Graph Embedding Algorithms Research Articles

EPCO-40. TRANSCRIPTIONAL TRAJECTORY INFERENCE OF IMAGE-LOCALIZED, MULTI-REGIONAL HIGH-GRADE GLIOMA BIOPSIES REVEALS DISTINCT POPULATION ECOLOGIES AND SEX-ASSOCIATED ENRICHED PATHWAYS

Abstract The intra- and inter-patient heterogeneity in high-grade glioma (HGG) continues to contribute to its poor prognosis. Clinical biopsies are often harvested from limited regions and typically are not image localized. Thus, they fail to capture the diversity within tumor regions, immune expression or normal cell abundances that play key roles in tumor development. It is important to gain an understanding of these subpopulation ecologies, their spatial resolution, and interactions between them that may then be exploited for future therapeutic benefit. Further, these may differ by patient characteristics such as sex, age at diagnosis and treatment status. Using an ongoing image-localized biopsy collection protocol, we have so far evaluated the bulk transcriptomics of 202 multi-regional biopsies from 58 patients to characterize HGG heterogeneity. These samples were processed through Monocle, a reverse graph embedding algorithm that groups samples into states and orders them along developmental trajectories. Deconvolution methods were previously used to predict relative abundances of 7 normal, 6 glioma, and 5 immune cell subpopulations for each sample, which we have now overlaid on the Monocle graph. Monocle classified HGG into 4 main states along a three-pronged trajectory. These states reveal distinct population ecologies with associated enriched gene pathways. We also note significant immune pathway enrichments that differ between state and patient-reported sex. Together, these algorithms reveal a simple transcriptomic trajectory that helps us understand the development and evolution of HGG. Characterizing the in vivo diversity within and between high grade gliomas is important for understanding prognosis, stratifying future treatments and ultimately improving patient outcome.

PLANARITY AND ITS APPLICATIONS: INVESTIGATING THE BOUNDARIES OF GRAPH EMBEDDINGS

Graph theory plays a critical role in numerous applications, particularly in understanding and analyzing the structural properties of networks. This paper focuses on the concept of planarity in graph theory, exploring how certain graphs can be embedded in a plane without edge crossings. The study investigates the criteria that determine graph planarity, including Kuratowski's and Wagner's theorems, and examines the implications of these concepts in various fields such as network design, circuit layout, and geography. Additionally, the paper delves into advanced techniques for testing planarity and embedding graphs in surfaces with higher genus, thus pushing the boundaries of how graph embeddings can be utilized in both theoretical and practical contexts. Through an in-depth analysis of graph embedding algorithms, real-world applications are discussed to highlight the importance of planarity in optimizing spatial layouts and reducing complexity in network structures. The results of this research demonstrate the vast potential of planar graphs in solving complex problems efficiently.

A Novel Method for Mining Regulatory sRNAs Related to Rice Resistance Against Blast Fungus from Multi-Omics Data

Background: Due to infection by the rice blast fungus, rice, a major global staple, faces yield challenges. While chemical control methods are common, their environmental and economic costs are growing concerns. Traditional biological experiments are also inefficient for exploring resistance genes. Therefore, understanding the interaction between rice and the rice blast fungus is urgent and important. Objective: This study aims to use multi-omics data to uncover key elements in rice's defense against rice blast fungus Magnaporthe oryzae. We built a detailed, multi-layered heterogeneous interaction network, employing an innovative graph embedding feature with a cross-layer random walk algorithm to identify crucial crucial resistance factors.This could inform strategies for enhancing disease resistance in rice. objective: This study aims to use multi-omics data to uncover key elements in rice's defense against rice blast fungus Magnaporthe oryzae. We built a detailed, multi-layered heterogeneous interaction network, employing an innovative graph embedding feature with a cross-layer random walk algorithm, to identify crucial crucial resistance factors. This could inform strategies for enhancing disease resistance in rice. Methods: We integrated genomics, transcriptomics, and proteomics data on Magnaporthe oryzae infecting rice. This multi-omics data was used to construct a multi-layer heterogeneous network.An advanced graph embedding algorithm (BINE) provided rich vector representations of network nodes. A multi-layer network walking algorithm was then used to analyze the network and identify key regulatory small RNA (sRNAs) in rice. Results: Node similarity rankings allowed us to identify significant regulatory sRNAs in rice that are integral to disease resistance. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses further revealed their roles in biological processes and key metabolic pathways.Our integrative method precisely and efficiently identified these crucial elements, offering a valuable systems biology tool. Conclusion: By integrating multi-omics data with computational analysis, this study reveals key regulatory sRNAs in rice's disease resistance mechanism. These findings enhance our understanding of rice disease resistance and provide genetic resources for breeding disease-resistant rice. Despite limitations in sRNA functional interpretation, this research demonstrates the power of applying multi- omics data to address complex biological problems.

MathEagle: Accurate prediction of drug-drug interaction events via multi-head attention and heterogeneous attribute graph learning

BackgroundDrug-drug interaction events influence the effectiveness of drug combinations and can lead to unexpected side effects or exacerbate underlying diseases, jeopardizing patient prognosis. Most existing methods are restricted to predicting whether two drugs interact or the type of drug-drug interactions, while very few studies endeavor to predict the specific risk levels of side effects of drug combinations. MethodsIn this study, we propose MathEagle, a novel approach to predict accurate risk levels of drug combinations based on multi-head attention and heterogeneous attribute graph learning. Initially, we model drugs and three distinct risk levels between drugs as a heterogeneous information graph. Subsequently, behavioral and chemical structure features of drugs are utilized by message passing neural networks and graph embedding algorithms, respectively. Ultimately, MathEagle employs heterogeneous graph convolution and multi-head attention mechanisms to learn efficient latent representations of drug nodes and estimates the risk levels of pairwise drugs in an end-to-end manner. ResultsTo assess the effectiveness and robustness of the model, five-fold cross-validation, ablation experiments, and case studies were conducted. MathEagle achieved an accuracy of 85.85 % and an AUC of 0.9701 on the drug risk level prediction task and is superior to all comparative models. The MathEagle predictor is freely accessible at http://120.77.11.78/MathEagle/. ConclusionsThe experimental results indicate that MathEagle can function as an effective tool for predicting accurate risk of drug combinations, aiding in guiding clinical medication, and enhancing patient outcomes.

VCGERG

Vulnerability can lead to data loss, privacy leakage and financial loss. Accurate detection and identification of vulnerabilities is essential to prevent information leakage and APT attacks. This paper explores the possibility of digging the valuable information in vulnerability reports deeply. We propose a new model, VCGERG, which products a graph using key information from vulnerability reports and embeds the graph into the vector space using a keywords-LINE graph embedding algorithm based on the attention of neighboring nodes. VCGERG model uses the OVR random forest algorithm to classify vulnerabilities. Our model can get the complicated local and global information of the graph in large-scale dataset and achieve better results. In order to verify the effectiveness of our model, it is evaluated on many experiments. Compared with other models, our method has a higher accuracy rate of 0.975.

Artificial Intelligence and Machine Learning in Financial Services: Risk Management and Fraud Detection

The field of financial risk management is undergoing a significant transformation due to the advancements in artificial intelligence (AI) and the underlying machine learning (ML) techniques that provide the foundation of AI. These developments hold the potential to revolutionize the way the user’s approach and address financial risk. The expansion of AI-driven solutions has opened up various opportunities for comprehending and managing risk. These opportunities encompass a wide range of activities, such as determining appropriate lending amounts for customers in banking, issuing warning signals to financial market traders regarding position risk, identifying instances of customer and insider fraud, enhancing compliance efforts, and mitigating model risk. The prime objective of this study is to investigate the application of AI and ML in the Financial Services industry, with a specific focus on Risk Management and Fraud Detection. This study proposes an intelligent and distributed approach for detecting Internet financial fraud using Big Data. The methodology entails the utilization of the graph embedding algorithm Node2Vec for the purpose of acquiring knowledge and representing the structural characteristics of the financial network graph in the form of compact vectors with reduced dimensions. This facilitates the intelligent and effective categorization and forecasting of data samples from a dataset of significant magnitude through the utilization of a deep neural network. Based on the study's findings, it was observed that the F1-Score test outcomes obtained from the Node2Vec algorithm range from 67.1% to 73.4%. These results surpass the outcomes achieved by the other two algorithms used for comparison. This finding demonstrates that Node2Vec has greater stability in terms of overall performance and yields superior categorization outcomes.

Particle Swarm Optimization for 5g and Beyond

Network embedding assigns nodes in a network to low dimensional representations and effectively preserves the network structure. Recently, a significant amount of progresses has been made toward this emerging network analysis paradigm. In this survey, we focus on categorizing and then reviewing the current development on network embedding methods, and point out its future research directions. We first summarize the motivation of network embedding. Particle Swarm Optimization (PSO) algorithm is used as the proposed method. We discuss the classical graph embedding algorithms on cognitive radio environment and their relationship with network embedding. Afterwards and primarily, we provide a comprehensive overview of a large number of networks embedding methods in a systematic manner, covering the structure- and property-preserving network embedding methods, the network embedding methods with side information and the advanced information preserving network embedding methods. Moreover, several evaluation approaches for network embedding and some useful online resources, including the network data sets and software, are reviewed, too. Finally, we discuss the framework of exploiting these network embedding methods to build an effective system and point out some potential future directions. Key Word: Particle Swarm Optimization (PSO), Beyond 5G (B5G), Internet of Think (IOT), Machine Learning (ML)etc..

Graph Representations for Reinforcement Learning

Graph analysis is becoming increasingly important due to the expressive power of graph models and the efficient algorithms available for processing them. Reinforcement Learning is one domain that could benefit from advancements in graph analysis, given that a learning agent may be integrated into an environment that can be represented as a graph. Nevertheless, the structural irregularity of graphs and the lack of prior labels make it difficult to integrate such a model into modern Reinforcement Learning frameworks that rely on artificial neural networks. Graph embedding enables the learning of low-dimensional vector representations that are more suited for machine learning algorithms, while retaining essential graph features. This paper presents a framework for evaluating graph embedding algorithms and their ability to preserve the structure and relevant features of graphs by means of an internal validation metric, without resorting to subsequent tasks that require labels for training. Based on this framework, three defined algorithms that meet the necessary requirements for solving a specific problem of Reinforcement Learning in graphs are selected, analyzed, and compared. These algorithms are Graph2Vec, GL2Vec, and Wavelet Characteristics, with the latter two demonstrating superior performance.

MTS2Graph: Interpretable multivariate time series classification with temporal evolving graphs

Conventional time series classification approaches based on bags of patterns or shapelets face significant challenges in dealing with a vast amount of feature candidates from high-dimensional multivariate data. In contrast, deep neural networks can learn low-dimensional features efficiently, and in particular, convolutional neural networks have shown promising results in classifying multivariate time series data. A key factor in the success of deep neural networks is this astonishing expressive power. However, this power comes at the cost of complex, black-boxed models, conflicting with the goals of building reliable and human-understandable models. In this work11The code can be found at https://github.com/raneeny/MTS2Graph., we introduce a new interpretable framework for multivariate time series data that by extracting and clustering the input quantifies the contribution of time-varying input variables and each signal’s role to the classification. We construct a graph that captures the temporal relationship between the extracted patterns for each layer and propose an effective merging strategy to aggregate those graphs into one. Finally, a graph embedding algorithm generates new representations of the created interpretable time-series features. Our extensive experiments indicate the benefit of our time-aware graph-based representation in multivariate time series classification while enriching them with more interpretability.

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).

GC-CDSS: Personalized gastric cancer treatment recommendations system based on knowledge graph

BackgroundGastric cancer (GC) is one of the most common malignant tumors in the world, posing a serious threat to human health. Currently, gastric cancer treatment strategies emphasize a multidisciplinary team (MDT) consultation approach. However, there are numerous treatment guidelines and insights from clinical trials. The application of AI-based Clinical Decision Support System (CDSS) in tumor diagnosis and screening is increasing rapidly. ObjectiveThe purpose of this study is to (1) summarize the treatment decision process for GC according to the treatment guidelines in China, and then create a knowledge graph (KG) for GC, (2) based on aforementioned KG, built a CDSS and conducted an initial feasibility evaluation for the current system. MethodsFirstly, we summarized the decision-making process for treatment of GC. Then, we extracted relevant decision nodes and relationships and utilized Neo4j to create the KG. After obtaining the initial node features for building the graph embedding model, graph embedding algorithm, such as Node2Vec and GraphSAGE, were used to construct the GC-CDSS. At last, a retrospective cohort study was used to compare the consistency between GC-CDSS and MDT in treatment decision making. ResultsIn current study, we introduce a GC-CDSS, which is constructed based on Chinese GC treatment guidelines knowledge graph (KG). In the KG, we define four types of nodes and four types of relationships, and it comprise a total of 207 nodes and 300 relationships. Regarding GC-CDSS, the system is capable of providing dynamic and personalized diagnostic and treatment recommendations based on the patient's condition. Furthermore, a retrospective cohort study is conducted to compare GC-CDSS recommendations with those of the MDT group, the overall consistency rate of treatment recommendations between the auxiliary decision system and MDT team is 92.96%. ConclusionsWe construct a GC treatment support system, GC-CDSS, based on KG. The GC-CDSS may help oncologists make treatment decisions more efficient and promote standardization in primary healthcare settings.

CR-TransR: A Knowledge Graph Embedding Model for Cultural Domain

As a combination of information computing technology and the cultural field, cultural computing is gaining more attention. The knowledge graph is also gradually applied as a particular data structure in the cultural area. Based on the domain knowledge graph data of the Beijing Municipal Social Science Project “Mining and Utilization of Cultural Resources in the Ancient Capital of Beijing,” this article proposes a graph representation learning model CR-TransR that integrates cultural attributes. Through the analysis of the data in the cultural field of the ancient capital of Beijing, a cultural feature dictionary is constructed, and a domain-specific feature matrix is constructed in the form of word vector splicing. The feature matrix is used to constrain the embedding graph model TransR, and then the feature matrix and the TransR model are jointly trained to complete the embedded expression of the knowledge graph. Finally, a comparative experiment is carried out on the Beijing ancient capital cultural knowledge graph dataset and the effects of the classic graph embedding algorithms TransE, TransH, and TransR. At the same time, we try to reproduce the embedding method with the core idea of neighbor node information aggregation as the core idea, and CRTransR are compared. The experimental tasks include link prediction and triplet classification, and the experimental results show that the CRTransR model performs better.

Biolinguistic graph fusion model for circRNA-miRNA association prediction.

Emerging clinical evidence suggests that sophisticated associations with circular ribonucleic acids (RNAs) (circRNAs) and microRNAs (miRNAs) are a critical regulatory factor of various pathological processes and play a critical role in most intricate human diseases. Nonetheless, the above correlations via wet experiments are error-prone and labor-intensive, and the underlying novel circRNA-miRNA association (CMA) has been validated by numerous existing computational methods that rely only on single correlation data. Considering the inadequacy of existing machine learning models, we propose a new model named BGF-CMAP, which combines the gradient boosting decision tree with natural language processing and graph embedding methods to infer associations between circRNAs and miRNAs. Specifically, BGF-CMAP extracts sequence attribute features and interaction behavior features by Word2vec and two homogeneous graph embedding algorithms, large-scale information network embedding and graph factorization, respectively. Multitudinous comprehensive experimental analysis revealed that BGF-CMAP successfully predicted the complex relationship between circRNAs and miRNAs with an accuracy of 82.90% and an area under receiver operating characteristic of 0.9075. Furthermore, 23 of the top 30 miRNA-associated circRNAs of the studies on data were confirmed in relevant experiences, showing that the BGF-CMAP model is superior to others. BGF-CMAP can serve as a helpful model to provide a scientific theoretical basis for the study of CMA prediction.

A Missing Traffic Data Imputation Method Based on a Diffusion Convolutional Neural Network–Generative Adversarial Network

Traffic state data are key to the proper operation of intelligent transportation systems (ITS). However, traffic detectors often receive environmental factors that cause missing values in the collected traffic state data. Therefore, aiming at the above problem, a method for imputing missing traffic state data based on a Diffusion Convolutional Neural Network–Generative Adversarial Network (DCNN-GAN) is proposed in this paper. The proposed method uses a graph embedding algorithm to construct a road network structure based on spatial correlation instead of the original road network structure; through the use of a GAN for confrontation training, it is possible to generate missing traffic state data based on the known data of the road network. In the generator, the spatiotemporal features of the reconstructed road network are extracted by the DCNN to realize the imputation. Two real traffic datasets were used to verify the effectiveness of this method, with the results of the proposed model proving better than those of the other models used for comparison.

Graph embedding and geometric deep learning relevance to network biology and structural chemistry.

Graphs are used as a model of complex relationships among data in biological science since the advent of systems biology in the early 2000. In particular, graph data analysis and graph data mining play an important role in biology interaction networks, where recent techniques of artificial intelligence, usually employed in other type of networks (e.g., social, citations, and trademark networks) aim to implement various data mining tasks including classification, clustering, recommendation, anomaly detection, and link prediction. The commitment and efforts of artificial intelligence research in network biology are motivated by the fact that machine learning techniques are often prohibitively computational demanding, low parallelizable, and ultimately inapplicable, since biological network of realistic size is a large system, which is characterised by a high density of interactions and often with a non-linear dynamics and a non-Euclidean latent geometry. Currently, graph embedding emerges as the new learning paradigm that shifts the tasks of building complex models for classification, clustering, and link prediction to learning an informative representation of the graph data in a vector space so that many graph mining and learning tasks can be more easily performed by employing efficient non-iterative traditional models (e.g., a linear support vector machine for the classification task). The great potential of graph embedding is the main reason of the flourishing of studies in this area and, in particular, the artificial intelligence learning techniques. In this mini review, we give a comprehensive summary of the main graph embedding algorithms in light of the recent burgeoning interest in geometric deep learning.

KSFinder-a knowledge graph model for link prediction of novel phosphorylated substrates of kinases.

Aberrant protein kinase regulation leading to abnormal substrate phosphorylation is associated with several human diseases. Despite the promise of therapies targeting kinases, many human kinases remain understudied. Most existing computational tools predicting phosphorylation cover less than 50% of known human kinases. They utilize local feature selection based on protein sequences, motifs, domains, structures, and/or functions, and do not consider the heterogeneous relationships of the proteins. In this work, we present KSFinder, a tool that predicts kinase-substrate links by capturing the inherent association of proteins in a network comprising 85% of the known human kinases. We also postulate the potential role of two understudied kinases based on their substrate predictions from KSFinder. KSFinder learns the semantic relationships in a phosphoproteome knowledge graph using a knowledge graph embedding algorithm and represents the nodes in low-dimensional vectors. A multilayer perceptron (MLP) classifier is trained to discern kinase-substrate links using the embedded vectors. KSFinder uses a strategic negative generation approach that eliminates biases in entity representation and combines data from experimentally validated non-interacting protein pairs, proteins from different subcellular locations, and random sampling. We assess KSFinder's generalization capability on four different datasets and compare its performance with other state-of-the-art prediction models. We employ KSFinder to predict substrates of 68 "dark" kinases considered understudied by the Illuminating the Druggable Genome program and use our text-mining tool, RLIMS-P along with manual curation, to search for literature evidence for the predictions. In a case study, we performed functional enrichment analysis for two dark kinases - HIPK3 and CAMKK1 using their predicted substrates. KSFinder shows improved performance over other kinase-substrate prediction models and generalized prediction ability on different datasets. We identified literature evidence for 17 novel predictions involving an understudied kinase. All of these 17 predictions had a probability score ≥0.7 (nine at >0.9, six at 0.8-0.9, and two at 0.7-0.8). The evaluation of 93,593 negative predictions (probability ≤0.3) identified four false negatives. The top enriched biological processes of HIPK3 substrates relate to the regulation of extracellular matrix and epigenetic gene expression, while CAMKK1 substrates include lipid storage regulation and glucose homeostasis. KSFinder outperforms the current kinase-substrate prediction tools with higher kinase coverage. The strategically developed negatives provide a superior generalization ability for KSFinder. We predicted substrates of 432 kinases, 68 of which are understudied, and hypothesized the potential functions of two dark kinases using their predicted substrates.

Insight extraction from e-Health bookings by means of Hypergraph and Machine Learning.

New technologies are transforming medicine, and this revolution starts with data. Usually, health services within public healthcare systems are accessed through a booking centre managed by local health authorities and controlled by the regional government. In this perspective, structuring e-health data through a Knowledge Graph (KG) approach can provide a feasible method to quickly and simply organize data and/or retrieve new information. Starting from raw health bookings data from the public healthcare system in Italy, a KG method is presented to support e-health services through the extraction of medical knowledge and novel insights. By exploiting graph embedding which arranges the various attributes of the entities into the same vector space, we are able to apply Machine Learning (ML) techniques to the embedded vectors. The findings suggest that KGs could be used to assess patients' medical booking patterns, either from unsupervised or supervised ML. In particular, the former can determine possible presence of hidden groups of entities that is not immediately available through the original legacy dataset structure. The latter, although the performance of the used algorithms is not very high, shows encouraging results in predicting a patient's likelihood to undergo a particular medical visit within a year. However, many technological advances remain to be made, especially in graph database technologies and graph embedding algorithms.

Graph embedding based on motif-aware feature propagation for community detection

Identifying communities plays an essential role in disclosing modular structures with specific functions or properties in different kinds of complex networks. However, the low accuracy can be attributed to the fact that traditional algorithms always pay more attention on networks’ structural information of lower-order, i.e. neglect that of higher-order. In this paper, we propose a novel algorithm, Graph Embedding based on Motif-aware Feature Propagation (GEMFP) for community detection. In graph embedding, the vector representation of each node in a graph is firstly initialized at random. Then, we reconstruct a weighted graph instead of the original one by considering the information of lower-order (adjacency interactions) as well as higher-order (motifs), which is further used to define the influence acceptance between nodes, and the representation of a node is determined by aggregating the information of its neighbors’ influence iteratively until the convergence of this process is reached. Finally, K-means algorithm is adopted to extract communities by using the above embedding information. We conduct extensive experiments on 14 real-world datasets, and the results show that our algorithm tends to be more effective for community detection compared with several traditional, and graph embedding algorithms. The code for GEMFP is accessible on GitHub at https://github.com/zhanghan1020/GEMFP.

Integrating platforms through content-based graph representation learning

The advancements in education technology have encouraged businesses to offer a wide range of educational resources aimed at teaching labor market-related skills. However, the ever-changing abundance of information in both course and job platforms makes it difficult for job seekers to identify the right learning resources for a particular job opportunity. As a result, it is important to integrate and analyze information from both platforms to recommend suitable courses and jobs to them. Meanwhile, integrating information from these distinct platforms for analysis purposes poses a challenge due to the presentation of data in free text. Previous studies have mainly focused on downstream tasks in one area and few have integrated both of them. Additionally, linking skills from these platforms through methods such as crowdsourcing or annotation mechanisms may not be reliable due to potential biases or inconsistencies. This study proposes a novel approach to integrate data from course and job advertising platforms using graph representation learning and embedding algorithms. The proposed approach predicts the relationship between the two platforms and has been tested in the form of link prediction tasks using several graph learning methods with RMSE scores below 0.1 and AUC scores between 70-75%. These results imply that our approach can be further refined and has the potential to be used in building recommendation systems that help address the problem of information overload among students and job seekers.

Local intrinsic dimensionality measures for graphs, with applications to graph embeddings

The notion of local intrinsic dimensionality (LID) is an important advancement in data dimensionality analysis, with applications in data mining, machine learning and similarity search problems. Existing distance-based LID estimators were designed for tabular datasets encompassing data points represented as vectors in a Euclidean space. After discussing their limitations for graph-structured data considering graph embeddings and graph distances, we propose NC-LID, a novel LID-related measure for quantifying the discriminatory power of the shortest-path distance with respect to natural communities of nodes as their intrinsic localities. It is shown how this measure can be used to design LID-aware graph embedding algorithms by formulating two LID-elastic variants of node2vec with personalized hyperparameters that are adjusted according to NC-LID values. Our empirical analysis of NC-LID on a large number of real-world graphs shows that this measure is able to point to nodes with high link reconstruction errors in node2vec embeddings better than node centrality metrics. The experimental evaluation also shows that the proposed LID-elastic node2vec extensions improve node2vec by better preserving graph structure in generated embeddings.