Exploring chemical space to find novel molecules that simultaneously satisfy multiple properties is crucial in drug discovery. However, existing methods often struggle with trading off multiple properties due to the conflicting or correlated nature of chemical properties. To tackle this issue, we introduce InversionGNN framework, an effective yet sample-efficient dual-path graph neural network (GNN) for multi-objective drug discovery. In the direct prediction path of InversionGNN, we train the model for multi-property prediction to acquire knowledge of the optimal combination of functional groups. Then the learned chemical knowledge helps the inversion generation path to generate molecules with required properties. In order to decode the complex knowledge of multiple properties in the inversion path, we propose a gradient-based Pareto search method to balance conflicting properties and generate Pareto optimal molecules. Additionally, InversionGNN is able to search the full Pareto front approximately in discrete chemical space. Comprehensive experimental evaluations show that InversionGNN is both effective and sample-efficient in various discrete multi-objective settings including drug discovery.
Cybersecurity threats are growing, making network intrusion detection essential. Traditional machine learning models remain effective in resource-limited environments due to their efficiency, requiring fewer parameters and less computational time. However, handling short and highly imbalanced datasets remains challenging. In this study, we propose the fusion of a Contrastive Attentive Graph Network and Graph Attention Network (CAGN-GAT Fusion) and benchmark it against 15 other models, including both Graph Neural Networks (GNNs) and traditional ML models. Our evaluation is conducted on four benchmark datasets (KDD-CUP-1999, NSL-KDD, UNSW-NB15, and CICIDS2017) using a short and proportionally imbalanced dataset with a constant size of 5000 samples to ensure fairness in comparison. Results show that CAGN-GAT Fusion demonstrates stable and competitive accuracy, recall, and F1-score, even though it does not achieve the highest performance in every dataset. Our analysis also highlights the impact of adaptive graph construction techniques, including small changes in connections (edge perturbation) and selective hiding of features (feature masking), improving detection performance. The findings confirm that GNNs, particularly CAGN-GAT Fusion, are robust and computationally efficient, making them well-suited for resource-constrained environments. Future work will explore GraphSAGE layers and multiview graph construction techniques to further enhance adaptability and detection accuracy.
Equivariant diffusion models have emerged as the prevailing approach for generating novel crystal materials due to their ability to leverage the physical symmetries of periodic material structures. However, current models do not effectively learn the joint distribution of atom types, fractional coordinates, and lattice structure of the crystal material in a cohesive end-to-end diffusion framework. Also, none of these models work under realistic setups, where users specify the desired characteristics that the generated structures must match. In this work, we introduce TGDMat, a novel text-guided diffusion model designed for 3D periodic material generation. Our approach integrates global structural knowledge through textual descriptions at each denoising step while jointly generating atom coordinates, types, and lattice structure using a periodic-E(3)-equivariant graph neural network (GNN). Extensive experiments using popular datasets on benchmark tasks reveal that TGDMat outperforms existing baseline methods by a good margin. Notably, for the structure prediction task, with just one generated sample, TGDMat outperforms all baseline models, highlighting the importance of text-guided diffusion. Further, in the generation task, TGDMat surpasses all baselines and their text-fusion variants, showcasing the effectiveness of the joint diffusion paradigm. Additionally, incorporating textual knowledge reduces overall training and sampling computational overhead while enhancing generative performance when utilizing real-world textual prompts from experts.
Soybean leaf disease detection is critical for agricultural productivity but faces challenges due to visually similar symptoms and limited interpretability in conventional methods. While Convolutional Neural Networks (CNNs) excel in spatial feature extraction, they often neglect inter-image relational dependencies, leading to misclassifications. This paper proposes an interpretable hybrid Sequential CNN-Graph Neural Network (GNN) framework that synergizes MobileNetV2 for localized feature extraction and GraphSAGE for relational modeling. The framework constructs a graph where nodes represent leaf images, with edges defined by cosine similarity-based adjacency matrices and adaptive neighborhood sampling. This design captures fine-grained lesion features and global symptom patterns, addressing inter-class similarity challenges. Cross-modal interpretability is achieved via Grad-CAM and Eigen-CAM visualizations, generating heatmaps to highlight disease-influential regions. Evaluated on a dataset of ten soybean leaf diseases, the model achieves $97.16\%$ accuracy, surpassing standalone CNNs ($\le95.04\%$) and traditional machine learning models ($\le77.05\%$). Ablation studies validate the sequential architecture's superiority over parallel or single-model configurations. With only 2.3 million parameters, the lightweight MobileNetV2-GraphSAGE combination ensures computational efficiency, enabling real-time deployment in resource-constrained environments. The proposed approach bridges the gap between accurate classification and practical applicability, offering a robust, interpretable tool for agricultural diagnostics while advancing CNN-GNN integration in plant pathology research.
The development of social media platforms has revolutionized the speed and manner in which information is disseminated, leading to both beneficial and detrimental effects on society. While these platforms facilitate rapid communication, they also accelerate the spread of rumors and extremist speech, impacting public perception and behavior significantly. This issue is particularly pronounced during election periods, where the influence of social media on election outcomes has become a matter of global concern. With the unprecedented number of elections in 2024, against this backdrop, the election ecosystem has encountered unprecedented challenges. This study addresses the urgent need for effective rumor detection on social media by proposing a novel method that combines semantic analysis with graph neural networks. We have meticulously collected a dataset from PolitiFact and Twitter, focusing on politically relevant rumors. Our approach involves semantic analysis using a fine-tuned BERT model to vectorize text content and construct a directed graph where tweets and comments are nodes, and interactions are edges. The core of our method is a graph neural network, SAGEWithEdgeAttention, which extends the GraphSAGE model by incorporating first-order differences as edge attributes and applying an attention mechanism to enhance feature aggregation. This innovative approach allows for the fine-grained analysis of the complex social network structure, improving rumor detection accuracy. The study concludes that our method significantly outperforms traditional content analysis and time-based models, offering a theoretically sound and practically efficient solution.
In causal inference, interference refers to the phenomenon in which the actions of peers in a network can influence an individual's outcome. Peer effect refers to the difference in counterfactual outcomes of an individual for different levels of peer exposure, the extent to which an individual is exposed to the treatments, actions, or behaviors of peers. Estimating peer effects requires deciding how to represent peer exposure. Typically, researchers define an exposure mapping function that aggregates peer treatments and outputs peer exposure. Most existing approaches for defining exposure mapping functions assume peer exposure based on the number or fraction of treated peers. Recent studies have investigated more complex functions of peer exposure which capture that different peers can exert different degrees of influence. However, none of these works have explicitly considered the problem of automatically learning the exposure mapping function. In this work, we focus on learning this function for the purpose of estimating heterogeneous peer effects, where heterogeneity refers to the variation in counterfactual outcomes for the same peer exposure but different individual's contexts. We develop EgoNetGNN, a graph neural network (GNN)-based method, to automatically learn the appropriate exposure mapping function allowing for complex peer influence mechanisms that, in addition to peer treatments, can involve the local neighborhood structure and edge attributes. We show that GNN models that use peer exposure based on the number or fraction of treated peers or learn peer exposure naively face difficulty accounting for such influence mechanisms. Our comprehensive evaluation on synthetic and semi-synthetic network data shows that our method is more robust to different unknown underlying influence mechanisms when estimating heterogeneous peer effects when compared to state-of-the-art baselines.
Attention-based transformers have played an important role in wireless sensor network (WSN) timing anomaly detection due to their ability to capture long-term dependencies. However, there are several issues that must be addressed, such as the fact that their ability to capture long-term dependencies is not completely reliable, their computational complexity levels are high, and the spatiotemporal features of WSN timing data are not sufficiently extracted for detecting the correlation anomalies of multinode WSN timing data. To address these limitations, this paper proposes a WSN anomaly detection method that integrates frequency-domain features with dynamic graph neural networks (GNN) under a designed self-encoder reconstruction framework. First, the discrete wavelet transform effectively decomposes trend and seasonal components of time series to solve the poor long-term reliability of transformers. Second, a frequency-domain attention mechanism is designed to make full use of the difference between the amplitude distributions of normal data and anomalous data in this domain. Finally, a multimodal fusion-based dynamic graph convolutional network (MFDGCN) is designed by combining an attention mechanism and a graph convolutional network (GCN) to adaptively extract spatial correlation features. A series of experiments conducted on public datasets and their results demonstrate that the anomaly detection method designed in this paper exhibits superior precision and recall than the existing methods do, with an F1 score of 93.5%, representing an improvement of 2.9% over that of the existing models.
Current autonomous vehicles operate primarily within limited regions, but there is increasing demand for broader applications. However, as models scale, their limited capacity becomes a significant challenge for adapting to novel scenarios. It is increasingly difficult to improve models for new situations using a single monolithic model. To address this issue, we introduce the concept of dynamically enhancing a basic driving planner with local driving data, without permanently modifying the planner itself. This approach, termed the Dynamically Local-Enhancement (DLE) Planner, aims to improve the scalability of autonomous driving systems without significantly expanding the planner's size. Our approach introduces a position-varying Markov Decision Process formulation coupled with a graph neural network that extracts region-specific driving features from local observation data. The learned features describe the local behavior of the surrounding objects, which is then leveraged to enhance a basic reinforcement learning-based policy. We evaluated our approach in multiple scenarios and compared it with a one-for-all driving model. The results show that our method outperforms the baseline policy in both safety (collision rate) and average reward, while maintaining a lighter scale. This approach has the potential to benefit large-scale autonomous vehicles without the need for largely expanding on-device driving models.
A surrogate model for particle-in-cell plasma simulations based on a graph neural network is presented. The graph is constructed in such a way as to enable the representation of electromagnetic fields on a fixed spatial grid. The model is applied to simulate beams of electrons in one dimension over a wide range of temperatures, drift momenta and densities, and is shown to reproduce two-stream instabilities - a common and fundamental plasma instability. Qualitatively, the characteristic phase-space mixing of counterpropagating electron beams is observed. Quantitatively, the model's performance is evaluated in terms of the accuracy of its predictions of number density distributions, the electric field, and their Fourier decompositions, particularly the growth rate of the fastest-growing unstable mode, as well as particle position, momentum distributions, energy conservation and run time. The model achieves high accuracy with a time step longer than conventional simulation by two orders of magnitude. This work demonstrates that complex plasma dynamics can be learned and shows promise for the development of fast differentiable simulators suitable for solving forward and inverse problems in plasma physics.
Visual localization involves estimating the 6-degree-of-freedom (6-DoF) camera pose within a known scene. A critical step in this process is identifying pixel-to-point correspondences between 2D query images and 3D models. Most advanced approaches currently rely on extensive visual descriptors to establish these correspondences, facing challenges in storage, privacy issues and model maintenance. Direct 2D-3D keypoint matching without visual descriptors is becoming popular as it can overcome those challenges. However, existing descriptor-free methods suffer from low accuracy or heavy computation. Addressing this gap, this paper introduces the Angle-Annular Graph Neural Network (A2-GNN), a simple approach that efficiently learns robust geometric structural representations with annular feature extraction. Specifically, this approach clusters neighbors and embeds each group's distance information and angle as supplementary information to capture local structures. Evaluation on matching and visual localization datasets demonstrates that our approach achieves state-of-the-art accuracy with low computational overhead among visual description-free methods. Our code will be released on https://github.com/YejunZhang/a2-gnn.
Recent advancements in protein design have leveraged diffusion models to generate structural scaffolds, followed by a process known as protein inverse folding, which involves sequence inference on these scaffolds. However, these methodologies face significant challenges when applied to hyper-variable structures such as antibody Complementarity-Determining Regions (CDRs), where sequence inference frequently results in non-functional sequences due to hallucinations. Distinguished from prevailing protein inverse folding approaches, this paper introduces Igseek, a novel structure-retrieval framework that infers CDR sequences by retrieving similar structures from a natural antibody database. Specifically, Igseek employs a simple yet effective multi-channel equivariant graph neural network to generate high-quality geometric representations of CDR backbone structures. Subsequently, it aligns sequences of structurally similar CDRs and utilizes structurally conserved sequence motifs to enhance inference accuracy. Our experiments demonstrate that Igseek not only proves to be highly efficient in structural retrieval but also outperforms state-of-the-art approaches in sequence recovery for both antibodies and T-Cell Receptors, offering a new retrieval-based perspective for therapeutic protein design.
Targeted protein degradation (TPD) induced by small molecules has emerged as a rapidly evolving modality in drug discovery, targeting proteins traditionally considered "undruggable". Proteolysis-targeting chimeras (PROTACs) and molecular glue degraders (MGDs) are the primary small molecules that induce TPD. Both types of molecules form a ternary complex linking an E3 ligase with a target protein, a crucial step for drug discovery. While significant advances have been made in binary structure prediction for proteins and small molecules, ternary structure prediction remains challenging due to obscure interaction mechanisms and insufficient training data. Traditional methods relying on manually assigned rules perform poorly and are computationally demanding due to extensive random sampling. In this work, we introduce DeepTernary, a novel deep learning-based approach that directly predicts ternary structures in an end-to-end manner using an encoder-decoder architecture. DeepTernary leverages an SE(3)-equivariant graph neural network (GNN) with both intra-graph and ternary inter-graph attention mechanisms to capture intricate ternary interactions from our collected high-quality training dataset, TernaryDB. The proposed query-based Pocket Points Decoder extracts the 3D structure of the final binding ternary complex from learned ternary embeddings, demonstrating state-of-the-art accuracy and speed in existing PROTAC benchmarks without prior knowledge from known PROTACs. It also achieves notable accuracy on the more challenging MGD benchmark under the blind docking protocol. Remarkably, our experiments reveal that the buried surface area calculated from predicted structures correlates with experimentally obtained degradation potency-related metrics. Consequently, DeepTernary shows potential in effectively assisting and accelerating the development of TPDs for previously undruggable targets.
Quantum error correction is crucial for large-scale quantum computing, but the absence of efficient decoders for new codes like quantum low-density parity-check (QLDPC) codes has hindered progress. Here we introduce a universal decoder based on linear attention sequence modeling and graph neural network that operates directly on any stabilizer code's graph structure. Our numerical experiments demonstrate that this decoder outperforms specialized algorithms in both accuracy and speed across diverse stabilizer codes, including surface codes, color codes, and QLDPC codes. The decoder maintains linear time scaling with syndrome measurements and requires no structural modifications between different codes. For the Bivariate Bicycle code with distance 12, our approach achieves a 39.4% lower logical error rate than previous best decoders while requiring only ~1% of the decoding time. These results provide a practical, universal solution for quantum error correction, eliminating the need for code-specific decoders.
In recent years, deep learning has achieved remarkable success in the field of image restoration. However, most convolutional neural network-based methods typically focus on a single scale, neglecting the incorporation of multi-scale information. In image restoration tasks, local features of an image are often insufficient, necessitating the integration of global features to complement them. Although recent neural network algorithms have made significant strides in feature extraction, many models do not explicitly model global features or consider the relationship between global and local features. This paper proposes multi-level attention-guided graph neural network. The proposed network explicitly constructs element block graphs and element graphs within feature maps using multi-attention mechanisms to extract both local structural features and global representation information of the image. Since the network struggles to effectively extract global information during image degradation, the structural information of local feature blocks can be used to correct and supplement the global information. Similarly, when element block information in the feature map is missing, it can be refined using global element representation information. The graph within the network learns real-time dynamic connections through the multi-attention mechanism, and information is propagated and aggregated via graph convolution algorithms. By combining local element block information and global element representation information from the feature map, the algorithm can more effectively restore missing information in the image. Experimental results on several classic image restoration tasks demonstrate the effectiveness of the proposed method, achieving state-of-the-art performance.
Sensor-based Human Activity Recognition (HAR) in smart home environments is crucial for several applications, especially in the healthcare domain. The majority of the existing approaches leverage deep learning models. While these approaches are effective, the rationale behind their outputs is opaque. Recently, eXplainable Artificial Intelligence (XAI) approaches emerged to provide intuitive explanations to the output of HAR models. To the best of our knowledge, these approaches leverage classic deep models like CNNs or RNNs. Recently, Graph Neural Networks (GNNs) proved to be effective for sensor-based HAR. However, existing approaches are not designed with explainability in mind. In this work, we propose the first explainable Graph Neural Network explicitly designed for smart home HAR. Our results on two public datasets show that this approach provides better explanations than state-of-the-art methods while also slightly improving the recognition rate.
Diabetic macular ischemia (DMI), marked by the loss of retinal capillaries in the macular area, contributes to vision impairment in patients with diabetes. Although color fundus photographs (CFPs), combined with artificial intelligence (AI), have been extensively applied in detecting various eye diseases, including diabetic retinopathy (DR), their applications in detecting DMI remain unexplored, partly due to skepticism among ophthalmologists regarding its feasibility. In this study, we propose a graph neural network-based multispectral view learning (GNN-MSVL) model designed to detect DMI from CFPs. The model leverages higher spectral resolution to capture subtle changes in fundus reflectance caused by ischemic tissue, enhancing sensitivity to DMI-related features. The proposed approach begins with computational multispectral imaging (CMI) to reconstruct 24-wavelength multispectral fundus images from CFPs. ResNeXt101 is employed as the backbone for multi-view learning to extract features from the reconstructed images. Additionally, a GNN with a customized jumper connection strategy is designed to enhance cross-spectral relationships, facilitating comprehensive and efficient multispectral view learning. The study included a total of 1,078 macula-centered CFPs from 1,078 eyes of 592 patients with diabetes, of which 530 CFPs from 530 eyes of 300 patients were diagnosed with DMI. The model achieved an accuracy of 84.7 percent and an area under the receiver operating characteristic curve (AUROC) of 0.900 (95 percent CI: 0.852-0.937) on eye-level, outperforming both the baseline model trained from CFPs and human experts (p-values less than 0.01). These findings suggest that AI-based CFP analysis holds promise for detecting DMI, contributing to its early and low-cost screening.
The orchestration of agents to optimize a collective objective without centralized control is challenging yet crucial for applications such as controlling autonomous fleets, and surveillance and reconnaissance using sensor networks. Decentralized controller design has been inspired by self-organization found in nature, with a prominent source of inspiration being flocking; however, decentralized controllers struggle to maintain flock cohesion. The graph neural network (GNN) architecture has emerged as an indispensable machine learning tool for developing decentralized controllers capable of maintaining flock cohesion, but they fail to exploit the symmetries present in flocking dynamics, hindering their generalizability. We enforce rotation equivariance and translation invariance symmetries in decentralized flocking GNN controllers and achieve comparable flocking control with 70% less training data and 75% fewer trainable weights than existing GNN controllers without these symmetries enforced. We also show that our symmetry-aware controller generalizes better than existing GNN controllers. Code and animations are available at http://github.com/Utah-Math-Data-Science/Equivariant-Decentralized-Controllers.
How can we subsample graph data so that a graph neural network (GNN) trained on the subsample achieves performance comparable to training on the full dataset? This question is of fundamental interest, as smaller datasets reduce labeling costs, storage requirements, and computational resources needed for training. Selecting an effective subset is challenging: a poorly chosen subsample can severely degrade model performance, and empirically testing multiple subsets for quality obviates the benefits of subsampling. Therefore, it is critical that subsampling comes with guarantees on model performance. In this work, we introduce new subsampling methods for graph datasets that leverage the Tree Mover's Distance to reduce both the number of graphs and the size of individual graphs. To our knowledge, our approach is the first that is supported by rigorous theoretical guarantees: we prove that training a GNN on the subsampled data results in a bounded increase in loss compared to training on the full dataset. Unlike existing methods, our approach is both model-agnostic, requiring minimal assumptions about the GNN architecture, and label-agnostic, eliminating the need to label the full training set. This enables subsampling early in the model development pipeline (before data annotation, model selection, and hyperparameter tuning) reducing costs and resources needed for storage, labeling, and training. We validate our theoretical results with experiments showing that our approach outperforms existing subsampling methods across multiple datasets.
Network tomography is a crucial problem in network monitoring, where the observable path performance metric values are used to infer the unobserved ones, making it essential for tasks such as route selection, fault diagnosis, and traffic control. However, most existing methods either assume complete knowledge of network topology and metric formulas-an unrealistic expectation in many real-world scenarios with limited observability-or rely entirely on black-box end-to-end models. To tackle this, in this paper, we argue that a good network tomography requires synergizing the knowledge from both data and appropriate inductive bias from (partial) prior knowledge. To see this, we propose Deep Network Tomography (DeepNT), a novel framework that leverages a path-centric graph neural network to predict path performance metrics without relying on predefined hand-crafted metrics, assumptions, or the real network topology. The path-centric graph neural network learns the path embedding by inferring and aggregating the embeddings of the sequence of nodes that compose this path. Training path-centric graph neural networks requires learning the neural netowrk parameters and network topology under discrete constraints induced by the observed path performance metrics, which motivates us to design a learning objective that imposes connectivity and sparsity constraints on topology and path performance triangle inequality on path performance. Extensive experiments on real-world and synthetic datasets demonstrate the superiority of DeepNT in predicting performance metrics and inferring graph topology compared to state-of-the-art methods.
Numerous real-world information networks form Heterogeneous Information Networks (HINs) with diverse objects and relations represented as nodes and edges in heterogeneous graphs. Similarity between nodes quantifies how closely two nodes resemble each other, mainly depending on the similarity of the nodes they are connected to, recursively. Users may be interested in only specific types of connections in the similarity definition, represented as meta-paths, i.e., a sequence of node and edge types. Existing Heterogeneous Graph Neural Network (HGNN)-based similarity search methods may accommodate meta-paths, but require retraining for different meta-paths. Conversely, existing path-based similarity search methods may switch flexibly between meta-paths but often suffer from lower accuracy, as they rely solely on path information. This paper proposes HetFS, a Fast Similarity method for ad-hoc queries with user-given meta-paths on Heterogeneous information networks. HetFS provides similarity results based on path information that satisfies the meta-path restriction, as well as node content. Extensive experiments demonstrate the effectiveness and efficiency of HetFS in addressing ad-hoc queries, outperforming state-of-the-art HGNNs and path-based approaches, and showing strong performance in downstream applications, including link prediction, node classification, and clustering.