Walks In Graphs Research Articles

Hermitian random walk graph Fourier transform for directed graphs and its applications

Signal processing on directed graphs present additional challenges since a complete set of eigenvectors is unavailable generally. To solve this problem, in this paper, a novel graph Fourier transform is constructed for representing and processing signals on directed graphs. Firstly, we introduce a Hermitian random walk Laplacian operator and derive that it is Hermitian positive semi-definite. Hence, the obtained Laplacian operator is diagonalizable and yields orthogonal eigenvectors as graph Fourier basis. Secondly, we propose the Hermitian random walk graph Fourier transform (HRWGFT) with good properties including unitary and preserving inner products. Furthermore, HRWGFT records the directionality of edges without sacrificing the information about the graph signal. Then, using these favorable properties, we derive spectral convolution to define the graph filter which is the core tool for processing graph signals. Finally, based on the proposed Laplacian matrix and HRWGFT, we present several applications on synthetic and real-world networks, including signal denoising, data classification. The rationality and validity of our work are verified by simulations.

Drug–target interaction prediction through fine-grained selection and bidirectional random walk methodology

The study of drug–target interaction plays an important role in the process of drug development. The subject of DTI forecasting has advanced significantly in the last several years, yielding numerous significant research findings and methodologies. Heterogeneous data sources provide richer information and comprehensive perspectives for drug–target interaction prediction, so many existing methods rely on heterogeneous networks, and graph embedding technology becomes an important technology to extract information from heterogeneous networks. These approaches, however, are less concerned with potential noisy information in heterogeneous networks and more focused on the extent of information extraction in those networks. Based on this, a potential DTI predictive network model called FBRWPC is proposed in this paper. It uses a fine-grained similarity selection program to first integrate similarity on similar networks and then a bidirectional random walk graph embedding learning method with restart to obtain an updated drug target interaction matrix. Through the use of similarity selection and fine-grained selection similarity integration, the framework can effectively filter out the noise present in heterogeneous networks and enhance the model's prediction performance. The experimental findings demonstrate that, even after being split up into four distinct types of data sets, FBRWPC can still retain great prediction performance, a sign of the model's resilience and good generalization.

Optimizing wireless sensor networks using centrality metrics: a strategic approach

This research paper presents a methodology for improving wireless sensor network (WSN) performance by leveraging centrality measures, including degree, betweenness, closeness, eigenvector, and Katz centrality. Employing a random walk graph model, this study constructs networks with 30 and 50 nodes to investigate the impact of these centrality metrics on routing decisions to optimize energy efficiency, minimize latency, and enhance overall network reliability. Additionally, the paper provides a comprehensive analysis of the relationships among these centrality measures through various correlation techniques, such as Pearson correlation, Kendall rank correlation, and Spearman correlation, offering insights into how these metrics can effectively improve WSN operations.

Failing to Hash Into Supersingular Isogeny Graphs

Abstract An important open problem in supersingular isogeny-based cryptography is to produce, without a trusted authority, concrete examples of ‘hard supersingular curves’ that is equations for supersingular curves for which computing the endomorphism ring is as difficult as it is for random supersingular curves. A related open problem is to produce a hash function to the vertices of the supersingular $\ell $-isogeny graph, which does not reveal the endomorphism ring, or a path to a curve of known endomorphism ring. Such a hash function would open up interesting cryptographic applications. In this paper, we document a number of (thus far) failed attempts to solve this problem, in the hope that we may spur further research, and shed light on the challenges and obstacles to this endeavour. The mathematical approaches contained in this article include: (i) iterative root-finding for the supersingular polynomial; (ii) gcd’s of specialized modular polynomials; (iii) using division polynomials to create small systems of equations; (iv) taking random walks in the isogeny graph of abelian surfaces, and applying Kummer surfaces and (v) using quantum random walks.

Multi-view contrastive learning with virtual social group influence for social recommendation

Social recommendation systems leverage user–item interaction and user–user social network data to model user preferences and provide recommendations. Previous research has shown that capturing the influence of high-order neighbors and social groups in social networks can help model user preferences. However, challenges still exist in identifying important high-order neighbors from many candidates and modeling social group influence without direct information on social groups. This paper proposes a Multi-view Contrastive Learning with Social Group Influence (MCLSGI) method to address these challenges. Our approach uses a graph walk method to identify users’ virtual social groups and a GNN-based framework to model user preferences in different views, capturing the influence of direct and high-order neighbors as well as social groups. We also adopt multi-view contrastive learning to fuse users’ preferences in different views. We conducted experiments on two real-world datasets (Ciao and Epinions) to validate our method’s effectiveness. Compared to the best baseline, we improved by 1.39% and 1.21% with MAE, and 1.79% and 0.96% with RMSE.

Hub‐aware random walk graph embedding methods for classification

AbstractIn the last two decades, we are witnessing a huge increase of valuable big data structured in the form of graphs or networks. To apply traditional machine learning and data analytic techniques to such data it is necessary to transform graphs into vector‐based representations that preserve the most essential structural properties of graphs. For this purpose, a large number of graph embedding methods have been proposed in the literature. Most of them produce general‐purpose embeddings suitable for a variety of applications such as node clustering, node classification, graph visualization and link prediction. In this article, we propose two novel graph embedding algorithms based on random walks that are specifically designed for the node classification problem. Random walk sampling strategies of the proposed algorithms have been designed to pay special attention to hubs–high‐degree nodes that have the most critical role for the overall connectedness in large‐scale graphs. The proposed methods are experimentally evaluated by analyzing the classification performance of three classification algorithms trained on embeddings of real‐world networks. The obtained results indicate that our methods considerably improve the predictive power of examined classifiers compared with currently the most popular random walk method for generating general‐purpose graph embeddings (node2vec).

Weighted Jump in Random Walk graph sampling

Graph sampling is a challenging problem in network analysis due to the complex structures of networks. Currently, a series of graph sampling algorithms based on random walks achieve good results in graph sampling tasks. However, the existing methods often reduce the conductance of graphs, causing the sampler to stay in the same node for a long time. This results in undersampling. In this paper, we propose a novel Weighted Jump Random Walk (WJRW) algorithm to generate representative samples. We design a parameter in the WJRW algorithm that can adjust the proportions of random walk and random jump in every step. According to the issue of repeated sample nodes in the Generalized Maximum Degree (GMD) method and the problem of large deviations in the Simple Random Walk (SRW), WJRW addresses the weaknesses of the GMD method and enhances the diffusion of a random walker on graphs, leading to a more representative sample. Then, WJRW addresses the issue of large deviations in SRW and enhances the efficiency of the unbiased estimator. By generating smoother stationary distributions. Numerical experiments with extensive real-world networks verify that our method achieves higher accuracy than classical and state-of-the-art methods in estimating distribution estimation.

Collaborative Learning in General Graphs With Limited Memorization: Complexity, Learnability, and Reliability

We consider a <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$K$</tex-math> </inline-formula> -armed bandit problem in general graphs where agents are arbitrarily connected and each of them has limited memorizing capabilities and communication bandwidth. The goal is to let each of the agents eventually learn the best arm. Although recent studies show the power of collaboration among the agents in improving the efficacy of learning, it is assumed in these studies that the communication graph should be complete or well-structured, whereas such an assumption is not always valid in practice. Furthermore, limited memorization and communication bandwidth also restrict the collaborations of the agents, since the agents memorize and communicate very few experiences. Additionally, an agent may be corrupted to share falsified experiences to its peers, while the resource limit in terms of memorization and communication may considerably restrict the reliability of the learning process. To address the above issues, we propose a three-staged collaborative learning algorithm. In each step, the agents share their latest experiences with each other through light-weight random walks in a general communication graph, and then make decisions on which arms to pull according to the recommendations received from their peers. The agents finally update their adoptions (i.e., preferences to the arms) based on the reward obtained by pulling the arms. Our theoretical analysis shows that, when there are a sufficient number of agents participating in the collaborative learning process, all the agents eventually learn the best arm with high probability, even with limited memorizing capabilities and light-weight communications. We also reveal in our theoretical analysis the upper bound on the number of corrupted agents our algorithm can tolerate. The efficacy of our proposed three-staged collaborative learning algorithm is finally verified by extensive experiments on both synthetic and real datasets.

A Graph-Based Context-Aware Model to Understand Online Conversations

Online forums that allow for participatory engagement between users have been transformative for the public discussion of many important issues. However, such conversations can sometimes escalate into full-blown exchanges of hate and misinformation. Existing approaches in natural language processing (NLP), such as deep learning models for classification tasks, use as inputs only a single comment or a pair of comments depending upon whether the task concerns the inference of properties of the individual comments or the replies between pairs of comments, respectively. However, in online conversations, comments and replies may be based on external context beyond the immediately relevant information that is input to the model. Therefore, being aware of the conversations’ surrounding contexts should improve the model’s performance for the inference task at hand. We propose GraphNLI , 1 a novel graph-based deep learning architecture that uses graph walks to incorporate the wider context of a conversation in a principled manner. Specifically, a graph walk starts from a given comment and samples “nearby” comments in the same or parallel conversation threads, which results in additional embeddings that are aggregated together with the initial comment’s embedding. We then use these enriched embeddings for downstream NLP prediction tasks that are important for online conversations. We evaluate GraphNLI on two such tasks - polarity prediction and misogynistic hate speech detection - and find that our model consistently outperforms all relevant baselines for both tasks. Specifically, GraphNLI with a biased root-seeking random walk performs with a macro- F 1 score of 3 and 6 percentage points better than the best-performing BERT-based baselines for the polarity prediction and hate speech detection tasks, respectively. We also perform extensive ablative experiments and hyperparameter searches to understand the efficacy of GraphNLI. This demonstrates the potential of context-aware models to capture the global context along with the local context of online conversations for these two tasks.

Infinite collision property for the three-dimensional uniform spanning tree

Let [Formula: see text] be the three-dimensional uniform spanning tree, whose probability law is denoted by [Formula: see text]. For [Formula: see text]-a.s. realization of [Formula: see text], the recurrence of the simple random walk on [Formula: see text] is proved in Benjamini et al. (2001) [I. Benjamini, R. Lyons, Y. Peres and O. Schramm, Uniform spanning forests, Ann. Probab. 29(1) (2001) 1–65] and it is also demonstrated in Hutchcroft and Peres (2015) [T. Hutchcroft and Y. Peres, Collisions of random walks in reversible random graphs, Electron. Commun. Probab. 20(63) (2015) 1–6] that two independent simple random walks on [Formula: see text] collide infinitely often. In this paper, we will give a quantitative estimate on the number of collisions of two independent simple random walks on [Formula: see text], which provides another proof of the infinite collision property of [Formula: see text].

NLRRC: A Novel Clustering Method of Jointing Non-Negative LRR and Random Walk Graph Regularized NMF for Single-Cell Type Identification.

The development of single-cell RNA sequencing (scRNA-seq) technology has opened up a new perspective for us to study disease mechanisms at the single cell level. Cell clustering reveals the natural grouping of cells, which is a vital step in scRNA-seq data analysis. However, the high noise and dropout of single-cell data pose numerous challenges to cell clustering. In this study, we propose a novel matrix factorization method named NLRRC for single-cell type identification. NLRRC joins non-negative low-rank representation (LRR) and random walk graph regularized NMF (RWNMFC) to accurately reveal the natural grouping of cells. Specifically, we find the lowest rank representation of single-cell samples by non-negative LRR to reduce the difficulty of analyzing high-dimensional samples and capture the global information of the samples. Meanwhile, by using random walk graph regularization (RWGR) and NMF, RWNMFC captures manifold structure and cluster information before generating a cluster allocation matrix. The cluster assignment matrix contains cluster labels, which can be used directly to get the clustering results. The performance of NLRRC is validated on simulated and real single-cell datasets. The results of the experiments illustrate that NLRRC has a significant advantage in single-cell type identification.

Quantum algorithm for de novo DNA sequence assembly based on quantum walks on graphs

De novo DNA sequence assembly is based on finding paths in overlap graphs, which is a NP-hard problem. We developed a quantum algorithm for de novo assembly based on quantum walks in graphs. The overlap graph is partitioned repeatedly to smaller graphs that form a hierarchical structure. We use quantum walks to find paths in low rank graphs and a quantum algorithm that finds Hamiltonian paths in high hierarchical rank. We tested the partitioning quantum algorithm, as well as the quantum algorithm that finds Hamiltonian paths in high hierarchical rank and confirmed its correct operation using Qiskit. We developed a custom simulation for quantum walks to search for paths in low rank graphs. The approach described in this paper may serve as a basis for the development of efficient quantum algorithms that solve the de novo DNA assembly problem.

Matrix Encryption Walks for Lightweight Cryptography

In this paper, we propose a new symmetric stream cipher encryption algorithm based on Graph Walks and 2-dimensional matrices, called Matrix Encryption Walks (MEW). We offer example Key Matrices and show the efficiency of the proposed method, which operates in linear complexity with an extremely large key space and low-resource requirements. We also provide the Proof of Concept code for the encryption algorithm and a detailed analysis of the security of our proposed MEW. The MEW algorithm is designed for low-resource environments such as IoT or smart devices and is therefore intended to be simple in operation. The encryption, decryption, and key generation time, along with the bytes required to store the key, are all discussed, and similar proposed algorithms are examined and compared. We further discuss the avalanche effect, key space, frequency analysis, Shannon entropy, and chosen/known plaintext-ciphertext attacks, and how MEW remains robust against these attacks. We have also discussed the potential for future research into algorithms such as MEW, which make use of alternative structures and graphic methods for improving encryption models.

ARGLRR: A Sparse Low-Rank Representation Single-Cell RNA-Sequencing Data Clustering Method Combined with a New Graph Regularization.

The development of single-cell transcriptome sequencing technologies has opened new ways to study biological phenomena at the cellular level. A key application of such technologies involves the employment of single-cell RNA sequencing (scRNA-seq) data to identify distinct cell types through clustering, which in turn provides evidence for revealing heterogeneity. Despite the promise of this approach, the inherent characteristics of scRNA-seq data, such as higher noise levels and lower coverage, pose major challenges to existing clustering methods and compromise their accuracy. In this study, we propose a method called Adjusted Random walk Graph regularization Sparse Low-Rank Representation (ARGLRR), a practical sparse subspace clustering method, to identify cell types. The fundamental low-rank representation (LRR) model is concerned with the global structure of data. To address the limited ability of the LRR method to capture local structure, we introduced adjusted random walk graph regularization in its framework. ARGLRR allows for the capture of both local and global structures in scRNA-seq data. Additionally, the imposition of similarity constraints into the LRR framework further improves the ability of the proposed model to estimate cell-to-cell similarity and capture global structural relationships between cells. ARGLRR surpasses other advanced comparison approaches on nine known scRNA-seq data sets judging by the results. In the normalized mutual information and Adjusted Rand Index metrics on the scRNA-seq data sets clustering experiments, ARGLRR outperforms the best-performing comparative method by 6.99% and 5.85%, respectively. In addition, we visualize the result using Uniform Manifold Approximation and Projection. Visualization results show that the usage of ARGLRR enhances the separation of different cell types within the similarity matrix.

Exposing the Self-Supervised Space-Time Correspondence Learning via Graph Kernels

Self-supervised space-time correspondence learning is emerging as a promising way of leveraging unlabeled video. Currently, most methods adapt contrastive learning with mining negative samples or reconstruction adapted from the image domain, which requires dense affinity across multiple frames or optical flow constraints. Moreover, video correspondence predictive models require mining more inherent properties in videos, such as structural information. In this work, we propose the VideoHiGraph, a space-time correspondence framework based on a learnable graph kernel. Concerning the video as the spatial-temporal graph, the learning objectives of VideoHiGraph are emanated in a self-supervised manner for predicting unobserved hidden graphs via graph kernel manner. We learn a representation of the temporal coherence across frames in which pairwise similarity defines the structured hidden graph, such that a biased random walk graph kernel along the sub-graph can predict long-range correspondence. Then, we learn a refined representation across frames on the node-level via a dense graph kernel. The self-supervision of the model training is formed by the structural and temporal consistency of the graph. VideoHiGraph achieves superior performance and demonstrates its robustness across the benchmark of label propagation tasks involving objects, semantic parts, keypoints, and instances. Our algorithm implementations have been made publicly available at https://github.com/zyqin19/VideoHiGraph.

An Algorithm for the Numbers of Homomorphisms from Paths to Rectangular Grid Graphs

Let G and H be graphs. A mapping f from the vertices of G to the vertices of H is known as a homomorphism from G to H if, for every pair of adjacent vertices x and y in G, the vertices f(x) and f(y) are adjacent in H. A rectangular grid graph is the Cartesian product of two path graphs. In this paper, we provide a formula to determine the number of homomorphisms from paths to rectangular grid graphs. This formula gives the solution to the problem concerning the number of walks in the rectangular grid graphs.

Representation Learning of Enhanced Graphs Using Random Walk Graph Convolutional Network

Nowadays, graph structure data has played a key role in machine learning because of its simple topological structure, and therefore, the graph representation learning methods have attracted great attention. And it turns out that the low-dimensional embedding representation obtained by graph representation learning is extremely useful in various typical tasks, such as node classification and content recommendation. However, most of the existing methods do not further dig out potential structural information on the original graph structure. Here, we propose wGCN, which utilizes random walk to obtain the node-specific mesoscopic structures (high-order local structure) of the graph and utilizes these mesoscopic structures to enhance the graph and organize the characteristic information of the nodes. Our method can effectively generate node embedding for data of previously unknown categories, which has been proven in a series of experiments conducted on many types of graph networks. And compared to baselines, our method shows the best performance on most datasets and achieves competitive results on others. It is believed that combining the mesoscopic structure to further explore the structural information of the graph will greatly improve the learning efficiency of the graph neural network.

Joint L2,p-norm and random walk graph constrained PCA for single-cell RNA-seq data

The development and widespread utilization of high-throughput sequencing technologies in biology has fueled the rapid growth of single-cell RNA sequencing (scRNA-seq) data over the past decade. The development of scRNA-seq technology has significantly expanded researchers’ understanding of cellular heterogeneity. Accurate cell type identification is the prerequisite for any research on heterogeneous cell populations. However, due to the high noise and high dimensionality of scRNA-seq data, improving the effectiveness of cell type identification remains a challenge. As an effective dimensionality reduction method, Principal Component Analysis (PCA) is an essential tool for visualizing high-dimensional scRNA-seq data and identifying cell subpopulations. However, traditional PCA has some defects when used in mining the nonlinear manifold structure of the data and usually suffers from over-density of principal components (PCs). Therefore, we present a novel method in this paper called joint -norm and random walk graph constrained PCA (RWPPCA). RWPPCA aims to retain the data’s local information in the process of mapping high-dimensional data to low-dimensional space, to more accurately obtain sparse principal components and to then identify cell types more precisely. Specifically, RWPPCA combines the random walk (RW) algorithm with graph regularization to more accurately determine the local geometric relationships between data points. Moreover, to mitigate the adverse effects of dense PCs, the -norm is introduced to make the PCs sparser, thus increasing their interpretability. Then, we evaluate the effectiveness of RWPPCA on simulated data and scRNA-seq data. The results show that RWPPCA performs well in cell type identification and outperforms other comparison methods.

Global eigenvalue fluctuations of random biregular bipartite graphs

We compute the eigenvalue fluctuations of uniformly distributed random biregular bipartite graphs with fixed and growing degrees for a large class of analytic functions. As a key step in the proof, we obtain a total variation distance bound for the Poisson approximation of the number of cycles and cyclically non-backtracking walks in random biregular bipartite graphs, which might be of independent interest. We also prove a semicircle law for random [Formula: see text]-biregular bipartite graphs when [Formula: see text]. As an application, we translate the results to adjacency matrices of uniformly distributed random regular hypergraphs.

Counting Homomorphic Cycles in Degenerate Graphs

Since counting subgraphs in general graphs is, by and large, a computationally demanding problem, it is natural to try and design fast algorithms for restricted families of graphs. One such family that has been extensively studied is that of graphs of bounded degeneracy (e.g., planar graphs). This line of work, which started in the early 80’s, culminated in a recent work of Gishboliner et al., which highlighted the importance of the task of counting homomorphic copies of cycles (i.e., cyclic walks) in graphs of bounded degeneracy. Our main result in this paper is a surprisingly tight relation between the above task and the well-studied problem of detecting (standard) copies of directed cycles in general directed graphs. More precisely, we prove the following: One can compute the number of homomorphic copies of C 2k and C 2k+1 in n -vertex graphs of bounded degeneracy in time Õ( n d k ), where the fastest known algorithm for detecting directed copies of C k in general m -edge digraphs runs in time Õ( m d k ). Conversely, one can transform any O(n b k ) algorithm for computing the number of homomorphic copies of C 2k or of C 2k+1 in n -vertex graphs of bounded degeneracy, into an Õ( m b k ) time algorithm for detecting directed copies of C k in general m -edge digraphs. We emphasize that our first result does not use a black-box reduction (as opposed to the second result which does). Instead, we design an algorithm for computing the number of C k -homomorphisms in degenerate graphs and show that one part of its analysis can be reduced to the analysis of the fastest known algorithm for detecting directed cycles in general digraphs, which was carried out in a recent breakthrough of Dalirrooyfard, Vuong and Vassilevska Williams. As a by-product of our algorithm, we obtain a new algorithm for detecting k -cycles in directed and undirected graphs of bounded degeneracy that is faster than all previously known algorithms for 7 ≤ k ≤ 11, and faster for all k ≥ 7 if the matrix multiplication exponent is 2.