Graphs Of Variation Research Articles

Graph neural network-based topological relationships automatic identification of geological boundaries

Topological relationship identification of geological boundaries greatly affects 3D geological modeling efficiency. However, due to the complex spatial distribution and unstructured data architecture of geological boundaries, the current topological identification still mainly depends on the manual operation and interpretation, which is time-consuming and labor-intensive. And geologists' judgments are based on knowledge and experience that are challenging to replicate through conventional algorithmic approaches. To address these challenges, a graph neural network-based geological boundary topological relationships automatic identification method is proposed. Based on graph theory, we conceptualize geological boundaries and their topological relationships as a graph transforming the identification task into an edge prediction problem within this topological graph. We employ the variational graph auto-encoder (VGAE) model to predict unknown edges in the topological graph, enabling automatic identification of geological boundary topological relationships. A geological information transformation method is proposed to extract and encode the geological boundaries’ features as inputs for VGAE. The proposed method is verified in an engineering case study. The results reveal that this method can efficiently and accurately analyze the geological boundary topological relationships. Moreover, it can greatly reduce the manual workload, requiring only 30% of the manual effort to obtain the geological boundary topological relationships, while achieving an average prediction accuracy of approximately 95%.

Expressway Vehicle Trajectory Prediction Based on Fusion Data of Trajectories and Maps from Vehicle Perspective

Research on vehicle trajectory prediction based on road monitoring video data often utilizes a global map as an input, disregarding the fact that drivers rely on the road structures observable from their own positions for path planning. This oversight reduces the accuracy of prediction. To address this, we propose the CVAE-VGAE model, a novel trajectory prediction approach. Initially, our method transforms global perspective map data into vehicle-centric map data, representing it through a graph structure. Subsequently, Variational Graph Auto-Encoders (VGAEs), an unsupervised learning framework tailored for graph-structured data, are employed to extract road environment features specific to each vehicle’s location from the map data. Finally, a prediction network based on the Conditional Variational Autoencoder (CVAE) structure is designed, which first predicts the driving endpoint and then fits the complete future trajectory. The proposed CVAE-VGAE model integrates a self-attention mechanism into its encoding and decoding modules to infer endpoint intent and incorporate road environment features for precise trajectory prediction. Through a series of ablation experiments, we demonstrate the efficacy of our method in enhancing vehicle trajectory prediction metrics. Furthermore, we compare our model with traditional and frontier approaches, highlighting significant improvements in prediction accuracy.

A parameterised model for link prediction using node centrality and similarity measure based on graph embedding

Link prediction is a crucial aspect of graph machine learning, with applications as diverse as disease prediction, social network recommendations, and drug discovery. It involves the prediction of potential new links between nodes within a network. Despite its importance, current models for link prediction exhibit notable limitations. Graph Convolutional Networks have shown high efficiency in link prediction across various datasets. However, they face significant challenges when applied to short-path networks and ego networks, resulting in poor performance. This issue represents a critical area of concern that our work seeks to address. This paper introduces the Node Centrality and Similarity-based Parameterised Model (NCSM), a novel method for link prediction tasks. NCSM uniquely integrates node centrality and similarity measures as edge features in a customised Graph Neural Network (GNN) layer, effectively leveraging the topological information of large networks. This model represents the first parameterised GNN-based link prediction model that considers topological information. The proposed model was evaluated on five benchmark graph datasets, each comprising thousands of nodes and edges. Experimental results highlight NCSM's superiority over existing state-of-the-art models like Graph Convolutional Networks and Variational Graph Autoencoder, as it outperforms them across various metrics and datasets. This exceptional performance can be attributed to NCSM's innovative integration of node centrality, similarity measures, and its efficient use of topological information.

A Construction Method for a Dynamic Weighted Protein Network Using Multi-Level Embedding

The rapid development of high-throughput technology has generated a large amount of protein–protein interaction (PPI) data, which provide a large amount of data support for constructing dynamic protein–protein interaction networks (PPINs). Constructing dynamic PPINs and applying them to recognize protein complexes has become a hot research topic. Most existing methods for complex recognition cannot fully mine the information of PPINs. To address this problem, we propose a construction method of dynamic weighted protein network by multi-level embedding (DWPNMLE). It can reflect the protein network’s dynamics and the protein network’s higher-order proximity. Firstly, the protein active period is calculated to divide the protein subnetworks at different time points. Then, the connection probability is used for the proteins possessing the same time points to judge whether there is an interaction relationship between them. Then, the corresponding protein subnetworks (multiple adjacency matrices) are constructed. Secondly, the multiple feature matrices are constructed using one-hot coding with the gene ontology (GO) information. Next, the first embedding is performed using variational graph auto-encoders (VGAEs) to aggregate features efficiently, followed by the second embedding using deep attributed network embedding (DANE) to strengthen the node representations learned in the first embedding and to maintain the first-order and higher-order proximity of the original network; finally, we compute the cosine similarity to obtain the final dynamic weighted PPIN. To evaluate the effectiveness of DWPNMLE, we apply four classical protein-complex-recognition algorithms on the DWPNMLE and compare them with two other dynamic protein network construction methods. The experimental results demonstrate that DWPNMLE significantly enhances the accuracy of complex recognition with high robustness, and the algorithms’ efficiency is also within a reasonable range.

VR-GNN: variational relation vector graph neural network for modeling homophily and heterophily

VR-GNN: variational relation vector graph neural network for modeling homophily and heterophily

VGE: Gene-Disease Association by Variational Graph Embedding

VGE: Gene-Disease Association by Variational Graph Embedding

RecGraph: recombination-aware alignment of sequences to variation graphs.

Bacterial genomes present more variability than human genomes, which requires important adjustments in computational tools that are developed for human data. In particular, bacteria exhibit a mosaic structure due to homologous recombinations, but this fact is not sufficiently captured by standard read mappers that align against linear reference genomes. The recent introduction of pangenomics provides some insights in that context, as a pangenome graph can represent the variability within a species. However, the concept of sequence-to-graph alignment that captures the presence of recombinations has not been previously investigated. In this paper, we present the extension of the notion of sequence-to-graph alignment to a variation graph that incorporates a recombination, so that the latter are explicitly represented and evaluated in an alignment. Moreover, we present a dynamic programming approach for the special case where there is at most a recombination-we implement this case as RecGraph. From a modelling point of view, a recombination corresponds to identifying a new path of the variation graph, where the new arc is composed of two halves, each extracted from an original path, possibly joined by a new arc. Our experiments show that RecGraph accurately aligns simulated recombinant bacterial sequences that have at most a recombination, providing evidence for the presence of recombination events. Our implementation is open source and available at https://github.com/AlgoLab/RecGraph.

A hepatitis B virus (HBV) sequence variation graph improves alignment and sample-specific consensus sequence construction.

Nearly 300 million individuals live with chronic hepatitis B virus (HBV) infection (CHB), for which no curative therapy is available. As viral diversity is associated with pathogenesis and immunological control of infection, improved methods to characterize this diversity could aid drug development efforts. Conventionally, viral sequencing data are mapped/aligned to a reference genome, and only the aligned sequences are retained for analysis. Thus, reference selection is critical, yet selecting the most representative reference a priori remains difficult. We investigate an alternative pangenome approach which can combine multiple reference sequences into a graph which can be used during alignment. Using simulated short-read sequencing data generated from publicly available HBV genomes and real sequencing data from an individual living with CHB, we demonstrate alignment to a phylogenetically representative 'genome graph' can improve alignment, avoid issues of reference ambiguity, and facilitate the construction of sample-specific consensus sequences more genetically similar to the individual's infection. Graph-based methods can, therefore, improve efforts to characterize the genetics of viral pathogens, including HBV, and have broader implications in host-pathogen research.

Design of an Iterative Method for Enhanced Multimodal Time Series Analysis Using Graph Attention Networks, Variational Graph Autoencoders, and Transfer Learning

In the ever-evolving landscape of data analysis, the need to efficiently and accurately interpret multimodal time series data has become paramount. Traditional methods often fall short in addressing the complex dependencies and dynamics inherent in such data, limiting their effectiveness in real-world applications. This work introduces a comprehensive approach that leverages Graph Attention Networks (GATs), Variational Graph Autoencoders (VGAEs), transfer learning with pretrained transformers, and Bayesian state-space models to overcome these limitations. GATs are selected for their ability to dynamically focus on relevant modalities through attention mechanisms, thereby capturing the intricate relationships between different data modalities. This method significantly enhances the model's ability to integrate multimodal information, leading to notable improvements in classification, prediction, and anomaly detection tasks. VGAEs are utilized to learn latent representations within a graph-based framework, promoting unsupervised learning while unveiling the underlying data structure. The resultant embeddings are pivotal for downstream tasks like clustering and visualization, encapsulating the interactions within multimodal time series data effectively. Furthermore, this work incorporates transfer learning with pretrained transformers to harness extensive knowledge from large datasets, adapting it to multimodal time series analysis. This strategy excels in capturing long-range dependencies, thereby augmenting generalization and performance in data-scarce scenarios. Bayesian state-space models are employed to elucidate the temporal dynamics and uncertainties of time series data, offering a robust framework for probabilistic inference and enhancing the interpretability and reliability of forecasting and anomaly detection. The efficacy of the proposed model is rigorously evaluated using diverse datasets, including the Yahoo! Stock Dataset, Forest Cover Dataset, and an empirical collection of 100k time series data samples. The results demonstrate a significant leap in performance metrics, including a 9.5% increase in precision, 8.5% boost in accuracy, 8.3% rise in recall, 10.4% reduction in delay, 9.4% enhancement in AUC, and a 5.9% improvement in specificity, alongside superior pre-emption capabilities compared to existing methods. This work not only addresses the pressing need for advanced multimodal time series analysis techniques but also sets a new benchmark for efficiency and accuracy. The integration of GATs, VGAEs, transfer learning with pretrained transformers, and Bayesian state-space models presents a formidable approach that significantly advances the field, offering profound impacts on a wide array of applications.

Attention-guided variational graph autoencoders reveal heterogeneity in spatial transcriptomics.

The latest breakthroughs in spatially resolved transcriptomics technology offer comprehensive opportunities to delve into gene expression patterns within the tissue microenvironment. However, the precise identification of spatial domains within tissues remains challenging. In this study, we introduce AttentionVGAE (AVGN), which integrates slice images, spatial information and raw gene expression while calibrating low-quality gene expression. By combining the variational graph autoencoder with multi-head attention blocks (MHA blocks), AVGN captures spatial relationships in tissue gene expression, adaptively focusing on key features and alleviating the need for prior knowledge of cluster numbers, thereby achieving superior clustering performance. Particularly, AVGN attempts to balance the model's attention focus on local and global structures by utilizing MHA blocks, an aspect that current graph neural networks have not extensively addressed. Benchmark testing demonstrates its significant efficacy in elucidating tissue anatomy and interpreting tumor heterogeneity, indicating its potential in advancing spatial transcriptomics research and understanding complex biological phenomena.

Explainable Origin-Destination Crowd Flow Interpolation via Variational Multi-Modal Recurrent Graph Auto-Encoder

Origin-destination (OD) crowd flow, if more accurately inferred at a fine-grained level, has the potential to enhance the efficacy of various urban applications. While in practice for mining OD crowd flow with effect, the problem of spatially interpolating OD crowd flow occurs since the ineluctable missing values. This problem is further complicated by the inherent scarcity and noise nature of OD crowd flow data. In this paper, we propose an uncertainty-aware interpolative and explainable framework, namely UApex, for realizing reliable and trustworthy OD crowd flow interpolation. Specifically, we first design a Variational Multi-modal Recurrent Graph Auto-Encoder (VMR-GAE) for uncertainty-aware OD crowd flow interpolation. A key idea here is to formulate the problem as semi-supervised learning on directed graphs. Next, to mitigate the data scarcity, we incorporate a distribution alignment mechanism that can introduce supplementary modals into variational inference. Then, a dedicated decoder with a Poisson prior is proposed for OD crowd flow interpolation. Moreover, to make VMR-GAE more trustworthy, we develop an efficient and uncertainty-aware explainer that can provide explanations from the spatiotemporal topology perspective via the Shapley value. Extensive experiments on two real-world datasets validate that VMR-GAE outperforms the state-of-the-art baselines. Also, an exploratory empirical study shows that the proposed explainer can generate meaningful spatiotemporal explanations.

Abstract 4912: Unsupervised detection of stromal phenotypes with distinct fibrogenic and inflamed properties in NSCLC

Abstract Background: Understanding the composition of cancer-associated stroma (CAS) is vital, as the number and location of immune cells and fibroblasts, as well as the degree of extracellular matrix deposition, have implications for cancer progression and response to treatment, including in non-small cell lung cancer (NSCLC). Manual analysis of CAS does not fully describe the stromal milieu, especially from a spatial perspective, and is highly subjective. To this end, we have developed an unsupervised machine learning (ML) model to characterize the CAS in NSCLC from hematoxylin and eosin (H&E) stained whole slide images (WSI) at scale. Methods: PathExploreTM models were deployed to predict stromal tissue and cell types, while another ML model was used to detect collagen fibers from H&E stained WSIs from the TCGA LUAD (N=536) and LUSC (N=464) datasets. Stroma was divided into small regions (median = 0.02 mm2), and 88 features characterizing cell distribution, tissue composition and fiber density were extracted from each region. Graphs were generated connecting neighboring regions (nodes), and an unsupervised variational graph auto-encoder (VGAE) model was trained to learn 8 latent features through dimensionality reduction. Stromal phenotypes were then derived from the latent features using k-means clustering. The fraction of each phenotype in the stroma was correlated against immune- and stroma-related gene expression signatures (GES) and overall survival (OS). Results: Deployment of VGAE on LUAD and LUSC WSIs revealed three distinct stromal phenotypes - P0, P1 and P2. Fibroblast density was elevated in P0 and P1 regions (p<0.001), immune cell density was elevated in P2 regions (p<0.001), and collagen fiber intensity was highest in P1 regions (p<0.001). P2 enrichment was correlated with elevated expression of the T cell-inflamed gene expression profile (TGEP; Spearman ρ = 0.43 in LUAD; ρ = 0.27 in LUSC) and with improved OS (HR = 0.696; 95% CIs: 0.571-0.847 in LUSC). Conversely, P1 enrichment was positively associated with a transforming growth factor-β-induced cancer associated fibroblast GES (TGFβ-CAF: ρ = 0.19 in LUAD and ρ = 0.12 in LUSC) and poor OS (HR = 1.358; 95% CIs: 1.149-1.603 in LUSC). These phenotypes are consistent with fibroblast-enriched, collagen-depleted stroma (P0), collagen-rich, fibroblast-enriched tumor-promoting stroma (P1), and immune cell-enriched, tumor-suppressive stroma (P2). Conclusions: We describe an unsupervised, data-driven method of predicting stromal regions with discrete patterns of cell composition and collagen deposition in NSCLC. This approach identified three phenotypes of NSCLC stroma. These results highlight the ability of ML models to characterize and find meaningful patterns within the cell, tissue, and matrix components of a tumor. This work provides further evidence of the potential of ML to discover novel precision medicine biomarkers in NSCLC. Citation Format: Neel Patel, Nhat Le, Tan Nguyen, Fedaa Najdawi, Sandhya Srinivasan, Adam Stanford-Moore, Deeksha Kartik, Jun Zhang, Jacqueline Brosnan-Cashman, Robert Egger, Justin Lee, Matthew Bronnimann. Unsupervised detection of stromal phenotypes with distinct fibrogenic and inflamed properties in NSCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4912.

Online course evaluation model based on graph auto-encoder

In the post-epidemic era, online learning has gained increasing attention due to the advancements in information and big data technology, leading to large-scale online course data with various student behaviors. Online data mining has become a popular and important way of extracting valuable insights from large amounts of data. However, previous online course analysis methods often focused on individual aspects of the data and neglected the correlation among the large-scale learning behavior data, which can lead to an incomplete understanding of the overall learning behavior and patterns within the online course. To solve the problems, this paper proposes an online course evaluation model based on a graph auto-encoder. In our method, the features of collected online course data are used to construct K-Nearest Neighbor(KNN) graphs to represent the association among the courses. Then the variational graph auto-encoder(VGAE) is introduced to learn the useful implicit features. Finally, we feed the learned implicit features into unsupervised and semi-supervised downstream tasks for online course evaluation, respectively. We conduct experiments on two datasets. In the clustering task, our method showed a more than tenfold increase in the Calinski-Harabasz index compared to unoptimized features, demonstrating significant structural distinction and group coherence. In the classification task, compared to traditional methods, our model exhibited an overall performance improvement of about 10%, indicating its effectiveness in handling complex network data.

Modeling vehicle U-turning behavior near intersections: A deep learning approach based on TCN and multi-head attention

In U-turn bays near intersections, the conflict between U-turning vehicles and those going straight-ahead results in traffic accidents since straight-ahead vehicles cannot reliably anticipate the behavior of oncoming U-turning vehicles. However, previous studies on modeling U-turning behavior do not effectively capture the spatial–temporal interaction between the U-turning and surrounding vehicles. To address this issue, a deep-learning framework based on a temporal convolutional network (TCN) and multi-head attention mechanism is developed. The TCN is utilized to capture long-term dependencies of vehicles in the shared left- and U-turn lanes by extracting vehicle historical motion features. The self-attention mechanism extracts salient features related to the U-turn intentions, classifying the vehicles into left- and U-turning vehicles based on their driving intentions. A parallel TCN and spatial multi-head attention structure is constructed to model vehicle–vehicle interactions to further predict the future trajectory of U-turning vehicles. Finally, the obtained features are input into a Transformer-based decoder module and trajectory generator to predict the future displacement and body orientation of U-turning vehicles. The model is validated via comparison with state-of-the-art models and the observed trajectories under various scenarios. Ablation studies are conducted to quantify the efficacy of each module. Further, the effect of the surrounding homogenous and heterogeneous vehicles on U-turning vehicles in four different U-turn scenarios is quantified using spatial–temporal variation graphs and attention matrices.

Recognition of Yuan blue and white porcelain produced in Jingdezhen based on graph anomaly detection combining portable X-ray fluorescence spectrometry

The blue and white porcelain produced in Jingdezhen during China’s Yuan Dynasty is an outstanding cultural heritage of ceramic art that has attracted wide attention for its identification. However, the traditional visual identification method is susceptible to misjudgment, thermoluminescence dating damages the samples, and the methods based on chemical analysis are limited by the accuracy and specificity of the elemental features. In this paper, we address the identification challenge by using machine learning techniques combined with portable X-ray Fluorescence Spectrometer (pXRF) analysis. We collect a large dataset of chemical compositions of Yuan blue and white porcelain from Jingdezhen using pXRF, and propose a graph anomaly detection method based on gradient attention map (GRAM) to identify the porcelain from different dynasties. We treat the porcelain produced in the Yuan dynasty as normal samples and those from other dynasties as abnormal samples. For GRAM, we merely train the variational graph autoencoder (VGAE) model with normal graphs and then use its encoder to extract graph features and compute the anomaly scores by utilizing the GRAM of the graph representations with respect to the node feature embeddings. Finally, we compare GRAM with state-of-the-art graph anomaly detection techniques and show that it achieves superior performance.

A Spatial-Temporal Variational Graph Attention Autoencoder Using Interactive Information for Fault Detection in Complex Industrial Processes.

Modern industry processes are typically composed of multiple operating units with reaction interaction and energy-mass coupling, which result in a mixed time-varying and spatial-temporal coupling of process variables. It is challenging to develop a comprehensive and precise fault detection model for the multiple interconnected units by simple superposition of the individual unit models. In this study, the fault detection problem is formulated as a spatial-temporal fault detection problem utilizing process data of multiple interconnected unit processes. A spatial-temporal variational graph attention autoencoder (STVGATE) using interactive information is proposed for fault detection, which aims to effectively capture the spatial and temporal features of the interconnected unit processes. First, slow feature analysis (SFA) is implemented to extract temporal information that reveals the dynamic relevance of the process data. Then, an integration method of metric learning and prior knowledge is proposed to construct coupled spatial relationships based on temporal information. In addition, a variational graph attention autoencoder (VGATE) is suggested to extract temporal and spatial information for fault detection, which incorporates the dominances of variational inference and graph attention mechanisms. The proposed method can automatically extract and deeply mine spatial-temporal interactive feature information to boost detection performance. Finally, three industrial process experiments are performed to verify the feasibility and effectiveness of the proposed method. The results demonstrate that the proposed method dramatically increases the fault detection rate (FDR) and reduces the false alarm rate (FAR).

Denoising Variational Graph of Graphs Auto-Encoder for Predicting Structured Entity Interactions

Denoising Variational Graph of Graphs Auto-Encoder for Predicting Structured Entity Interactions

Application of Variational Graph Autoencoder in Traction Control of Energy-Saving Driving for High-Speed Train

In a high-speed rail system, the driver repeatedly adjusts the train’s speed and traction while driving, causing a high level of energy consumption. This also leads to the instability of the train’s operation, affecting passengers’ experiences and the operational efficiency of the system. To solve this problem, we propose a variational graph auto-encoder (VGAE) model using a neural network to learn the posterior distribution. This model can effectively capture the correlation between the components of a high-speed rail system and simulate drivers’ operating state accurately. The specific traction control is divided into two parts. The first part employs an algorithm based on the K-Nearest Neighbors (KNN) algorithm and undersampling to address the negative impact of imbalanced quantities in the training dataset. The second part utilizes a variational graph autoencoder to derive the initial traction control of drivers, thereby predicting the energy performance of the drivers’ operation. An 83,786 m long high-speed train driving section is used as an example for verification. By using a confusion matrix for our comparative analysis, it was concluded that the energy consumption is approximately 18.78% less than that of manual traction control. This shows the potential and effect of the variational graph autoencoder model for optimizing energy consumption in high-speed rail systems.

MAVGAE: a multimodal framework for predicting asymmetric drug–drug interactions based on variational graph autoencoder

Drug-drug interactions refer to the phenomena wherein the potency, duration, or effectiveness of one or multiple drugs undergo alterations of varying degrees as a result of their concurrent or sequential usage. The accurate identification of potential drug interactions plays a pivotal role in mitigating the risks associated with drug administration in patients, it also helps in minimizing the likelihood of hazardous situations arising during a patient’s course of treatment. However, researchers have found that there is a problem of asymmetric drug interactions, where one drug may affect another but not vice versa. This adds to the difficulty of prediction, so in polypharmacy, the order of drug administration is critical to efficacy and safety, and few current studies predict asymmetric DDIs. Aiming at the above problems, we propose a framework based on multimodal data and a variational graph autoencoder named MAVGAE for predicting asymmetric drug interactions. The framework initially encodes multimodal data into low-dimensional representations and then utilizes a variational graph autoencoder for encoding and decoding. During the model training process, supervised learning is employed for the classification task with the incorporation of heterogeneity information, ensuring accurate prediction of drug interactions. Experimental validation on a large-scale drug dataset demonstrates the framework’s high accuracy and reliability in predicting non-symmetrical drug interactions, offering effective support and guidance for drug research.

Prediction of Associations between Nanoparticle, Drug and Cancer Using Variational Graph Autoencoder

Predicting implicit drug-disease associations is critical to the development of new drugs, with the aim of minimizing side effects and development costs. Existing drug-disease prediction methods typically focus on either single or multiple drug-disease networks. Recent advances in nanoparticles particularly in cancer research show improvements in bioavailability and pharmacokinetics by reducing toxic side effects. Thus, the interaction of the nanoparticles with drugs and diseases tends to improve during the development phase. In this study, it presents a variational graph autoencoder model to the cell-specific drug delivery data, including the class interactions between nanoparticle, drug, and cancer types as a knowledge base for targeted drug delivery. The cell-specific drug delivery data is transformed into a bipartite graph where relations only exist between sequences of these class interactions. Experimental results show that the knowledge graph enhanced Variational Graph Autoencoder model with VGAE-ROC-AUC (0.9627) and VGAE-AP (0.9566) scores performs better than the Graph Autoencoder model.