Nodes In Graph Research Articles

Sequence Flow: interactive web application for visualizing partial order alignments

BackgroundMultiple sequence alignment (MSA) has proven extremely useful in computational biology, especially in inferring evolutionary relationships via phylogenetic analysis and providing insight into protein structure and function. An alternative to the standard MSA model is partial order alignment (POA), in which aligned sequences are represented as paths in a graph rather than rows in a matrix. While the POA model has proven useful in several applications (e.g. sequencing reads assembly and pangenome structure exploration), we lack efficient visualization tools that could highlight its advantages.ResultsWe propose Sequence Flow – a web application designed to address the above problem. Sequence Flow presents the POA as a Sankey diagram, a kind of graph visualisation typically used for graphs representing flowcharts. Sequence Flow enables interactive alignment exploration, including fragment selection, highlighting a selected group of sequences, modification of the position of graph nodes, structure simplification etc. After adjustment, the visualization can be saved as a high-quality graphic file. Thanks to the use of SanKEY.js – a JavaScript library for creating Sankey diagrams, designed specifically to visualize POAs, Sequence Flow provides satisfactory performance even with large alignments.ConclusionsWe provide Sankey diagram-based POA visualization tools for both end users (Sequence Flow) and bioinformatic software developers (SanKEY.js). Sequence Flow webservice is available at https://sequenceflow.mimuw.edu.pl/. The source code for SanKEY.js is available at https://github.com/Krzysiekzd/SanKEY.js and for Sequence Flow at https://github.com/Krzysiekzd/SequenceFlow.

Development of Whole System Digital Twins for Advanced Reactors: Leveraging Graph Neural Networks and SAM Simulations

In this work, we introduce a novel method to develop whole system digital twins (DTs) for advanced nuclear reactors. This method treats a complex reactor system as a heterogeneous graph: with the system components as different types of graph nodes and their physical interconnections as edges. Based on the heterogeneous graph, a graph neural network combining graph convolution and temporal node attention is developed as the DT, facilitating a comprehensive understanding of the system’s dynamic behavior. By utilizing the System Analysis Module (SAM) code for simulating various operational transients, we develop a graph-based database that trains the DT. This DT is characterized by two primary functions: It can infer the entire system’s status using sparse node information, and it can predict the progress of transients based on current and historical system information. Our approach is validated through case studies on the Experimental Breeder Reactor II (EBR-II) system and a generic Fluoride-salt-cooled High-temperature Reactor (gFHR), demonstrating the DT’s accuracy in forecasting operational transients. The DT’s rapid computation capabilities enhance its potential for supporting advanced reactor operations, offering benefits in intelligent simulation, autonomous control, and anomaly detection, paving the way for improved safety analysis and intelligent component health management for advanced reactor systems and reducing their operations and maintenance cost.

HOW MANY SUBSETS WHICH THEIR OPERATIONS WITH A FIXED SUBSET CONTAIN AT LEAST ONE ELEMENT OF A GIVEN COLLECTION?

We pose the following problem related to binary set operations on finite sets. Given a finite set . Let a binary set operation and be a non-empty collection of non-empty subsets of . For a fixed subset of , where , how many subsets of which their operation with contains at least one element of ?. In this paper, we give the solution of this problem, especially for the subsets of size , using the inclusion-exclusion principle, Corrádi’s lemma, and Bonferroni’s inequality. In this context, the problem is related to determining the degree of nodes in certain graphs, such as graphs constructed with the adjacency rule depends on and the node set is a hypergraph.

Dual-level adaptive incongruity-enhanced model for multimodal sarcasm detection

Multimodal sarcasm detection leverages multimodal information, such as image, text, etc. to identify special instances whose superficial emotional expression is contrary to the actual emotion. Existing methods primarily focused on the incongruity between text and image information for sarcasm detection. Existing sarcasm methods in which the tendency of image encoders to encode similar images into similar vectors, and the introduction of noise in graph-level feature extraction due to negative correlations caused by the accumulation of GAT layers and the lack of representations for non-neighboring nodes. To address these limitations, we propose a Dual-Level Adaptive Incongruity-Enhanced Model (DAIE) to extract the incongruity between the text and image at both token and graph levels. At the token level, we bolster token-level contrastive learning with patch-based reconstructed image to capture common and specific features of images, thereby amplifying incongruities between text and images. At the graph level, we introduce adaptive graph contrast learning, coupled with negative pair similarity weights, to refine the feature representation of the model’s textual and visual graph nodes, while also enhancing the information exchange among neighboring nodes. We conduct experiments using a publicly available sarcasm detection dataset. The results demonstrate the effectiveness of our method, outperforming several state-of-the-art approaches by 3.33% and 4.34% on accuracy and F1 score, respectively.

RT-APT: A real-time APT anomaly detection method for large-scale provenance graph

Advanced Persistent Threats (APTs) are prevalent in the field of cyber attacks, where attackers employ advanced techniques to control targets and exfiltrate data without being detected by the system. Existing APT detection methods heavily rely on expert rules or specific training scenarios, resulting in the lack of both generality and reliability. Therefore, this paper proposes a novel real-time APT attack anomaly detection system for large-scale provenance graphs, named RT-APT. Firstly, a provenance graph is constructed with kernel logs, and the WL subtree kernel algorithm is utilized to aggregate contextual information of nodes in the provenance graph. In this way we obtain vector representations. Secondly, the FlexSketch algorithm transforms the streaming provenance graph into a sequence of feature vectors. Finally, the K-means clustering algorithm is performed on benign feature vector sequences, where each cluster represents a different system state. Thus, we can identify abnormal behaviors during system execution. Therefore RT-APT enables to detect unknown attacks and extract long-term system behaviors. Experiments have been carried out to explore the optimal parameter settings under which RT-APT can perform best. In addition, we compare RT-APT and the state-of-the-art approaches on three datasets, Laboratory, StreamSpot and Unicorn. Results demonstrate that our proposed method outperforms the state-of-the-art approaches from the perspective of runtime performance, memory overhead and CPU usage.

GeoHi-GNN: Geometry-aware hierarchical graph representation learning for normal estimation

Normal estimation has been one of the key tasks in point cloud analysis, while it is challenging when facing with severe noises or complex regions. The challenges mainly come from the selection of supporting points for estimation, that is, improper selections of points and points' scale will lead to insufficient information, loss of details, etc. To this end, this paper proposes one feature-centric fitting scheme, GeoHi-GNN, by learning geometry-aware hierarchical graph representation for fitting weights estimation. The main functional module is the continuously conducted Hierarchically Geometric-aware (HG) module, consisting of two core operations, namely, the graph node construction (GNC) and the geometric-aware dynamic graph convolution (GDGC). GNC aims to aggregate the feature information onto a smaller number of nodes, providing global-to-local information while avoiding the interferences from noises in larger scales. With these nodes distributed in different scales, GDGC dynamically updates the node features regarding to both intrinsic feature and extrinsic geometric information. Finally, the hierarchical graphical features are cascaded to estimate the weights for supporting points in the surface fitting. Through the extensive experiments and comprehensive comparisons with the state-of-the-arts, our scheme has exhibited many attractive advantages such as being geometry-aware and robust, empowering further applications like more accurate surface reconstruction.

A Fast Algorithm for All-Pairs-Shortest-Paths Suitable for Neural Networks.

Given a directed graph of nodes and edges connecting them, a common problem is to find the shortest path between any two nodes. Here we show that the shortest path distances can be found by a simple matrix inversion: if the edges are given by the adjacency matrix Aij, then with a suitably small value of γ, the shortest path distances are Dij=ceil(logγ[(I-γA)-1]ij).We derive several graph-theoretic bounds on the value of γ and explore its useful range with numerics on different graph types. Even when the distance function is not globally accurate across the entire graph, it still works locally to instruct pursuit of the shortest path. In this mode, it also extends to weighted graphs with positive edge weights. For a wide range of dense graphs, this distance function is computationally faster than the best available alternative. Finally, we show that this method leads naturally to a neural network solution of the all-pairs-shortest-path problem.

Graph node classification algorithm based on similarity random walk aggregation

Aiming at the relatively low accuracy of methods such as MLP and GCN in heterogeneous graph node classification tasks, this paper proposes a graph neural network based on similarity random walk aggregation (SRW-GNN). Most existing node classification methods usually take neighbor nodes as neighborhoods, but the target node and its neighbors in heterogeneous graphs usually belong to different categories. To reduce the impact of heterogeneity on node embedding, SRW-GNN uses the similarity between nodes as probability to perform random walks and takes the sampled paths as neighborhoods to obtain more homogeneous information. The order in which nodes appear in the path is particularly critical for capturing neighborhood information. However, most existing GNN aggregators are insensitive to node order. This paper introduces a path aggregator based on recurrent neural network (RNN) to simultaneously extract the features and order information of nodes in the path. In addition, nodes have different preferences for different paths. In order to adaptively learn the importance of different paths in node encoding, an attention mechanism is used to dynamically adjust the contribution of each path to the final embedding. Experimental results on multiple commonly used heterogeneous graph datasets show that the accuracy of this method is significantly better than that of MLP, GCN, H2GCN, HOG-GCN and other methods, verifying its effectiveness in heterogeneous graph node classification tasks.

Node classification based on Attribute Fuse Edge Features and Label Adaptive Adjustment

Most of existing graph representation learning methods only extract information from nodes and ignore the hidden information of edges. Nodes carry weak structural information thus affecting the specificity of node embeddings.To solve these problems, this paper proposes a node classification algorithm based on Attribute Fuse Edge Features and Label Adaptive Adjustment (AFEF_LAA).Firstly, Intimate-Relationship-Attribute of node is designed based on edge embeddings.Rz-Cos rule is constructed to perform the similarity metric between nodes and their neighbors to select intimate neighbor nodes.After that Reverse-TransE is constructed to encode embedding vectors of the edges connected to intimate neighborhood nodes.Secondly, a multi-fusion method based on smoothed neighborhood information is constructed.Each node in the original graph is smoothed together with its neighbor nodes.The smoothed original graph is multi-fused with multiple twin graphs. Finally, a strategy of label adaptive adjustment is proposed to select the label embedding vectors for input to the next-generation trainer by comparing accuracy.This strategy can improve the quality of graph embeddings while effectively avoiding the overfitting problem when processing high-dimensional data.AFEF_LAA is compared with the state-of-the-art algorithms on six graph datasets.Experimental results show that AFEF_LAA can achieve higher node classification accuracy.

BioSAM: Generating SAM Prompts From Superpixel Graph for Biological Instance Segmentation.

Proposal-free instance segmentation methods have significantly advanced the field of biological image analysis. Recently, the Segment Anything Model (SAM) has shown an extraordinary ability to handle challenging instance boundaries. However, directly applying SAM to biological images that contain instances with complex morphologies and dense distributions fails to yield satisfactory results. In this work, we propose BioSAM, a new biological instance segmentation framework generating SAM prompts from a superpixel graph. Specifically, to avoid over-merging, we first generate sufficient superpixels as graph nodes and construct an initialized graph. We then generate initial prompts from each superpixel and aggregate them through a graph neural network (GNN) by predicting the relationship of superpixels to avoid over-segmentation. We employ the SAM encoder embeddings and the SAM-assisted superpixel similarity as new features for the graph to enhance its discrimination capability. With the graph-based prompt aggregation, we utilize the aggregated prompts in SAM to refine the segmentation and generate more accurate instance boundaries. Comprehensive experiments on four representative biological datasets demonstrate that our proposed method outperforms state-of-the-art methods.

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.

Comprehensive Graph Gradual Pruning for Sparse Training in Graph Neural Networks.

Graph neural networks (GNNs) tend to suffer from high computation costs due to the exponentially increasing scale of graph data and a large number of model parameters, which restricts their utility in practical applications. To this end, some recent works focus on sparsifying GNNs (including graph structures and model parameters) with the lottery ticket hypothesis (LTH) to reduce inference costs while maintaining performance levels. However, the LTH-based methods suffer from two major drawbacks: 1) they require exhaustive and iterative training of dense models, resulting in an extremely large training computation cost, and 2) they only trim graph structures and model parameters but ignore the node feature dimension, where vast redundancy exists. To overcome the above limitations, we propose a comprehensive graph gradual pruning framework termed CGP. This is achieved by designing a during-training graph pruning paradigm to dynamically prune GNNs within one training process. Unlike LTH-based methods, the proposed CGP approach requires no retraining, which significantly reduces the computation costs. Furthermore, we design a cosparsifying strategy to comprehensively trim all the three core elements of GNNs: graph structures, node features, and model parameters. Next, to refine the pruning operation, we introduce a regrowth process into our CGP framework, to reestablish the pruned but important connections. The proposed CGP is evaluated over a node classification task across six GNN architectures, including shallow models [graph convolutional network (GCN) and graph attention network (GAT)], shallow-but-deep-propagation models [simple graph convolution (SGC) and approximate personalized propagation of neural predictions (APPNP)], and deep models [GCN via initial residual and identity mapping (GCNII) and residual GCN (ResGCN)], on a total of 14 real-world graph datasets, including large-scale graph datasets from the challenging Open Graph Benchmark (OGB). Experiments reveal that the proposed strategy greatly improves both training and inference efficiency while matching or even exceeding the accuracy of the existing methods.

Exploiting Neighbor Effect: Conv-Agnostic GNN Framework for Graphs With Heterophily.

Due to the homophily assumption in graph convolution networks (GCNs), a common consensus in the graph node classification task is that graph neural networks (GNNs) perform well on homophilic graphs but may fail on heterophilic graphs with many interclass edges. However, the previous interclass edges' perspective and related homo-ratio metrics cannot well explain the GNNs' performance under some heterophilic datasets, which implies that not all the interclass edges are harmful to GNNs. In this work, we propose a new metric based on the von Neumann entropy to reexamine the heterophily problem of GNNs and investigate the feature aggregation of interclass edges from an entire neighbor identifiable perspective. Moreover, we propose a simple yet effective Conv-Agnostic GNN framework (CAGNNs) to enhance the performance of most GNNs on the heterophily datasets by learning the neighbor effect for each node. Specifically, we first decouple the feature of each node into the discriminative feature for downstream tasks and the aggregation feature for graph convolution (GC). Then, we propose a shared mixer module to adaptively evaluate the neighbor effect of each node to incorporate the neighbor information. The proposed framework can be regarded as a plug-in component and is compatible with most GNNs. The experimental results over nine well-known benchmark datasets indicate that our framework can significantly improve performance, especially for the heterophily graphs. The average performance gain is 9.81%, 25.81%, and 20.61% compared with graph isomorphism network (GIN), graph attention network (GAT), and GCN, respectively. Extensive ablation studies and robustness analysis further verify the effectiveness, robustness, and interpretability of our framework. Code is available at https://github.com/JC-202/CAGNN.

Hierarchical Graph Neural Network: A Lightweight Image Matching Model with Enhanced Message Passing of Local and Global Information in Hierarchical Graph Neural Networks

Graph Neural Networks (GNNs) have gained popularity in image matching methods, proving useful for various computer vision tasks like Structure from Motion (SfM) and 3D reconstruction. A well-known example is SuperGlue. Lightweight variants, such as LightGlue, have been developed with a focus on stacking fewer GNN layers compared to SuperGlue. This paper proposes the h-GNN, a lightweight image matching model, with improvements in the two processing modules, the GNN and matching modules. After image features are detected and described as keypoint nodes of a base graph, the GNN module, which primarily aims at increasing the h-GNN’s depth, creates successive hierarchies of compressed-size graphs from the base graph through a clustering technique termed SC+PCA. SC+PCA combines Principal Component Analysis (PCA) with Spectral Clustering (SC) to enrich nodes with local and global information during graph clustering. A dual non-contrastive clustering loss is used to optimize graph clustering. Additionally, four message-passing mechanisms have been proposed to only update node representations within a graph cluster at the same hierarchical level or to update node representations across graph clusters at different hierarchical levels. The matching module performs iterative pairwise matching on the enriched node representations to obtain a scoring matrix. This matrix comprises scores indicating potential correct matches between the image keypoint nodes. The score matrix is refined with a ‘dustbin’ to further suppress unmatched features. There is a reprojection loss used to optimize keypoint match positions. The Sinkhorn algorithm generates a final partial assignment from the refined score matrix. Experimental results demonstrate the performance of the proposed h-GNN against competing state-of-the-art (SOTA) GNN-based methods on several image matching tasks under homography, estimation, indoor and outdoor camera pose estimation, and 3D reconstruction on multiple datasets. Experiments also demonstrate improved computational memory and runtime, approximately 38.1% and 26.14% lower than SuperGlue, and an average of about 6.8% and 7.1% lower than LightGlue. Future research will explore the effects of integrating more recent simplicial message-passing mechanisms, which concurrently update both node and edge representations, into our proposed model.

Optimizing the Effectiveness of Moving Target Defense in a Probabilistic Attack Graph: A Deep Reinforcement Learning Approach

Moving target defense (MTD) technology baffles potential attacks by dynamically changing the software in use and/or its configuration while maintaining the application’s running states. But it incurs a deployment cost and various performance overheads, degrading performance. An attack graph is capable of evaluating the balance between the effectiveness and cost of an MTD deployment. In this study, we consider a network scenario in which each node in the attack graph can deploy MTD technology. We aim to achieve MTD deployment effectiveness optimization (MTD-DO) in terms of minimizing the network security loss under a limited budget. The existing related works either considered only a single node for deploying an MTD or they ignored the deployment cost. We first establish a non-linear MTD-DO formulation. Then, two deep reinforcement learning-based algorithms are developed, namely, deep Q-learning (DQN) and proximal policy optimization (PPO). Moreover, two metrics are defined in order to effectively evaluate MTD-DO algorithms with varying network scales and budgets. The experimental results indicate that both PPO- and DQN-based algorithms perform better than Q-learning-based and random algorithms. The DQN-based algorithm converges more quickly and performs, in terms of reward, marginally better than the PPO-based algorithm.

Graph Node Scoring for the Analysis and Visualisation of Mobility Networks and Data

Graph Node Scoring for the Analysis and Visualisation of Mobility Networks and Data

Approximate sequential optimization for informative path planning

We consider the problem of finding an informative path through a graph, given initial and terminal nodes and a given maximum path length. We assume that a linear noise corrupted measurement is taken at each node of an underlying unknown vector that we wish to estimate. The informativeness is measured by the reduction in uncertainty in our estimate, evaluated using several Gaussian process-based metrics. We present a convex relaxation for this informative path planning problem, which we can readily solve to obtain a bound on the possible performance. We develop an approximate sequential method where the path is constructed segment by segment through dynamic programming. This involves solving an orienteering problem, with the node reward acting as a surrogate for informativeness, taking the first step, and then repeating the process. The method scales to very large problem instances and achieves performance close to the bound produced by the convex relaxation. We also demonstrate our method’s ability to handle adaptive objectives, multimodal sensing, and multi-agent variations of the informative path planning problem.

Denoising Alignment with Large Language Model for Recommendation

The mainstream approach of GNN-based recommendation aggregates high-order ID information associated with the node in the user-item graph. The aggregation pattern using ID as signal has two disadvantages: lack of textual semantics and the impact of interaction noise. These disadvantages pose a threat to effectively learn user preferences, especially in capturing intricate user-item semantic relationships. Although large language models (LLMs) allow the integration of rich textual information into recommenders and have had groundbreaking applications in recommender systems, current works need to bridge the gap between different representation spaces. This is because LLMs-based methods align the representations of GNN-based models only by using text embedding of LLM, leading to unsatisfactory results. To address this challenge, we propose a D enoising A lignment framework with L LMs for GNN-based R ecommenders (DALR), which aims to align structural representation with textual representation and mitigate the effects of noise. Specifically, We propose a modeling framework that integrates the representation of graph structure with textual information from LLMs to capture intricate user-item interactions. We also suggest an alignment paradigm to enhance representation performance by aligning semantic signals from LLMs and structural features from GNN models. Additionally, we introduce a contrastive learning scheme to relieve the impact of noise and improve model performance. Extensive experiments on public datasets demonstrate that our model consistently outperforms the state-of-the-art methods. DALR achieves improvements ranging from 2.82% to 12.20% in Recall@5 and from 1.04% to 3.48% in NDCG@5 compared to the strongest baseline model, using the Steam dataset as an example.

A short-term wind power prediction method via self-adaptive adjacency matrix and spatiotemporal graph neural networks

Graph neural networks (GNN) recently have been successfully applied in wind power prediction by employing geo-information to construct the graphs that serve as the GNN-based prediction model. However, these graphs cannot maintain the latent correlation and attribute of the wind turbines, leading to inferior performance. This research proposes an optimizing wind power prediction model through attention mechanism and spatiotemporal graph neural networks. Initially, the spectral clustering and a self-adjacency matrix to construct the graph nodes and edges. Subsequently, the proposed ASTGNN combined from graph convolutional networks and a gated recurrent unit with an attention mechanism is designed to act as the prediction model. A comprehensive set of experiments has been carried out and the proposed method not only improved prediction accuracy but also enhanced computational efficiency. According to the results obtained, the developed model demonstrated an improvement that is up to 13 % in terms of RMSE and 6.7 % in terms of computation time compared to the latest models.

Advancing microbial diagnostics: a universal phylogeny guided computational algorithm to find unique sequences for precise microorganism detection.

Sequences derived from organisms sharing common evolutionary origins exhibit similarity, while unique sequences, absent in related organisms, act as good diagnostic marker candidates. However, the approach focused on identifying dissimilar regions among closely-related organisms poses challenges as it requires complex multiple sequence alignments, making computation and parsing difficult. To address this, we have developed a biologically inspired universal NAUniSeq algorithm to find the unique sequences for microorganism diagnosis by traveling through the phylogeny of life. Mapping through a phylogenetic tree ensures a low number of cross-contamination and false positives. We have downloaded complete taxonomy data from Taxadb database and sequence data from National Center for Biotechnology Information Reference Sequence Database (NCBI-Refseq) and, with the help of NetworkX, created a phylogenetic tree. Sequences were assigned over the graph nodes, k-mers were created for target and non-target nodes and search was performed over the graph using the depth first search algorithm. In a memory efficient alternative NoSQL approach, we created a collection of Refseq sequences in MongoDB database using tax-id and path of FASTA files. We queried the MongoDB collection for the target and non-target sequences. In both the approaches, we used an alignment free sliding window k-mer-based procedure that quickly compares k-mers of target and non-target sequences and returns unique sequences that are not present in the non-target. We have validated our algorithm with target nodes Mycobacterium tuberculosis, Neisseria gonorrhoeae, and Monkeypox and generated unique sequences. This universal algorithm is a powerful tool for generating diagnostic sequences, enabling the accurate identification of microbial strains with high phylogenetic precision.