches, offering a reliable and efficient solution for microscopy based patient diagnosis.

Multilayer GNN for Predictive Maintenance and Clustering in Power Grids

Unplanned power outages cost the US economy over $150 billion annually, partly due to predictive maintenance (PdM) models that overlook spatial, temporal, and causal dependencies in grid failures. This study introduces a multilayer Graph Neural Network (GNN) framework to enhance PdM and enable resilience-based substation clustering. Using seven years of incident data from Oklahoma Gas & Electric (292,830 records across 347 substations), the framework integrates Graph Attention Networks (spatial), Graph Convolutional Networks (temporal), and Graph Isomorphism Networks (causal), fused through attention-weighted embeddings. Our model achieves a 30-day F1-score of 0.8935 +/- 0.0258, outperforming XGBoost and Random Forest by 3.2% and 2.7%, and single-layer GNNs by 10 to 15 percent. Removing the causal layer drops performance to 0.7354 +/- 0.0418. For resilience analysis, HDBSCAN clustering on HierarchicalRiskGNN embeddings identifies eight operational risk groups. The highest-risk cluster (Cluster 5, 44 substations) shows 388.4 incidents/year and 602.6-minute recovery time, while low-risk groups report fewer than 62 incidents/year. ANOVA (p < 0.0001) confirms significant inter-cluster separation. Our clustering outperforms K-Means and Spectral Clustering with a Silhouette Score of 0.626 and Davies-Bouldin index of 0.527. This work supports proactive grid management through improved failure prediction and risk-aware substation clustering.

When Graph Contrastive Learning Backfires: Spectral Vulnerability and Defense in Recommendation

Graph Contrastive Learning (GCL) has demonstrated substantial promise in enhancing the robustness and generalization of recommender systems, particularly by enabling models to leverage large-scale unlabeled data for improved representation learning. However, in this paper, we reveal an unexpected vulnerability: the integration of GCL inadvertently increases the susceptibility of a recommender to targeted promotion attacks. Through both theoretical investigation and empirical validation, we identify the root cause as the spectral smoothing effect induced by contrastive optimization, which disperses item embeddings across the representation space and unintentionally enhances the exposure of target items. Building on this insight, we introduce CLeaR, a bi-level optimization attack method that deliberately amplifies spectral smoothness, enabling a systematic investigation of the susceptibility of GCL-based recommendation models to targeted promotion attacks. Our findings highlight the urgent need for robust countermeasures; in response, we further propose SIM, a spectral irregularity mitigation framework designed to accurately detect and suppress targeted items without compromising model performance. Extensive experiments on multiple benchmark datasets demonstrate that, compared to existing targeted promotion attacks, GCL-based recommendation models exhibit greater susceptibility when evaluated with CLeaR, while SIM effectively mitigates these vulnerabilities.

Transferable Parasitic Estimation via Graph Contrastive Learning and Label Rebalancing in AMS Circuits

Graph representation learning on Analog-Mixed Signal (AMS) circuits is crucial for various downstream tasks, e.g., parasitic estimation. However, the scarcity of design data, the unbalanced distribution of labels, and the inherent diversity of circuit implementations pose significant challenges to learning robust and transferable circuit representations. To address these limitations, we propose CircuitGCL, a novel graph contrastive learning framework that integrates representation scattering and label rebalancing to enhance transferability across heterogeneous circuit graphs. CircuitGCL employs a self-supervised strategy to learn topology-invariant node embeddings through hyperspherical representation scattering, eliminating dependency on large-scale data. Simultaneously, balanced mean squared error (MSE) and softmax cross-entropy (bsmCE) losses are introduced to mitigate label distribution disparities between circuits, enabling robust and transferable parasitic estimation. Evaluated on parasitic capacitance estimation (edge-level task) and ground capacitance classification (node-level task) across TSMC 28nm AMS designs, CircuitGCL outperforms all state-of-the-art (SOTA) methods, with the $R^2$ improvement of $33.64\% \sim 44.20\%$ for edge regression and F1-score gain of $0.9\times \sim 2.1\times$ for node classification. Our code is available at \href{https://anonymous.4open.science/r/CircuitGCL-099B/README.md}{here}.

FuDoBa: Fusing Document and Knowledge Graph-based Representations with Bayesian Optimisation

Building on the success of Large Language Models (LLMs), LLM-based representations have dominated the document representation landscape, achieving great performance on the document embedding benchmarks. However, the high-dimensional, computationally expensive embeddings from LLMs tend to be either too generic or inefficient for domain-specific applications. To address these limitations, we introduce FuDoBa a Bayesian optimisation-based method that integrates LLM-based embeddings with domain-specific structured knowledge, sourced both locally and from external repositories like WikiData. This fusion produces low-dimensional, task-relevant representations while reducing training complexity and yielding interpretable early-fusion weights for enhanced classification performance. We demonstrate the effectiveness of our approach on six datasets in two domains, showing that when paired with robust AutoML-based classifiers, our proposed representation learning approach performs on par with, or surpasses, those produced solely by the proprietary LLM-based embedding baselines.