An efficient mining algorithm for maximal frequent patterns in uncertain graph database

2020 ◽  
Vol 39 (5) ◽  
pp. 7021-7033
Author(s):  
Feng Li
Keyword(s):  
State Of The Art ◽  
Cost Savings ◽  
Search Tree ◽  
Subgraph Isomorphism ◽  
Frequent Patterns ◽  
Graph Database ◽  
Graph Databases ◽  
Uncertain Graph ◽  
Mining Algorithm ◽  
Real World Datasets

Mining maximal frequent patterns is significant in many fields, but the mining efficiency is often low. The bottleneck lies in too many candidate subgraphs and extensive subgraph isomorphism tests. In this paper we propose an efficient mining algorithm. There are two key ideas behind the proposed methods. The first is to divide each edge of every certain graph (converted from equivalent uncertain graph) and build search tree, avoiding too many candidate subgraphs. The second is to search the tree built in the first step in order, avoiding extensive subgraph isomorphism tests. The evaluation of our approach demonstrates the significant cost savings with respect to the state-of-the-art approach not only on the real-world datasets as well as on synthetic uncertain graph databases.

scholarly journals G-Tric: generating three-way synthetic datasets with triclustering solutions

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
João Lobo ◽  
Rui Henriques ◽  
Sara C. Madeira
Keyword(s):  
State Of The Art ◽  
Synthetic Data ◽  
Ground Truth ◽  
Real Data ◽  
Three Dimensions ◽  
Additional Advantage ◽  
Urban Dynamics ◽  
Data Generator ◽  
Real World Datasets ◽  
Synthetic Datasets

Abstract Background Three-way data started to gain popularity due to their increasing capacity to describe inherently multivariate and temporal events, such as biological responses, social interactions along time, urban dynamics, or complex geophysical phenomena. Triclustering, subspace clustering of three-way data, enables the discovery of patterns corresponding to data subspaces (triclusters) with values correlated across the three dimensions (observations $$\times$$ × features $$\times$$ × contexts). With increasing number of algorithms being proposed, effectively comparing them with state-of-the-art algorithms is paramount. These comparisons are usually performed using real data, without a known ground-truth, thus limiting the assessments. In this context, we propose a synthetic data generator, G-Tric, allowing the creation of synthetic datasets with configurable properties and the possibility to plant triclusters. The generator is prepared to create datasets resembling real 3-way data from biomedical and social data domains, with the additional advantage of further providing the ground truth (triclustering solution) as output. Results G-Tric can replicate real-world datasets and create new ones that match researchers needs across several properties, including data type (numeric or symbolic), dimensions, and background distribution. Users can tune the patterns and structure that characterize the planted triclusters (subspaces) and how they interact (overlapping). Data quality can also be controlled, by defining the amount of missing, noise or errors. Furthermore, a benchmark of datasets resembling real data is made available, together with the corresponding triclustering solutions (planted triclusters) and generating parameters. Conclusions Triclustering evaluation using G-Tric provides the possibility to combine both intrinsic and extrinsic metrics to compare solutions that produce more reliable analyses. A set of predefined datasets, mimicking widely used three-way data and exploring crucial properties was generated and made available, highlighting G-Tric’s potential to advance triclustering state-of-the-art by easing the process of evaluating the quality of new triclustering approaches.

scholarly journals TransET: Knowledge Graph Embedding with Entity Types

Electronics ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1407
Author(s):  
Peng Wang ◽  
Jing Zhou ◽  
Yuzhang Liu ◽  
Xingchen Zhou
Keyword(s):  
Link Prediction ◽  
State Of The Art ◽  
Score Function ◽  
Graph Embedding ◽  
Vector Spaces ◽  
Knowledge Graph ◽  
Semantic Features ◽  
Knowledge Graphs ◽  
Real World Datasets ◽  
Low Dimensional

Knowledge graph embedding aims to embed entities and relations into low-dimensional vector spaces. Most existing methods only focus on triple facts in knowledge graphs. In addition, models based on translation or distance measurement cannot fully represent complex relations. As well-constructed prior knowledge, entity types can be employed to learn the representations of entities and relations. In this paper, we propose a novel knowledge graph embedding model named TransET, which takes advantage of entity types to learn more semantic features. More specifically, circle convolution based on the embeddings of entity and entity types is utilized to map head entity and tail entity to type-specific representations, then translation-based score function is used to learn the presentation triples. We evaluated our model on real-world datasets with two benchmark tasks of link prediction and triple classification. Experimental results demonstrate that it outperforms state-of-the-art models in most cases.

scholarly journals Density Guarantee on Finding Multiple Subgraphs and Subtensors

2021 ◽  
Vol 15 (5) ◽  
pp. 1-32
Author(s):  
Quang-huy Duong ◽  
Heri Ramampiaro ◽  
Kjetil Nørvåg ◽  
Thu-lan Dam
Keyword(s):  
Lower Bound ◽  
State Of The Art ◽  
The State ◽  
The Other ◽  
Exact Methods ◽  
Practical Solution ◽  
Novel Approach ◽  
Wide Range ◽  
Real World Datasets ◽  
Tensor Data

Dense subregion (subgraph & subtensor) detection is a well-studied area, with a wide range of applications, and numerous efficient approaches and algorithms have been proposed. Approximation approaches are commonly used for detecting dense subregions due to the complexity of the exact methods. Existing algorithms are generally efficient for dense subtensor and subgraph detection, and can perform well in many applications. However, most of the existing works utilize the state-or-the-art greedy 2-approximation algorithm to capably provide solutions with a loose theoretical density guarantee. The main drawback of most of these algorithms is that they can estimate only one subtensor, or subgraph, at a time, with a low guarantee on its density. While some methods can, on the other hand, estimate multiple subtensors, they can give a guarantee on the density with respect to the input tensor for the first estimated subsensor only. We address these drawbacks by providing both theoretical and practical solution for estimating multiple dense subtensors in tensor data and giving a higher lower bound of the density. In particular, we guarantee and prove a higher bound of the lower-bound density of the estimated subgraph and subtensors. We also propose a novel approach to show that there are multiple dense subtensors with a guarantee on its density that is greater than the lower bound used in the state-of-the-art algorithms. We evaluate our approach with extensive experiments on several real-world datasets, which demonstrates its efficiency and feasibility.

scholarly journals Advantages of using graph databases to explore chromatin conformation capture experiments

2021 ◽  
Vol 22 (S2) ◽  
Author(s):  
Daniele D’Agostino ◽  
Pietro Liò ◽  
Marco Aldinucci ◽  
Ivan Merelli
Keyword(s):  
Web Application ◽  
High Throughput Sequencing ◽  
Cell Types ◽  
Graph Database ◽  
Graph Databases ◽  
Sources Of Information ◽  
Chromosome Conformation ◽  
Wide Scale ◽  
User Friendly ◽  
Different Cell Types

Abstract Background High-throughput sequencing Chromosome Conformation Capture (Hi-C) allows the study of DNA interactions and 3D chromosome folding at the genome-wide scale. Usually, these data are represented as matrices describing the binary contacts among the different chromosome regions. On the other hand, a graph-based representation can be advantageous to describe the complex topology achieved by the DNA in the nucleus of eukaryotic cells. Methods Here we discuss the use of a graph database for storing and analysing data achieved by performing Hi-C experiments. The main issue is the size of the produced data and, working with a graph-based representation, the consequent necessity of adequately managing a large number of edges (contacts) connecting nodes (genes), which represents the sources of information. For this, currently available graph visualisation tools and libraries fall short with Hi-C data. The use of graph databases, instead, supports both the analysis and the visualisation of the spatial pattern present in Hi-C data, in particular for comparing different experiments or for re-mapping omics data in a space-aware context efficiently. In particular, the possibility of describing graphs through statistical indicators and, even more, the capability of correlating them through statistical distributions allows highlighting similarities and differences among different Hi-C experiments, in different cell conditions or different cell types. Results These concepts have been implemented in NeoHiC, an open-source and user-friendly web application for the progressive visualisation and analysis of Hi-C networks based on the use of the Neo4j graph database (version 3.5). Conclusion With the accumulation of more experiments, the tool will provide invaluable support to compare neighbours of genes across experiments and conditions, helping in highlighting changes in functional domains and identifying new co-organised genomic compartments.

scholarly journals Applying graph database technology for analyzing perturbed co-expression networks in cancer

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Claire M Simpson ◽  
Florian Gnad
Keyword(s):  
Relational Databases ◽  
Molecular Mechanisms ◽  
Biological Data ◽  
Database Management System ◽  
Graph Database ◽  
Graph Databases ◽  
Graph Representations ◽  
Rnaseq Data ◽  
Database Technology ◽  
Speed Accuracy

Abstract Graph representations provide an elegant solution to capture and analyze complex molecular mechanisms in the cell. Co-expression networks are undirected graph representations of transcriptional co-behavior indicating (co-)regulations, functional modules or even physical interactions between the corresponding gene products. The growing avalanche of available RNA sequencing (RNAseq) data fuels the construction of such networks, which are usually stored in relational databases like most other biological data. Inferring linkage by recursive multiple-join statements, however, is computationally expensive and complex to design in relational databases. In contrast, graph databases store and represent complex interconnected data as nodes, edges and properties, making it fast and intuitive to query and analyze relationships. While graph-based database technologies are on their way from a fringe domain to going mainstream, there are only a few studies reporting their application to biological data. We used the graph database management system Neo4j to store and analyze co-expression networks derived from RNAseq data from The Cancer Genome Atlas. Comparing co-expression in tumors versus healthy tissues in six cancer types revealed significant perturbation tracing back to erroneous or rewired gene regulation. Applying centrality, community detection and pathfinding graph algorithms uncovered the destruction or creation of central nodes, modules and relationships in co-expression networks of tumors. Given the speed, accuracy and straightforwardness of managing these densely connected networks, we conclude that graph databases are ready for entering the arena of biological data.

scholarly journals Chi-Squared Distance Metric Learning for Histogram Data

2015 ◽  
Vol 2015 ◽  
pp. 1-12 ◽  
Author(s):  
Wei Yang ◽  
Luhui Xu ◽  
Xiaopan Chen ◽  
Fengbin Zheng ◽  
Yang Liu
Keyword(s):  
Nearest Neighbor ◽  
State Of The Art ◽  
Metric Learning ◽  
Nearest Neighbors ◽  
Distance Metric Learning ◽  
Distance Metric ◽  
Projected Gradient Method ◽  
Proper Distance ◽  
Chi Squared ◽  
Real World Datasets

Learning a proper distance metric for histogram data plays a crucial role in many computer vision tasks. The chi-squared distance is a nonlinear metric and is widely used to compare histograms. In this paper, we show how to learn a general form of chi-squared distance based on the nearest neighbor model. In our method, the margin of sample is first defined with respect to the nearest hits (nearest neighbors from the same class) and the nearest misses (nearest neighbors from the different classes), and then the simplex-preserving linear transformation is trained by maximizing the margin while minimizing the distance between each sample and its nearest hits. With the iterative projected gradient method for optimization, we naturally introduce thel2,1norm regularization into the proposed method for sparse metric learning. Comparative studies with the state-of-the-art approaches on five real-world datasets verify the effectiveness of the proposed method.

scholarly journals A Rule-based Conversion of an EER Schema to Neo4j Schema Constraints

2021 ◽  
Author(s):  
Telmo Henrique Valverde da Silva ◽  
Ronaldo dos Santos Mello
Keyword(s):  
Data Model ◽  
Design Methodology ◽  
A Priori ◽  
Database Management System ◽  
Conversion Process ◽  
Graph Database ◽  
Graph Databases ◽  
Rule Based ◽  
Promising Solution ◽  
Entity Relationship

Several application domains hold highly connected data, like supply chain and social network. In this context, NoSQL graph databases raise as a promising solution since relationships are first class citizens in their data model. Nevertheless, a traditional database design methodology initially defines a conceptual schema of the domain data, and the Enhanced Entity-Relationship (EER) model is a common tool. This paper presents a rule-based conversion process from an EER schema to Neo4j schema constraints, as Neo4j is the most representative NoSQL graph database management system with an expressive data model. Different from related work, our conversion process deals with all EER model concepts and generates rules for ensuring schema constraints through a set of Cypher instructions ready to run into a Neo4j database instance, as Neo4J is a schemaless system, and it is not possible to create a schema a priori. We also present an experimental evaluation that demonstrates the viability of our process in terms of performance.

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