Accurately predicting adsorption properties in nanoporous materials using Deep Learning models remains a challenging task. This challenge becomes even more pronounced when attempting to generalize to structures that were not part of the training data.. In this work, we introduce SymGNN, a graph neural network architecture that leverages material symmetries to improve adsorption property prediction. By incorporating symmetry operations into the message-passing mechanism, our model enhances parameter sharing across different zeolite topologies, leading to improved generalization. We evaluate SymGNN on both interpolation and generalization tasks, demonstrating that it successfully captures key adsorption trends, including the influence of both the framework and aluminium distribution on CO$_2$ adsorption. Furthermore, we apply our model to the characterization of experimental adsorption isotherms, using a genetic algorithm to infer likely aluminium distributions. Our results highlight the effectiveness of machine learning models trained on simulations for studying real materials and suggest promising directions for fine-tuning with experimental data and generative approaches for the inverse design of multifunctional nanomaterials.
The increasing penetration of renewable energy sources introduces significant variability and uncertainty in modern power systems, making accurate state prediction critical for reliable grid operation. Conventional forecasting methods often neglect the power grid's inherent topology, limiting their ability to capture complex spatio temporal dependencies. This paper proposes a topology aware Graph Neural Network (GNN) framework for predicting power system states under high renewable integration. We construct a graph based representation of the power network, modeling buses and transmission lines as nodes and edges, and introduce a specialized GNN architecture that integrates GraphSAGE convolutions with Gated Recurrent Units (GRUs) to model both spatial and temporal correlations in system dynamics. The model is trained and evaluated on the NREL 118 test system using realistic, time synchronous renewable generation profiles. Our results show that the proposed GNN outperforms baseline approaches including fully connected neural networks, linear regression, and rolling mean models, achieving substantial improvements in predictive accuracy. The GNN achieves average RMSEs of 0.13 to 0.17 across all predicted variables and demonstrates consistent performance across spatial locations and operational conditions. These results highlight the potential of topology aware learning for scalable and robust power system forecasting in future grids with high renewable penetration.
Existing foundation models, such as CLIP, aim to learn a unified embedding space for multimodal data, enabling a wide range of downstream web-based applications like search, recommendation, and content classification. However, these models often overlook the inherent graph structures in multimodal datasets, where entities and their relationships are crucial. Multimodal graphs (MMGs) represent such graphs where each node is associated with features from different modalities, while the edges capture the relationships between these entities. On the other hand, existing graph foundation models primarily focus on text-attributed graphs (TAGs) and are not designed to handle the complexities of MMGs. To address these limitations, we propose UniGraph2, a novel cross-domain graph foundation model that enables general representation learning on MMGs, providing a unified embedding space. UniGraph2 employs modality-specific encoders alongside a graph neural network (GNN) to learn a unified low-dimensional embedding space that captures both the multimodal information and the underlying graph structure. We propose a new cross-domain multi-graph pre-training algorithm at scale to ensure effective transfer learning across diverse graph domains and modalities. Additionally, we adopt a Mixture of Experts (MoE) component to align features from different domains and modalities, ensuring coherent and robust embeddings that unify the information across modalities. Extensive experiments on a variety of multimodal graph tasks demonstrate that UniGraph2 significantly outperforms state-of-the-art models in tasks such as representation learning, transfer learning, and multimodal generative tasks, offering a scalable and flexible solution for learning on MMGs.
Financial institutions are required by regulation to report suspicious financial transactions related to money laundering. Therefore, they need to constantly monitor vast amounts of incoming and outgoing transactions. A particular challenge in detecting money laundering is that money launderers continuously adapt their tactics to evade detection. Hence, detection methods need constant fine-tuning. Traditional machine learning models suffer from catastrophic forgetting when fine-tuning the model on new data, thereby limiting their effectiveness in dynamic environments. Continual learning methods may address this issue and enhance current anti-money laundering (AML) practices, by allowing models to incorporate new information while retaining prior knowledge. Research on continual graph learning for AML, however, is still scarce. In this review, we critically evaluate state-of-the-art continual graph learning approaches for AML applications. We categorise methods into replay-based, regularization-based, and architecture-based strategies within the graph neural network (GNN) framework, and we provide in-depth experimental evaluations on both synthetic and real-world AML data sets that showcase the effect of the different hyperparameters. Our analysis demonstrates that continual learning improves model adaptability and robustness in the face of extreme class imbalances and evolving fraud patterns. Finally, we outline key challenges and propose directions for future research.
Event cameras asynchronously output low-latency event streams, promising for state estimation in high-speed motion and challenging lighting conditions. As opposed to frame-based cameras, the motion-dependent nature of event cameras presents persistent challenges in achieving robust event feature detection and matching. In recent years, learning-based approaches have demonstrated superior robustness over traditional handcrafted methods in feature detection and matching, particularly under aggressive motion and HDR scenarios. In this paper, we propose SuperEIO, a novel framework that leverages the learning-based event-only detection and IMU measurements to achieve event-inertial odometry. Our event-only feature detection employs a convolutional neural network under continuous event streams. Moreover, our system adopts the graph neural network to achieve event descriptor matching for loop closure. The proposed system utilizes TensorRT to accelerate the inference speed of deep networks, which ensures low-latency processing and robust real-time operation on resource-limited platforms. Besides, we evaluate our method extensively on multiple public datasets, demonstrating its superior accuracy and robustness compared to other state-of-the-art event-based methods. We have also open-sourced our pipeline to facilitate research in the field: https://github.com/arclab-hku/SuperEIO.
High hospital readmission rates are associated with significant costs and health risks for patients. Therefore, it is critical to develop predictive models that can support clinicians to determine whether or not a patient will return to the hospital in a relatively short period of time (e.g, 30-days). Nowadays, it is possible to collect both structured (electronic health records - EHR) and unstructured information (clinical notes) about a patient hospital event, all potentially containing relevant information for a predictive model. However, their integration is challenging. In this work we explore the combination of clinical notes and EHRs to predict 30-day hospital readmissions. We address the representation of the various types of information available in the EHR data, as well as exploring LLMs to characterize the clinical notes. We collect both information sources as the nodes of a graph neural network (GNN). Our model achieves an AUROC of 0.72 and a balanced accuracy of 66.7\%, highlighting the importance of combining the multimodal information.
This work proposes a Graph Neural Network (GNN) modeling approach to predict the resulting surface from a particle based fabrication process. The latter consists of spray-based printing of cementitious plaster on a wall and is facilitated with the use of a robotic arm. The predictions are computed using the robotic arm trajectory features, such as position, velocity and direction, as well as the printing process parameters. The proposed approach, based on a particle representation of the wall domain and the end effector, allows for the adoption of a graph-based solution. The GNN model consists of an encoder-processor-decoder architecture and is trained using data from laboratory tests, while the hyperparameters are optimized by means of a Bayesian scheme. The aim of this model is to act as a simulator of the printing process, and ultimately used for the generation of the robotic arm trajectory and the optimization of the printing parameters, towards the materialization of an autonomous plastering process. The performance of the proposed model is assessed in terms of the prediction error against unseen ground truth data, which shows its generality in varied scenarios, as well as in comparison with the performance of an existing benchmark model. The results demonstrate a significant improvement over the benchmark model, with notably better performance and enhanced error scaling across prediction steps.
Graph neural networks, recently introduced into the field of fluid flow surrogate modeling, have been successfully applied to model the temporal evolution of various fluid flow systems. Existing applications, however, are mostly restricted to cases where the domain is time-invariant. The present work extends the application of graph neural network-based modeling to fluid flow around structures rotating with respect to a certain axis. Specifically, we propose to apply a graph neural network-based surrogate modeling for fluid flow with the mesh corotating with the structure. Unlike conventional data-driven approaches that rely on structured Cartesian meshes, our framework operates on unstructured co-rotating meshes, enforcing rotation equivariance of the learned model by leveraging co-rotating polar (2D) and cylindrical (3D) coordinate systems. To model the pressure for systems without Dirichlet pressure boundaries, we propose a novel local directed pressure difference formulation that is invariant to the reference pressure point and value. For flow systems with large mesh sizes, we introduce a scheme to train the network in single or distributed graphics processing units by accumulating the backpropagated gradients from partitions of the mesh. The effectiveness of our proposed framework is examined on two test cases: (i) fluid flow in a 2D rotating mixer, and (ii) the flow past a 3D rotating cube. Our results show that the model achieves stable and accurate rollouts for over 2000 time steps in periodic regimes while capturing accurate short-term dynamics in chaotic flow regimes. In addition, the drag and lift force predictions closely match the CFD calculations, highlighting the potential of the framework for modeling both periodic and chaotic fluid flow around rotating structures.
Existing methods for graph out-of-distribution (OOD) detection typically depend on training graph neural network (GNN) classifiers using a substantial amount of labeled in-distribution (ID) data. However, acquiring high-quality labeled nodes in text-attributed graphs (TAGs) is challenging and costly due to their complex textual and structural characteristics. Large language models (LLMs), known for their powerful zero-shot capabilities in textual tasks, show promise but struggle to naturally capture the critical structural information inherent to TAGs, limiting their direct effectiveness. To address these challenges, we propose LLM-GOOD, a general framework that effectively combines the strengths of LLMs and GNNs to enhance data efficiency in graph OOD detection. Specifically, we first leverage LLMs' strong zero-shot capabilities to filter out likely OOD nodes, significantly reducing the human annotation burden. To minimize the usage and cost of the LLM, we employ it only to annotate a small subset of unlabeled nodes. We then train a lightweight GNN filter using these noisy labels, enabling efficient predictions of ID status for all other unlabeled nodes by leveraging both textual and structural information. After obtaining node embeddings from the GNN filter, we can apply informativeness-based methods to select the most valuable nodes for precise human annotation. Finally, we train the target ID classifier using these accurately annotated ID nodes. Extensive experiments on four real-world TAG datasets demonstrate that LLM-GOOD significantly reduces human annotation costs and outperforms state-of-the-art baselines in terms of both ID classification accuracy and OOD detection performance.
Entity alignment aims to use pre-aligned seed pairs to find other equivalent entities from different knowledge graphs (KGs) and is widely used in graph fusion-related fields. However, as the scale of KGs increases, manually annotating pre-aligned seed pairs becomes difficult. Existing research utilizes entity embeddings obtained by aggregating single structural information to identify potential seed pairs, thus reducing the reliance on pre-aligned seed pairs. However, due to the structural heterogeneity of KGs, the quality of potential seed pairs obtained using only a single structural information is not ideal. In addition, although existing research improves the quality of potential seed pairs through semi-supervised iteration, they underestimate the impact of embedding distortion produced by noisy seed pairs on the alignment effect. In order to solve the above problems, we propose a seed expanded-aware graph neural network with iterative optimization for semi-supervised entity alignment, named SE-GNN. First, we utilize the semantic attributes and structural features of entities, combined with a conditional filtering mechanism, to obtain high-quality initial potential seed pairs. Next, we designed a local and global awareness mechanism. It introduces initial potential seed pairs and combines local and global information to obtain a more comprehensive entity embedding representation, which alleviates the impact of KGs structural heterogeneity and lays the foundation for the optimization of initial potential seed pairs. Then, we designed the threshold nearest neighbor embedding correction strategy. It combines the similarity threshold and the bidirectional nearest neighbor method as a filtering mechanism to select iterative potential seed pairs and also uses an embedding correction strategy to eliminate the embedding distortion.
The relationship between RNA structure and function has recently attracted interest within the deep learning community, a trend expected to intensify as nucleic acid structure models advance. Despite this momentum, a lack of standardized, accessible benchmarks for applying deep learning to RNA 3D structures hinders progress. To this end, we introduce a collection of seven benchmarking datasets specifically designed to support RNA structure-function prediction. Built on top of the established Python package rnaglib, our library streamlines data distribution and encoding, provides tools for dataset splitting and evaluation, and offers a comprehensive, user-friendly environment for model comparison. The modular and reproducible design of our datasets encourages community contributions and enables rapid customization. To demonstrate the utility of our benchmarks, we report baseline results for all tasks using a relational graph neural network.
The development of biologically interpretable and explainable models remains a key challenge in computational pathology, particularly for multistain immunohistochemistry (IHC) analysis. We present BioX-CPath, an explainable graph neural network architecture for whole slide image (WSI) classification that leverages both spatial and semantic features across multiple stains. At its core, BioX-CPath introduces a novel Stain-Aware Attention Pooling (SAAP) module that generates biologically meaningful, stain-aware patient embeddings. Our approach achieves state-of-the-art performance on both Rheumatoid Arthritis and Sjogren's Disease multistain datasets. Beyond performance metrics, BioX-CPath provides interpretable insights through stain attention scores, entropy measures, and stain interaction scores, that permit measuring model alignment with known pathological mechanisms. This biological grounding, combined with strong classification performance, makes BioX-CPath particularly suitable for clinical applications where interpretability is key. Source code and documentation can be found at: https://github.com/AmayaGS/BioX-CPath.
Gene expression datasets offer insights into gene regulation mechanisms, biochemical pathways, and cellular functions. Additionally, comparing gene expression profiles between disease and control patients can deepen the understanding of disease pathology. Therefore, machine learning has been used to process gene expression data, with patient diagnosis emerging as one of the most popular applications. Although gene expression data can provide valuable insights, challenges arise because the number of patients in expression datasets is usually limited, and the data from different datasets with different gene expressions cannot be easily combined. This work proposes a novel methodology to address these challenges by integrating multiple gene expression datasets and domain-specific knowledge using knowledge graphs, a unique tool for biomedical data integration. Then, vector representations are produced using knowledge graph embedding techniques, which are used as inputs for a graph neural network and a multi-layer perceptron. We evaluate the efficacy of our methodology in three settings: single-dataset learning, multi-dataset learning, and transfer learning. The experimental results show that combining gene expression datasets and domain-specific knowledge improves patient diagnosis in all three settings.
Steering estimation is a critical task in autonomous driving, traditionally relying on 2D image-based models. In this work, we explore the advantages of incorporating 3D spatial information through hybrid architectures that combine 3D neural network models with recurrent neural networks (RNNs) for temporal modeling, using LiDAR-based point clouds as input. We systematically evaluate four hybrid 3D models, all of which outperform the 2D-only baseline, with the Graph Neural Network (GNN) - RNN model yielding the best results. To reduce reliance on LiDAR, we leverage a pretrained unified model to estimate depth from monocular images, reconstructing pseudo-3D point clouds. We then adapt the GNN-RNN model, originally designed for LiDAR-based point clouds, to work with these pseudo-3D representations, achieving comparable or even superior performance compared to the LiDAR-based model. Additionally, the unified model provides semantic labels for each point, enabling a more structured scene representation. To further optimize graph construction, we introduce an efficient connectivity strategy where connections are predominantly formed between points of the same semantic class, with only 20\% of inter-class connections retained. This targeted approach reduces graph complexity and computational cost while preserving critical spatial relationships. Finally, we validate our approach on the KITTI dataset, achieving a 71% improvement over 2D-only models. Our findings highlight the advantages of 3D spatial information and efficient graph construction for steering estimation, while maintaining the cost-effectiveness of monocular images and avoiding the expense of LiDAR-based systems.
Visual Question Answering (VQA) requires reasoning across visual and textual modalities, yet Large Vision-Language Models (LVLMs) often lack integrated commonsense knowledge, limiting their robustness in real-world scenarios. To address this, we introduce MAGIC-VQA, a novel framework that enhances VQA by systematically integrating commonsense knowledge with LVLMs. MAGIC-VQA employs a three-stage process: (1) Explicit Knowledge Integration from external sources, (2) By-Type Post-Processing for contextual refinement, and (3) Implicit Knowledge Augmentation using a Graph Neural Network (GNN) for structured reasoning. While GNNs bring greater depth to structured inference, they enable superior relational inference beyond LVLMs. MAGIC-VQA bridges a key gap by unifying commonsensse knowledge with LVLM-driven reasoning, eliminating the need for extensive pre-training or complex prompt tuning. Our framework achieves state-of-the-art performance on benchmark datasets, significantly improving commonsense reasoning in VQA.
Transparency and interpretability are crucial for enhancing customer confidence and user engagement, especially when dealing with black-box Machine Learning (ML)-based recommendation systems. Modern recommendation systems leverage Graph Neural Network (GNN) due to their ability to produce high-quality recommendations in terms of both relevance and diversity. Therefore, the explainability of GNN is especially important for Link Prediction (LP) tasks since recommending relevant items can be viewed as predicting links between users and items. GNN explainability has been a well-studied field, existing methods primarily focus on node or graph-level tasks, leaving a gap in LP explanation techniques. This work introduces Z-REx, a GNN explanation framework designed explicitly for heterogeneous link prediction tasks. Z-REx utilizes structural and attribute perturbation to identify critical sub-structures and important features while reducing the search space by leveraging domain-specific knowledge. In our experimentation, we show the efficacy of Z-REx in generating contextually relevant and human-interpretable explanations for ZiGNN, a GNN-based recommendation engine, using a real-world real-estate dataset from Zillow Group, Inc. We also compare Z-REx to State-of-The-Art (SOTA) GNN explainers to show Z-REx's superiority in producing high-quality human-interpretable explanations.
Computer networks are the foundation of modern digital infrastructure, facilitating global communication and data exchange. As demand for reliable high-bandwidth connectivity grows, advanced network modeling techniques become increasingly essential to optimize performance and predict network behavior. Traditional modeling methods, such as packet-level simulators and queueing theory, have notable limitations --either being computationally expensive or relying on restrictive assumptions that reduce accuracy. In this context, the deep learning-based RouteNet family of models has recently redefined network modeling by showing an unprecedented cost-performance trade-off. In this work, we revisit RouteNet's sophisticated design and uncover its hidden connection to Topological Deep Learning (TDL), an emerging field that models higher-order interactions beyond standard graph-based methods. We demonstrate that, although originally formulated as a heterogeneous Graph Neural Network, RouteNet serves as the first instantiation of a new form of TDL. More specifically, this paper presents OrdGCCN, a novel TDL framework that introduces the notion of ordered neighbors in arbitrary discrete topological spaces, and shows that RouteNet's architecture can be naturally described as an ordered topological neural network. To the best of our knowledge, this marks the first successful real-world application of state-of-the-art TDL principles --which we confirm through extensive testbed experiments--, laying the foundation for the next generation of ordered TDL-driven applications.
The ability of machine learning (ML) classification models to resist small, targeted input perturbations - known as adversarial attacks - is a key measure of their safety and reliability. We show that floating-point non associativity (FPNA) coupled with asynchronous parallel programming on GPUs is sufficient to result in misclassification, without any perturbation to the input. Additionally, we show this misclassification is particularly significant for inputs close to the decision boundary and that standard adversarial robustness results may be overestimated up to 4.6% when not considering machine-level details. We first study a linear classifier, before focusing on standard Graph Neural Network (GNN) architectures and datasets. We present a novel black-box attack using Bayesian optimization to determine external workloads that bias the output of reductions on GPUs and reliably lead to misclassification. Motivated by these results, we present a new learnable permutation (LP) gradient-based approach, to learn floating point operation orderings that lead to misclassifications, making the assumption that any reduction or permutation ordering is possible. This LP approach provides a worst-case estimate in a computationally efficient manner, avoiding the need to run identical experiments tens of thousands of times over a potentially large set of possible GPU states or architectures. Finally, we investigate parallel reduction ordering across different GPU architectures for a reduction under three conditions: (1) executing external background workloads, (2) utilizing multi-GPU virtualization, and (3) applying power capping. Our results demonstrate that parallel reduction ordering varies significantly across architectures under the first two conditions. The results and methods developed here can help to include machine-level considerations into adversarial robustness assessments.
This paper presents a novel framework for compactly representing a 3D indoor scene using a set of polycuboids through a deep learning-based fitting method. Indoor scenes mainly consist of man-made objects, such as furniture, which often exhibit rectilinear geometry. This property allows indoor scenes to be represented using combinations of polycuboids, providing a compact representation that benefits downstream applications like furniture rearrangement. Our framework takes a noisy point cloud as input and first detects six types of cuboid faces using a transformer network. Then, a graph neural network is used to validate the spatial relationships of the detected faces to form potential polycuboids. Finally, each polycuboid instance is reconstructed by forming a set of boxes based on the aggregated face labels. To train our networks, we introduce a synthetic dataset encompassing a diverse range of cuboid and polycuboid shapes that reflect the characteristics of indoor scenes. Our framework generalizes well to real-world indoor scene datasets, including Replica, ScanNet, and scenes captured with an iPhone. The versatility of our method is demonstrated through practical applications, such as virtual room tours and scene editing.
Genomic studies, including CRISPR-based PerturbSeq analyses, face a vast hypothesis space, while gene perturbations remain costly and time-consuming. Gene expression models based on graph neural networks are trained to predict the outcomes of gene perturbations to facilitate such experiments. Active learning methods are often employed to train these models due to the cost of the genomic experiments required to build the training set. However, poor model initialization in active learning can result in suboptimal early selections, wasting time and valuable resources. While typical active learning mitigates this issue over many iterations, the limited number of experimental cycles in genomic studies exacerbates the risk. To this end, we propose graph-based one-shot data selection methods for training gene expression models. Unlike active learning, one-shot data selection predefines the gene perturbations before training, hence removing the initialization bias. The data selection is motivated by theoretical studies of graph neural network generalization. The criteria are defined over the input graph and are optimized with submodular maximization. We compare them empirically to baselines and active learning methods that are state-of-the-art on this problem. The results demonstrate that graph-based one-shot data selection achieves comparable accuracy while alleviating the aforementioned risks.