Neighborhood Graph Research Articles

Analysis and knowledge extraction of newborn resuscitation activities from annotation files.

Deprivation of oxygen in an infant during and after birth leads to birth asphyxia, which is considered one of the leading causes of death in the neonatal period. Adequate resuscitation activities are performed immediately after birth to save the majority of newborns. The primary resuscitation activities include ventilation, stimulation, drying, suction, and chest compression. While resuscitation guidelines exist, little research has been conducted on measured resuscitation episodes. Objective data collected for measuring and registration of the executed resuscitation activities can be used to generate temporal timelines. This paper is primarily aimed to introduce methods for analyzing newborn resuscitation activity timelines, through visualization, aggregation, redundancy and dimensionality reduction. We are using two datasets: 1) from Stavanger University Hospital with 108 resuscitation episodes, and 2) from Haydom Lutheran Hospital with 76 episodes. The resuscitation activity timelines were manually annotated, but in future work we will use the proposed method on automatically generated timelines from video and sensor data. We propose an encoding generator with unique codes for combination of activities. A visualization of aggregated episodes is proposed using sparse nearest neighbor graph, shown to be useful to compare datasets and give insights. Finally, we propose a method consisting of an autoencoder trained for reducing redundancy in encoded resuscitation timeline descriptions, followed by a neighborhood component analysis for dimensionality reduction. Visualization of the resulting features shows very good class separability and potential for clustering the resuscitation files according to the outcome of the newborns as dead, admitted to NICU or normal. This shows great potential for extracting important resuscitation patterns when tested on larger datasets.

Urban Land Use Classification Model Fusing Multimodal Deep Features

Urban land use classification plays a significant role in urban studies and provides key guidance for urban development. However, existing methods predominantly rely on either raster structure deep features through convolutional neural networks (CNNs) or topological structure deep features through graph neural networks (GNNs), making it challenging to comprehensively capture the rich semantic information in remote sensing images. To address this limitation, we propose a novel urban land use classification model by integrating both raster and topological structure deep features to enhance the accuracy and robustness of the classification model. First, we divide the urban area into block units based on road network data and further subdivide these units using the fractal network evolution algorithm (FNEA). Next, the K-nearest neighbors (KNN) graph construction method with adaptive fusion coefficients is employed to generate both global and local graphs of the blocks and sub-units. The spectral features and subgraph features are then constructed, and a graph convolutional network (GCN) is utilized to extract the node relational features from both the global and local graphs, forming the topological structure deep features while aggregating local features into global ones. Subsequently, VGG-16 (Visual Geometry Group 16) is used to extract the image convolutional features of the block units, obtaining the raster structure deep features. Finally, the transformer is used to fuse both topological and raster structure deep features, and land use classification is completed using the softmax function. Experiments were conducted using high-resolution Google images and Open Street Map (OSM) data, with study areas on the third ring road of Shenyang and the fourth ring road of Chengdu. The results demonstrate that the proposed method improves the overall accuracy and Kappa coefficient by 9.32% and 0.17, respectively, compared to single deep learning models. Incorporating subgraph structure features further enhances the overall accuracy and Kappa by 1.13% and 0.1. The adaptive KNN graph construction method achieves accuracy comparable to that of the empirical threshold method. This study enables accurate large-scale urban land use classification with reduced manual intervention, improving urban planning efficiency. The experimental results verify the effectiveness of the proposed method, particularly in terms of classification accuracy and feature representation completeness.

Graph attention automatic encoder based on contrastive learning for domain recognition of spatial transcriptomics

Spatial transcriptomics is an emerging technology that enables the profiling of gene expression in tissues while preserving spatial location information. This innovative approach is anticipated to provide a comprehensive understanding of the spatial distribution of different cells within tissues and facilitate in-depth analysis of tissue structure. To accurately recognize spatial domains from spatial transcriptomics, we have introduced a generalized deep learning method called GAAEST (Graph Attention-based Autoencoder for Spatial Transcriptomics). Our proposed approach effectively integrates both spatial location information and gene expression data from spatial transcriptomics. Specifically, it leverages spatial location details to construct a neighborhood graph and employs a graph attention network-based encoder to embed gene expression information into a spatially informed space. At the same time, to further optimize the learned potential embedding, self-supervised contrastive learning is introduced to capture spatial information at three levels: local, global and contextual feature of spots. Finally, the decoder reconstructs gene expressions, which are then clustered to identify spatial domains with similar expression patterns and spatial proximity. Based on our experiments conducted on multiple datasets, GAAEST consistently outperforms existing state-of-the-art methods. The proposed GAAEST demonstrates excellent capabilities in spatial domain recognition, positioning it as an ideal tool for advancing spatial transcriptomics research.

Dynamic Spatial-Temporal Memory Augmentation Network for Traffic Prediction.

Traffic flow prediction plays a crucial role in the development of smart cities. However, existing studies face challenges in effectively capturing spatio-temporal contexts, handling hierarchical temporal features, and understanding spatial heterogeneity. To better manage the spatio-temporal correlations inherent in traffic flow, we present a novel model called Dynamic Spatio-Temporal Memory-Augmented Network (DSTMAN). Firstly, we design three spatial-temporal embeddings to capture dynamic spatial-temporal contexts and encode the unique characteristics of time units and spatial states. Secondly, these three spatial-temporal components are integrated to form a multi-scale spatial-temporal block, which effectively extracts hierarchical spatial-temporal dependencies. Finally, we introduce a meta-memory node bank to construct an adaptive neighborhood graph, implicitly representing spatial relationships and enhancing the learning of spatial heterogeneity through a secondary memory mechanism. Evaluation on four public datasets, including METR-LA and PEMS-BAY, demonstrates that the proposed model outperforms benchmark models such as MTGNN, DCRNN, and AGCRN. On the METR-LA dataset, our model reduces the MAE by 4% compared to MTGNN, 6.9% compared to DCRNN, and 5.8% compared to AGCRN, confirming its efficacy in traffic flow prediction.

GSSCL: A framework for Graph Self-Supervised Curriculum Learning based on clustering label smoothing

Graph self-supervised learning is an effective technique for learning common knowledge from unlabeled graph data through pretext tasks. To capture the interrelationships between nodes and their essential roles globally, existing methods use clustering labels as self-supervised signals. However, in some cases, these methods may introduce noise, leading to over-fitting of the model and a reduction in performance. To address these issues, a novel framework for Graph Self-Supervised Curriculum Learning based on clustering label smoothing called GSSCL has been proposed. GSSCL clusters knowledge in an easy-to-difficult manner, reducing the heavy dependence on the reliability of clustering and improving the generalizability of the model. Moreover, the Silhouette Coefficient is employed to evaluate the clustering confident scores for all nodes. Some nodes are selected based on high confident scores to perform self-supervised learning. To account for the possibility of complex heterophilous information in graphs (e.g., noisy links), clustering pseudo-label smoothing is performed on K-nearest neighbor graphs built upon the similarities between node features instead of the original graph structures. The obtained multi-scale knowledge is then applied to curriculum learning. Finally, comprehensive experiments conducted across diverse public graph benchmarks demonstrate the superior performance of the proposed framework. It exhibits comparable results to state-of-the-art methods across semi-supervised node classification and clustering tasks.

A simulation data-driven semi-supervised framework based on MK-KNN graph and ESSGAT for bearing fault diagnosis

Current supervised intelligent fault diagnosis relies on abundant labeled data. However, collecting and labeling data are typically both expensive and time-consuming. Fault diagnosis with unlabeled data remains a significant challenge. To address this issue, a simulation data-driven semi-supervised framework based on multi-kernel K-nearest neighbor (MK-KNN) and edge self-supervised graph attention network (ESSGAT) is proposed. The novel MK-KNN establishes the neighborhood relationships between simulation data and real data. The developed multi-kernel function mitigates the risks of overfitting and underfitting, thereby enhancing the robustness of the simulation-real graphs. The designed ESSGAT employs two forms of self-supervised attention to predict the presence of edges, increasing the weights of crucial neighboring nodes in the MK-KNN graph. The performance of the proposed method is evaluated using a public bearing dataset and a self-constructed dataset of high-speed train axle box bearings. The results show that the proposed method achieves better diagnostic performance compared with other state-of-the-art graph construction methods and graph convolutional networks.

Elucidation of characteristics of networks where every node has its own lifetime

Growth is regarded as an important mechanism for explaining the structures of real networks. However, when the increase in the number of nodes is suppressed owing to their lifetime, the growth property alone is not sufficient to explain even fundamental network properties, such as the scale-free property. In this paper, we propose a network model that considers the lifetime of nodes and the excess addition of local internal links as a mechanism that supports network structures. By investigating the model network, we aimed to elucidate the network characteristics supported by local interactions between nodes via their common neighbors even when the rates of node addition and deletion were balanced. We found that the stationary state of the number of nodes is characterized by a scale-free property with the power-law exponent γ≃1 and localization of the peaks at l=2 in the distance distributions of neighboring nodes (DDN) as the node degree k increases. The specific behavior of the DDN explains the very slow decrease in the clustering strength C(k) with k compared with the normal behavior C(k)∼k−1 and the accelerated growth of the neighborhood graph of each node. Moreover, we showed that some real networks share local structures similar to those of the model network. These findings suggest that the same mechanism as that of the proposed model plays an essential role in supporting the local structures of some real networks.

Pair-EGRET: Enhancing the prediction of protein-protein interaction sites through graph attention networks and protein language models.

Proteins are responsible for most biological functions, many of which require the interaction of more than one protein molecule. However, accurately predicting protein-protein interaction (PPI) sites (the interfacial residues of a protein that interact with other protein molecules) remains a challenge. The growing demand and cost associated with the reliable identification of PPI sites using conventional experimental methods call for computational tools for automated prediction and understanding of PPIs. We present Pair-EGRET, an edge-aggregated graph attention network that leverages the features extracted from pre-trained transformer-like models to accurately predict PPI sites. Pair-EGRET works on a k-nearest neighbor graph, representing the three-dimensional structure of a protein, and utilizes the cross-attention mechanism for accurate identification of interfacial residues of a pair of proteins. Through an extensive evaluation study using a diverse array of experimental data, evaluation metrics, and case studies on representative protein sequences, we demonstrate that Pair-EGRET can achieve remarkable performance in predicting PPI sites. Moreover, Pair-EGRET can provide interpretable insights from the learned cross-attention matrix. Pair-EGRET is freely available in open source form at the GitHub Repository https://github.com/1705004/Pair-EGRET. Supplementary data are available at Bioinformatics online.

Properties of Cubic Fuzzy Competition Graphs with Applications

This study extends the concept of competition graphs to cubic fuzzy competition graphs by introducing additional variations including cubic fuzzy out-neighbourhoods, cubic fuzzy in-neighbourhoods, open neighbourhood cubic fuzzy graphs, closed neighbourhood cubic fuzzy graphs, cubic fuzzy (k) neighbourhood graphs and cubic fuzzy [k]-neighbourhood graphs. These variations provide further insights into the relationships and competition within the graph structure, each with its own defined characteristics and examples. These cubic fuzzy CMGs are further classified as cubic fuzzy k-competition graphs that show competition in the k th order between components, p -competition cubic fuzzy graphs that concentrate on competition in terms of membership degrees, and m -step cubic fuzzy competition graphs that analyze competition in terms of steps. Further, some related results about independent strong vertices and edges have been obtained for these cubic fuzzy competition graph classes. Finally, the proposed concept of cubic fuzzy competition graphs is supported by a numerical example. This example showcases how the framework of cubic fuzzy competition graphs can be practically applied to the predator-prey model to illustrate the representation and analysis of ambiguous information within the graph structures.

Adaptive Neighbors Graph Learning for Large-Scale Data Clustering using Vector Quantization and Self-Regularization

In traditional adaptive neighbors graph learning (ANGL)-based clustering, the time complexity is more than O(n2), where n is the number of data points, which is not scalable for large-scale data problems in real applications. Subsequently, ANGL adds a balance regularization to its objective function to avoid the sparse over-fitting problem in the learned similarity graph matrix. Still, the regularization may leads to many weak connections between data points in different clusters. To address these problems, we propose a new fast clustering method, namely, Adaptive Neighbors Graph Learning for Large-Scale Data Clustering using Vector Quantization and Self-Regularization (ANGL-LDC), to perform vector quantization (VQ) on original data and feed the obtained VQ data as the input in the n×n similarity graph matrix learning. Hence, the n×n similarity graph matrix learning problem is simplified to weighted m×m(m≪n) graph learning problem, where m is the number of distinct points and weight is the duplicate times of distinct points in VQ data. Consequently, the time complexity of ANGL-LDC is much lower than that of ANGL. At the same time, we propose a new ANGL objective function with a graph connection self-regularization mechanism, where the ANGL-LDC objective function will get an infinity value if the value of one graph connection is equal to 1. Therefore, ANGL-LDC naturally avoids obtaining the sparse over-fitting problem since we need to minimize the value of ANGL-LDC’s objective function. Experimental results on synthetic and real-world datasets demonstrate the scalability and effectiveness of ANGL-LDC.

Graph attention networks with adaptive neighbor graph aggregation for cold-start recommendation

Graph attention networks with adaptive neighbor graph aggregation for cold-start recommendation

L-FNNG: Accelerating Large-Scale KNN Graph Construction on CPU-FPGA Heterogeneous Platform

Due to the high complexity of constructing exact k -nearest neighbor graphs, approximate construction has become a popular research topic. The NN-Descent algorithm is one of the representative in-memory algorithms. To effectively handle large datasets, existing state-of-the-art solutions combine the divide-and-conquer approach and the NN-Descent algorithm, where large datasets are divided into multiple partitions, and a subgraph is constructed for each partition before all the subgraphs are merged, reducing the memory pressure significantly. However, such solutions fail to address inefficiencies in large-scale k -nearest neighbor graph construction. In this paper, we propose L-FNNG, a novel solution for accelerating large-scale k -nearest neighbor graph construction on CPU-FPGA heterogeneous platform. The CPU is responsible for dividing data and determining the order of partition processing, while the FPGA executes all construction tasks to utilize the acceleration capability fully. To accelerate the execution of construction tasks, we design an efficient FPGA accelerator, which includes the Block-based Scheduling (BS) and Useless Computation Aborting (UCA) techniques to address the problems of memory access and computation in the NN-Descent algorithm. We also propose an efficient scheduling strategy that includes a KD-tree-based data partitioning method and a hierarchical processing method to address scheduling inefficiency. We evaluate L-FNNG on a Xilinx Alveo U280 board hosted by a 64-core Xeon server. On multiple large-scale datasets, L-FNNG achieves, on average, 2.3× construction speedup over the state-of-the-art GPU-based solution.

Neighbourhood and competition graphs under fuzzy incidence graph and its application

Neighbourhood and competition graphs under fuzzy incidence graph and its application

Asymmetry index for data and its verification in dimensionality reduction and data visualization

We propose an asymmetry index as a measure of degree of asymmetry of a given dataset. It provides an additional information on a dataset allowing to guide and improve any further analysis. The index reflects the intensity of the asymmetric relationships among data resulting from hierarchical data structure. Using the information retrieved by our asymmetry index, one obtains a justification and explanation of the effectiveness of the subsequent asymmetric data analysis methods, as well as helpful preparation to asymmetrizing the tools for the further analysis. The asymmetry index is based on the k-nearest neighbors graph representing the considered data. Therefore, it uses the intrinsic geometry-based information on the data, in this way, providing an insight into the data structure. Our experiments on real data are designed to verify the usefulness of the asymmetry index and the correctness of its theoretical fundamentals. In our empirical validation, we employ the symmetric and asymmetric dimensionality reduction algorithms and evaluate their results on the basis of clustering in the 2-dimensional visualization space. We test, whether our index indeed predicts the level of superiority of the asymmetric methods over their symmetric counterparts.

Benchmarking computational methods for single-cell chromatin data analysis

BackgroundSingle-cell chromatin accessibility assays, such as scATAC-seq, are increasingly employed in individual and joint multi-omic profiling of single cells. As the accumulation of scATAC-seq and multi-omics datasets continue, challenges in analyzing such sparse, noisy, and high-dimensional data become pressing. Specifically, one challenge relates to optimizing the processing of chromatin-level measurements and efficiently extracting information to discern cellular heterogeneity. This is of critical importance, since the identification of cell types is a fundamental step in current single-cell data analysis practices.ResultsWe benchmark 8 feature engineering pipelines derived from 5 recent methods to assess their ability to discover and discriminate cell types. By using 10 metrics calculated at the cell embedding, shared nearest neighbor graph, or partition levels, we evaluate the performance of each method at different data processing stages. This comprehensive approach allows us to thoroughly understand the strengths and weaknesses of each method and the influence of parameter selection.ConclusionsOur analysis provides guidelines for choosing analysis methods for different datasets. Overall, feature aggregation, SnapATAC, and SnapATAC2 outperform latent semantic indexing-based methods. For datasets with complex cell-type structures, SnapATAC and SnapATAC2 are preferred. With large datasets, SnapATAC2 and ArchR are most scalable.

Graph-based spatial co-location pattern mining: integrate geospatial analysis and logical reasoning

ABSTRACT Spatial co-location patterns reflect the inherent correlations among geographical elements. Mining co-location patterns of POIs can provide valuable insights for urban planning and resource management. Generally, co-location mining comprises two steps: proximity relationship determination (geospatial analysis) and frequent pattern recursion (logical reasoning). Previous methods often separate these two steps: serializing proximity relationships to enumerate frequent sequences. However, this approach suffers from limited flexibility and intuitiveness: as continuous spatial contexts are segmented into numerous small parts, it fails to adequately represent geographic correlations and hinders the effective visualization of logical reasoning. Facing these challenges, this study proposes a novel graph-based spatial co-location mining method (GSCM), which leverages graphs to integrate geospatial analysis and logical reasoning. Initially, to establish adjacency relationships, GSCM constructs the adaptive neighborhood graph, which dynamically adjusts proximity thresholds to accommodate geographic heterogeneity. Subsequently, the Apriori logical recursive process is realized on the graph structure. By leveraging graph searching, pruning, and growing, the potential growth directions of co-location patterns are identified, enhancing both the efficiency and intuition of frequent pattern recursion. Through experiments conducted on large-scale POI datasets from Wuhan, GSCM is compared with existing baseline methods, verifying its potential to uncover co-location patterns in complex spatial contexts.

HTFSMMA: Higher-Order Topological Guided Small Molecule-MicroRNA Associations Prediction.

Small molecules (SMs) play a pivotal role in regulating microRNAs (miRNAs). Existing prediction methods for associations between SM-miRNA have overlooked crucial aspects: the incorporation of local topological features between nodes, which represent either SMs or miRNAs, and the effective fusion of node features with topological features. This study introduces a novel approach, termed high-order topological features for SM-miRNA association prediction (HTFSMMA), which specifically addresses these limitations. Initially, an association graph is formed by integrating SM-miRNA association data, SM similarity, and miRNA similarity. Subsequently, we focus on the local information of links and propose target neighborhood graph convolutional network for extracting local topological features. Then, HTFSMMA employs graph attention networks to amalgamate these local features, thereby establishing a platform for the acquisition of high-order features through random walks. Finally, the extracted features are integrated into the multilayer perceptron to derive the association prediction scores. To demonstrate the performance of HTFSMMA, we conducted comprehensive evaluations including five-fold cross-validation, leave-one-out cross-validation (LOOCV), SM-fixed local LOOCV, and miRNA-fixed local LOOCV. The area under receiver operating characteristic curve values were 0.9958 ± 0.0024 (0.8722 ± 0.0021), 0.9986 (0.9504), 0.9974 (0.9111), and 0.9977 (0.9074), respectively. Our findings demonstrate the superior performance of HTFSMMA over existing approaches. In addition, three case studies and the DeLong test have confirmed the effectiveness of the proposed method. These results collectively underscore the significance of HTFSMMA in facilitating the inference of associations between SMs and miRNAs.

HGOD: Outlier detection based on a hybrid graph

Outlier detection is one of the core problems in the field of data mining. Graph-based approaches are widely acknowledged for their robust performance in outlier detection, yet constructing a comprehensive graph to represent the original data remains challenging. Some methods rely solely on the global distribution of the data, leading to low detection accuracy; in addition, when incorporating the local information of the data, the problem of dangling links may arise. To improve the graph construction process, this paper proposes an outlier detection algorithm based on a hybrid graph (HGOD). First, the neighbors of each object are obtained in an adaptive manner, and a neighborhood graph is created. Subsequently, a global connectivity graph is constructed using a minimum spanning tree. Then, these two graphs are merged into a hybrid graph, and Markov random walks are conducted on it. Finally, outliers are identified based on the converged stationary distribution. The performance of HGOD is evaluated on both real-world and synthetic datasets. The precision and AUC of HGOD algorithm surpasses that of the other seven algorithms. Ablation and analysis experiments further demonstrate that the HGOD algorithm is effective and has outstanding performance in outlier detection.

AKNNO: single-cell and spatial transcriptomics clustering with an optimized adaptive k-nearest neighbor graph

Typical clustering methods for single-cell and spatial transcriptomics struggle to identify rare cell types, while approaches tailored to detect rare cell types gain this ability at the cost of poorer performance for grouping abundant ones. Here, we develop aKNNO to simultaneously identify abundant and rare cell types based on an adaptive k-nearest neighbor graph with optimization. Benchmarking on 38 simulated and 20 single-cell and spatial transcriptomics datasets demonstrates that aKNNO identifies both abundant and rare cell types more accurately than general and specialized methods. Using only gene expression aKNNO maps abundant and rare cells more precisely compared to integrative approaches.

Graph-Regularized Non-Negative Matrix Factorization for Single-Cell Clustering in scRNA-Seq Data.

The advent of single-cell RNA sequencing (scRNA-seq) has brought forth fresh perspectives on intricate biological processes, revealing the nuances and divergences present among distinct cells. Accurate single-cell analysis is a crucial prerequisite for in-depth investigation into the underlying mechanisms of heterogeneity. Due to various technical noises, like the impact of dropout values, scRNA-seq data remains challenging to interpret. In this work, we propose an unsupervised learning framework for scRNA-seq data analysis (aka Sc-GNNMF). Based on the non-negativity and sparsity of scRNA-seq data, we propose employing graph-regularized non-negative matrix factorization (GNNMF) algorithm for the analysis of scRNA-seq data, which involves estimating cell-cell sparse similarity and gene-gene sparse similarity through Laplacian kernels and p-nearest neighbor graphs ( p-NNG). By assuming intrinsic geometric local invariance, we use a weighted p-nearest known neighbors ( p-NKN) to optimize the scRNA-seq data. The optimized scRNA-seq data then participates in the matrix decomposition process, promoting the closeness of cells with similar types in cell-gene data space and determining a more suitable embedding space for clustering. Sc-GNNMF demonstrates superior performance compared to other methods and maintains satisfactory compatibility and robustness, as evidenced by experiments on 11 real scRNA-seq datasets. Furthermore, Sc-GNNMF yields excellent results in clustering tasks, extracting useful gene markers, and pseudo-temporal analysis.