Search results for: multiplex graph

Authors: Montaceur Zaghdoud, Mohamed Moussaoui, Jalel Akaichi

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Frequent subgraph mining refers usually to graph matching and it is widely used in when analyzing big data with large graphs. A lot of research works dealt with structural exact or inexact graph matching but a little attention is paid to semantic matching when graph vertices and/or edges are attributed and typed. Therefore, it seems very interesting to integrate background knowledge into the analysis and that extracted frequent subgraphs should become more pruned by applying a new semantic filter instead of using only structural similarity in graph matching process. Consequently, this paper focuses on developing a new hybrid approximate structuralsemantic graph matching to discover a set of frequent subgraphs. It uses simultaneously an approximate structural similarity function based on graph edit distance function and a possibilistic vertices similarity function based on affinity function. Both structural and semantic filters contribute together to prune extracted frequent set. Indeed, new hybrid structural-semantic frequent subgraph mining approach searches will be suitable to be applied to several application such as community detection in social networks.

Keywords: approximate graph matching, hybrid frequent subgraph mining, graph mining, possibility theory

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Authors: David Pham, Yongfeng Zhang

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Graphs are an important structure for data storage and computation. Recent years have seen the success of deep learning on graphs such as Graph Neural Networks (GNN) on various data mining and machine learning tasks. However, most of the deep learning models on graphs cannot easily explain their predictions and are thus often labelled as “black boxes.” For example, Graph Attention Network (GAT) is a frequently used GNN architecture, which adopts an attention mechanism to carefully select the neighborhood nodes for message passing and aggregation. However, it is difficult to explain why certain neighbors are selected while others are not and how the selected neighbors contribute to the final classification result. In this paper, we present a graph learning model called Explainable Graph Attention Network (XGAT), which integrates graph attention modeling and explainability. We use a single model to target both the accuracy and explainability of problem spaces and show that in the context of graph attention modeling, we can design a unified neighborhood selection strategy that selects appropriate neighbor nodes for both better accuracy and enhanced explainability. To justify this, we conduct extensive experiments to better understand the behavior of our model under different conditions and show an increase in both accuracy and explainability.

Keywords: explainable AI, graph attention network, graph neural network, node classification

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Authors: Zainab Yasir Al-Rekaby, Abdul Jalil M. Khalaf

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Coloring the vertices of a graph such that every two adjacent vertices have different color is a very common problem in the graph theory. This is known as proper coloring of graphs. The possible number of different proper colorings on a graph with a given number of colors can be represented by a function called the chromatic polynomial. Two graphs G and H are said to be chromatically equivalent, if they share the same chromatic polynomial. A Graph G is chromatically unique, if G is isomorphic to H for any graph H such that G is chromatically equivalent to H. The study of chromatically equivalent and chromatically unique problems is called chromaticity. This paper shows that a wheel W14 is chromatically unique.

Keywords: chromatic polynomial, chromatically Equivalent, chromatically unique, wheel

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Authors: A. I. Khalafalla, K. A. Al-Busada, I. M. El-Sabagh

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Pox and pox-like diseases of camels are a group of exanthematous skin conditions that have become increasingly important economically. They may be caused by three distinct viruses: camelpox virus (CMPV), camel contagious ecthyma virus (CCEV) and camel papillomavirus (CAPV). These diseases are difficult to differentiate based on clinical presentation in disease outbreaks. Molecular methods such as PCR targeting species-specific genes have been developed and used to identify CMPV and CCEV, but not simultaneously in a single tube. Recently, multiplex PCR has gained reputation as a convenient diagnostic method with cost- and time–saving benefits. In the present communication, we describe the development, optimization and validation a multiplex PCR assays able to detect simultaneously the genome of the three viruses in one single test allowing for rapid and efficient molecular diagnosis. The assay was developed based on the evaluation and combination of published and new primer sets, and was applied to the detection of 110 tissue samples. The method showed high sensitivity, and the specificity was confirmed by PCR-product sequencing. In conclusion, this rapid, sensitive and specific assay is considered a useful method for identifying three important viruses in specimens from camels and as part of a molecular diagnostic regime.

Keywords: multiplex PCR, diagnosis, pox and pox-like diseases, camels

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Authors: Kanokon Chaicom, Chitima Sirijerachai, Kanchana Chansung, Pinsuda Klangsang, Boonpeng Palaeng, Prajuab Chaimanee, Pimjai Ananta

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Chronic myeloid leukemia (CML) is characterized by the consistent involvement of the Philadelphia chromosome (Ph), which is derived from a reciprocal translocation between chromosome 9 and 22, the main product of the t(9;22) (q34;q11) translocation, is found in the leukemic clone of at least 95% of CML patients. There are two major forms of the BCR/ABL fusion gene, involving ABL exon 2, but including different exons of BCR gene. The transcripts b2a2 (e13a2) or b3a2 (e14a2) code for a p210 protein. Another fusion gene leads to the expression of an e1a2 transcript, which codes for a p190 protein. Other less common fusion genes are b3a3 or b2a3, which codes for a p203 protein and e19a2 (c3a2) transcript, which codes for a p230 protein. Its frequency varies in different populations. In this study, we aimed to report the frequency of BCR-ABL fusion transcript types with CML by multiplex PCR (polymerase chain reaction) in Srinagarind Hospital, Khon Kaen, Thailand. Multiplex PCR for BCR-ABL was performed on 58 patients, to detect different types of BCR-ABL transcripts of the t (9; 22). All patients examined were positive for some type of BCR/ABL rearrangement. The majority of the patients (93.10%) expressed one of the p210 BCR-ABL transcripts, b3a2 and b2a2 transcripts were detected in 53.45% and 39.65% respectively. The expression of an e1a2 transcript showed 3.75%. Co-expression of p210/p230 was detected in 3.45%. Co-expression of p210/p190 was not detected. Multiplex PCR is useful, saves time and reliable in the detection of BCR-ABL transcript types. The frequency of one or other rearrangement in CML varies in different population.

Keywords: chronic myeloid leukemia, BCR-ABL fusion transcript types, multiplex PCR, frequency of BCR-ABL fusion

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Authors: Junjie Zhong, Kai Hong, Lei Wang

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Passage Retrieval (PR) plays an important role in many Natural Language Processing (NLP) tasks. Traditional efficient retrieval models relying on exact term-matching, such as TF-IDF or BM25, have nowadays been exceeded by pre-trained language models which match by semantics. Though they gain effectiveness, deep language models often require large memory as well as time cost. To tackle the trade-off between efficiency and effectiveness in PR, this paper proposes Graph Passage Retriever (GraphPR), a graph-based model inspired by the development of graph learning techniques. Different from existing works, GraphPR is end-to-end and integrates both term-matching information and semantics. GraphPR constructs a passage-level graph from BM25 retrieval results and trains a GCN-like model on the graph with graph-based objectives. Passages were regarded as nodes in the constructed graph and were embedded in dense vectors. PR can then be implemented using embeddings and a fast vector-similarity search. Experiments on a variety of real-world retrieval datasets show that the proposed model outperforms related models in several evaluation metrics (e.g., mean reciprocal rank, accuracy, F1-scores) while maintaining a relatively low query latency and memory usage.

Keywords: efficiency, effectiveness, graph learning, language model, passage retrieval, term-matching model

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Authors: Soner Nandappa D., Ahmed Mohammed Naji

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In a graph G = (V, E), the distance from a vertex v to a vertex u is the length of shortest v to u path. The eccentricity e(v) of v is the distance to a farthest vertex from v. The diameter diam(G) is the maximum eccentricity. The k-distance neighborhood of v, for 0 ≤ k ≤ e(v), is Nk(v) = {u ϵ V (G) : d(v, u) = k}. In this paper, we introduce a new distance degree based topological polynomial of a graph G is called a k- distance neighborhood polynomial, denoted Nk(G, x). It is a polynomial with the coefficient of the term k, for 0 ≤ k ≤ e(v), is the sum of the cardinalities of Nk(v) for every v ϵ V (G). Some properties of k- distance neighborhood polynomials are obtained. Exact formulas of the k- distance neighborhood polynomial for some well-known graphs, Cartesian product and join of graphs are presented.

Keywords: vertex degrees, distance in graphs, graph operation, Nk-polynomials

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Authors: Shuo Liu

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In Chinese text classification tasks, redundant words and phrases can interfere with the formation of extracted and analyzed text information, leading to a decrease in the accuracy of the classification model. To reduce irrelevant elements, extract and utilize text content information more efficiently and improve the accuracy of text classification models. In this paper, the text in the corpus is first extracted using the TextRank algorithm for abstraction, the words in the abstract are used as nodes to construct a text graph, and then the graph attention network (GAT) is used to complete the task of classifying the text. Testing on a Chinese dataset from the network, the classification accuracy was improved over the direct method of generating graph structures using text.

Keywords: Chinese natural language processing, text classification, abstract extraction, graph attention network

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Authors: Mehrshad Khosraviani, Sepehr Najjarpour

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Considering the usage of graph-based approaches in systems and synthetic biology, and the various types of ‎the graphs employed by them, a comprehensive graph library based ‎on the three-tier architecture (3TA) was previously introduced for full representation of the biological systems. Although proposing a 3TA-based graph library, three following reasons motivated us to redesign the graph ‎library based on the service-oriented architecture (SOA): (1) Maintaining the accuracy of the data related to an input graph (including its edges, its ‎vertices, its topology, etc.) without involving the end user:‎ Since, in the case of using 3TA, the library files are available to the end users, they may ‎be utilized incorrectly, and consequently, the invalid graph data will be provided to the ‎computer algorithms. However, considering the usage of the SOA, the operation of the ‎graph registration is specified as a service by encapsulation of the library files. In other words, overall control operations needed for registration of the valid data will be the ‎responsibility of the services. (2) Partitioning of the library product into some different parts: Considering 3TA, a whole library product was provided in general. While here, the product ‎can be divided into smaller ones, such as an AND/OR graph drawing service, and each ‎one can be provided individually. As a result, the end user will be able to select any ‎parts of the library product, instead of all features, to add it to a project. (3) Reduction of the complexities: While using 3TA, several other libraries must be needed to add for connecting to the ‎database, responsibility of the provision of the needed library resources in the SOA-‎based graph library is entrusted with the services by themselves. Therefore, the end user ‎who wants to use the graph library is not involved with its complexity. In the end, in order to ‎make ‎the library easier to control in the system, and to restrict the end user from accessing the files, ‎it was preferred to use the service-oriented ‎architecture ‎‎(SOA) over the three-tier architecture (3TA) and to redevelop the previously proposed graph library based on it‎.

Keywords: Bio-Design Automation, Biological System, Graph Library, Service-Oriented Architecture, Systems and Synthetic Biology

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Authors: Shaowei Sun

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Let G be a graph with vertex set V(G)={v_1,v_2,...,v_n} and edge set E(G). For any vertex v belong to V(G), let d_v denote the degree of v. The normalized Laplacian matrix of the graph G is the matrix where the non-diagonal (i,j)-th entry is -1/(d_id_j) when vertex i is adjacent to vertex j and 0 when they are not adjacent, and the diagonal (i,i)-th entry is the di. In this paper, we discuss some bounds on the largest and the second smallest normalized Laplacian eigenvalue of trees and graphs. As following, we found some new bounds on the second smallest normalized Laplacian eigenvalue of tree T in terms of graph parameters. Moreover, we use Sage to give some conjectures on the second largest and the third smallest normalized eigenvalues of graph.

Keywords: graph, normalized Laplacian eigenvalues, normalized Laplacian matrix, tree

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Authors: Alfi Y. Zakiyyah, Hanni Garminia, M. Salman, A. N. Irawati

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In the terminology of the hypergraph, there is a relation with the terminology graph. In the theory of graph, the edges connected two vertices. In otherwise, in hypergraph, the edges can connect more than two vertices. There is representation matrix of a graph such as adjacency matrix, Laplacian matrix, and incidence matrix. The adjacency matrix is symmetry matrix so that all eigenvalues is real. This matrix is a nonnegative matrix. The all diagonal entry from adjacency matrix is zero so that the trace is zero. Another representation matrix of the graph is the Laplacian matrix. Laplacian matrix is symmetry matrix and semidefinite positive so that all eigenvalues are real and non-negative. According to the spectral study in the graph, some that result is generalized to hypergraph. A hypergraph can be represented by a matrix such as adjacency, incidence, and Laplacian matrix. Throughout for this term, we use Laplacian matrix to represent a complete tripartite hypergraph. The aim from this research is to determine second smallest eigenvalues from this matrix and find a relation this eigenvalue with the connectivity of that hypergraph.

Keywords: connectivity, graph, hypergraph, Laplacian matrix

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Authors: Walaa Obaidallah Alqarafi, Wafaa Mohammed Fakieh, Alaa Abdallah Altassan

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Algebraic graph theory is defined as a bridge between algebraic structures and graphs. It has several uses in many fields, including chemistry, physics, and computer science. The prime graph is a type of graph associated with a ring R, where the vertex set is the whole ring R, and two vertices x and y are adjacent if either xRy=0 or yRx=0. However, the investigation of the prime graph over rings remains relatively limited. The behavior of this graph in extended rings, like R[x] and R[[x]], where R is a non-commutative ring, deserves more attention because of the wider applicability in algebra and other mathematical fields. To study the prime graphs over polynomials and power series rings, we used a combination of ring-theoretic and graph-theoretic techniques. This paper focuses on two invariants: the diameter and the girth of these graphs. Furthermore, the work discusses how the graph structures change when passing from R to R[x] and R[[x]]. In our study, we found that the set of strong zero-divisors of ring R represents the set of vertices in prime graphs. Based on this discovery, we redefined the vertices of prime graphs using the definition of strong zero divisors. Additionally, our results show that although the prime graphs of R[x] and R[[x]] are comparable to the graph of R, they have different combinatorial characteristics since these extensions contain new strong zero-divisors. In particular, we find conditions in which the diameter and girth of the graphs, as they expand from R to R[x] and R[[x]], do not change or do change. In conclusion, this study shows how extending a non-commutative ring R to R[x] and R[[x]] affects the structure of their prime graphs, particularly in terms of diameter and girth. These findings enhance the understanding of the relationship between ring extensions and graph properties.

Keywords: prime graph, diameter, girth, polynomial ring, power series ring

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Authors: Shin-Shin Kao, Yuan-Kang Shih, Hsun Su

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In this paper, we show that the conjecture of Chv tal, which states that any 1-tough graph is either a Hamiltonian graph or its complement contains a specific graph denoted by F, does not hold in general. More precisely, it is true only for graphs with six or seven vertices, and is false for graphs with eight or more vertices. A theorem is derived as a correction for the conjecture.

Keywords: complement, degree sum, hamiltonian, tough

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Authors: Kay Thi Yar, Khin Mar Lar Tun

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Nowadays, social networks are so popular and widely used in all over the world. In addition, searching personal information of each person and searching connection between them (peoples’ relation in real world) becomes interesting issue in our society. In this paper, we propose a framework with three portions for exploring peoples’ relations from their connected information. The first portion focuses on the Graph database structure to store the connected data of peoples’ information. The second one proposes the graph database searching algorithm, the Modified-SoS-ACO (Sense of Smell-Ant Colony Optimization). The last portion proposes the Deductive Reasoning Algorithm to define two persons’ relationship. This study reveals the proper storage structure for connected information, graph searching algorithm and deductive reasoning algorithm to predict and analyze the personnel relationship from peoples’ relation in their connected information.

Keywords: personnel information, graph storage structure, graph searching algorithm, deductive reasoning algorithm

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Authors: Amir Bahrami

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In the fields of chemical graph theory, molecular topology, and mathematical chemistry, a topological index or a descriptor index also known as a connectivity index is a type of a molecular descriptor that is calculated based on the molecular graph of a chemical compound. Topological indices are numerical parameters of a graph which characterize its topology and are usually graph invariant. Topological indices are used for example in the development of quantitative structure-activity relationships (QSARs) in which the biological activity or other properties of molecules are correlated with their chemical structure. In this paper some descriptor index (descriptor index) of single-walled carbon nanotubes, is determined.

Keywords: chemical graph theory, molecular topology, molecular descriptor, single-walled carbon nanotubes

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Authors: Zheng Zhihao

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Recently, Knowledge Graph Framework Network (KGCN) has developed powerful capabilities in knowledge representation and reasoning tasks. However, traditional KGCN often uses a fixed weight mechanism when aggregating information, failing to make full use of rich structural information, resulting in a certain expression ability of node representation, and easily causing over-smoothing problems. In order to solve these challenges, the paper proposes an new graph neural network model called KGCN-STAR (Knowledge Graph Convolutional Network with Structural Adaptive Receptive Fields). This model dynamically adjusts the perception of each node by introducing a structural adaptive receptive field. wild range, and a subgraph aggregator is designed to capture local structural information more effectively. Experimental results show that KGCN-STAR shows significant performance improvement on multiple knowledge graph data sets, especially showing considerable capabilities in the task of representation learning of complex structures.

Keywords: knowledge graph, graph neural networks, structural adaptive receptive fields, information aggregation

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Authors: Shokofeh Ebrtahimi

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Let G be the chemical graph of a molecule. The matrix D = [dij ] is called the detour matrix of G, if dij is the length of longest path between atoms i and j. The sum of all entries above the main diagonal of D is called the detour index of G.Chemical graph theory is the topology branch of mathematical chemistry which applies graph theory to mathematical modelling of chemical phenomena.[1] The pioneers of the chemical graph theory are Alexandru Balaban, Ante Graovac, Ivan Gutman, Haruo Hosoya, Milan Randić and Nenad TrinajstićLet G be the chemical graph of a molecule. The matrix D = [dij ] is called the detour matrix of G, if dij is the length of longest path between atoms i and j. The sum of all entries above the main diagonal of D is called the detour index of G. In this paper, a new program for computing the detour index of molecular graphs of nanotubes by heptagons is determineded. Some Conjectures about detour index of Molecular graphs of nanotubes is included.

Keywords: chemical graph, detour matrix, Detour index, carbon nanotube

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Authors: Yingqi Cui, Changran Huang, Raymond Lee

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In this paper, we proposed an AI Tutor using ontology and natural language process techniques to generate a computer science domain knowledge graph and answer users’ questions based on the knowledge graph. We define eight types of relation to extract relationships between entities according to the computer science domain text. The AI tutor is separated into two agents: learning agent and Question-Answer (QA) agent and developed on JADE (a multi-agent system) platform. The learning agent is responsible for reading text to extract information and generate a corresponding knowledge graph by defined patterns. The QA agent can understand the users’ questions and answer humans’ questions based on the knowledge graph generated by the learning agent.

Keywords: artificial intelligence, natural Language processing, knowledge graph, intelligent agents, QA system

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Authors: Mustafa Elfituri, Jonathan Cook

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Recently, graph-based computations have become more important in large-scale scientific computing as they can provide a methodology to model many types of relations between independent objects. They are being actively used in fields as varied as biology, social networks, cybersecurity, and computer networks. At the same time, graph problems have some properties such as irregularity and poor locality that make their performance different than regular applications performance. Therefore, parallelizing graph algorithms is a hard and challenging task. Initial evidence is that standard computer architectures do not perform very well on graph algorithms. Little is known exactly what causes this. The Graph500 benchmark is a representative application for parallel graph-based computations, which have highly irregular data access and are driven more by traversing connected data than by computation. In this paper, we present results from analyzing the performance of various example implementations of Graph500, including a shared memory (OpenMP) version, a distributed (MPI) version, and a hybrid version. We measured and analyzed all the factors that affect its performance in order to identify possible changes that would improve its performance. Results are discussed in relation to what factors contribute to performance degradation.

Keywords: graph computation, graph500 benchmark, parallel architectures, parallel programming, workload characterization.

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Authors: Bin Sheng, Changhong Lu

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Let G be a simple undirected graph with no isolated vertex. A paired dominating set of G is a dominating set which induces a subgraph that has a perfect matching. The paired domination number of G, denoted by γₚᵣ(G), is the size of its smallest paired dominating set. Goddard and Henning conjectured that γₚᵣ(G) ≤ 4n/7 holds for every graph G with δ(G) ≥ 3, except the Petersen Graph. In this paper, we prove this conjecture for cubic graphs.

Keywords: paired dominating set, upper bound, cubic graphs, weight function

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Authors: Rihab Ben Lamine, Raoudha Ben Jemaa, Ikram Amous Ben Amor

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This paper proposes a graph planning technique for semantic adaptable Web Services composition. First, we use an ontology based context model for extending Web Services descriptions with information about the most suitable context for its use. Then, we transform the composition problem into a semantic context aware graph planning problem to build the optimal service composition based on user's context. The construction of the planning graph is based on semantic context aware Web Service discovery that allows for each step to add most suitable Web Services in terms of semantic compatibility between the services parameters and their context similarity with the user's context. In the backward search step, semantic and contextual similarity scores are used to find best composed Web Services list. Finally, in the ranking step, a score is calculated for each best solution and a set of ranked solutions is returned to the user.

Keywords: semantic web service, web service composition, adaptation, context, graph planning

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Authors: I. Gahlouz, A. Chellil

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The paper concerns the estimation of system components faults by using an unknown inputs observer. To reach this goal, we used the Bond Graph approach to physical modelling. We showed that this graphical tool is allowing the representation of system components faults as unknown inputs within the state representation of the considered physical system. The study of the causal and structural features of the system (controllability, observability, finite structure, and infinite structure) based on the Bond Graph approach was hence fulfilled in order to design an unknown inputs observer which is used for the system component fault estimation.

Keywords: estimation, bond graph, controllability, observability

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Authors: Shin-Shin Kao, Hsiu-Chunj Pan

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Given a graph G. A cycle of G is a sequence of vertices of G such that the first and the last vertices are the same. A hamiltonian cycle of G is a cycle containing all vertices of G. The graph G is k-ordered (resp. k-ordered hamiltonian) if for any sequence of k distinct vertices of G, there exists a cycle (resp. hamiltonian cycle) in G containing these k vertices in the specified order. Obviously, any cycle in a graph is 1-ordered, 2-ordered and 3-ordered. Thus the study of any graph being k-ordered (resp. k-ordered hamiltonian) always starts with k = 4. Most studies about this topic work on graphs with no real applications. To our knowledge, the chordal ring families were the first one utilized as the underlying topology in interconnection networks and shown to be 4-ordered [1]. Furthermore, based on computer experimental results in [1], it was conjectured that some of them are 4-ordered hamiltonian. In this paper, we intend to give some possible directions in proving the conjecture.

Keywords: Hamiltonian cycle, 4-ordered, Chordal rings, 3-regular

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Authors: Desouky Abd El Haleem, Sahar Zaki

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This work was conducted to develop a one-step multiplex PCR system for rapid, sensitive, and specific detection of three different bacterial pathogens, Escherichia coli, Pseudomonas aeruginosa, and Salmonella spp, directly in wastewater without prior isolation on selective media. As a molecular confirmatory test after isolation of the pathogens by classical microbiological methods, PCR-RFLP of their amplified 16S rDNA genes was performed. It was observed that the developed protocols have significance impact in the ability to detect sensitively, rapidly and specifically the three pathogens directly in water within short-time, represents a considerable advancement over more time-consuming and less-sensitive methods for identification and characterization of these kinds of pathogens.

Keywords: multiplex PCR, bacterial pathogens, Escherichia coli, Pseudomonas aeruginosa, Salmonella spp.

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Authors: Sanju Vaidya, Aihua Li

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Vulnerability measures and topological indices are crucial in solving various problems such as the stability of the communication networks and development of mathematical models for chemical compounds. In 1947, Harry Wiener introduced a topological index related to molecular branching. Now there are more than 100 topological indices for graphs. For example, Hosoya polynomials (also called Wiener polynomials) were introduced to derive formulas for certain vulnerability measures and topological indices for various graphs. In this paper, we will find a relation between the Hosoya polynomials of any graph and its Mycielskian graph. Additionally, using this we will compute vulnerability measures, closeness and betweenness centrality, and extended Wiener indices. It is fascinating to see how Hosoya polynomials are useful in the two diverse fields, cybersecurity and chemistry.

Keywords: hosoya polynomial, mycielskian graph, graph vulnerability measure, topological index

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Authors: Jaco Oosthuizen, Nerina C. Van Der Merwe

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The National Health Laboratory Services in Bloemfontien has been the diagnostic testing facility for 1830 patients for familial breast cancer since 1997. From the cohort, 540 were comprehensively screened using High-Resolution Melting Analysis or Next Generation Sequencing for the presence of point mutations and/or indels. Approximately 90% of these patients stil remain undiagnosed as they are BRCA1/2 negative. Multiplex ligation-dependent probe amplification was initially added to screen for copy number variation detection, but with the introduction of next generation sequencing in 2017, was substituted and is currently used as a confirmation assay. The aim was to investigate the viability of utilizing internationally designed copy number variation detection assays based on mostly European/Caucasian genomic data for use within a South African context. The multiplex ligation-dependent probe amplification technique is based on the hybridization and subsequent ligation of multiple probes to a targeted exon. The ligated probes are amplified using conventional polymerase chain reaction, followed by fragment analysis by means of capillary electrophoresis. The experimental design of the assay was performed according to the guidelines of MRC-Holland. For BRCA1 (P002-D1) and BRCA2 (P045-B3), both multiplex assays were validated, and results were confirmed using a secondary probe set for each gene. The next generation sequencing technique is based on target amplification via multiplex polymerase chain reaction, where after the amplicons are sequenced parallel on a semiconductor chip. Amplified read counts are visualized as relative copy numbers to determine the median of the absolute values of all pairwise differences. Various experimental parameters such as DNA quality, quantity, and signal intensity or read depth were verified using positive and negative patients previously tested internationally. DNA quality and quantity proved to be the critical factors during the verification of both assays. The quantity influenced the relative copy number frequency directly whereas the quality of the DNA and its salt concentration influenced denaturation consistency in both assays. Multiplex ligation-dependent probe amplification produced false positives due to ligation failure when ligation was inhibited due to a variant present within the ligation site. Next generation sequencing produced false positives due to read dropout when primer sequences did not meet optimal multiplex binding kinetics due to population variants in the primer binding site. The analytical sensitivity and specificity for the South African population have been proven. Verification resulted in repeatable reactions with regards to the detection of relative copy number differences. Both multiplex ligation-dependent probe amplification and next generation sequencing multiplex panels need to be optimized to accommodate South African polymorphisms present within the genetically diverse ethnic groups to reduce the false copy number variation positive rate and increase performance efficiency.

Keywords: familial breast cancer, multiplex ligation-dependent probe amplification, next generation sequencing, South Africa

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Authors: Wongsakorn Charoenpanitseri

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The total chromatic number χ"(G) of a graph G is the minimum number of colors needed to color the elements (vertices and edges) of G such that no incident or adjacent pair of elements receive the same color Let G be a graph with maximum degree Δ(G). Considering a total coloring of G and focusing on a vertex with maximum degree. A vertex with maximum degree needs a color and all Δ(G) edges incident to this vertex need more Δ(G) + 1 distinct colors. To color all vertices and all edges of G, it requires at least Δ(G) + 1 colors. That is, χ"(G) is at least Δ(G) + 1. However, no one can find a graph G with the total chromatic number which is greater than Δ(G) + 2. The Total Coloring Conjecture states that for every graph G, χ"(G) is at most Δ(G) + 2. In this paper, we prove that the Total Coloring Conjectur for a Δ-claw-free 3-degenerated graph. That is, we prove that the total chromatic number of every Δ-claw-free 3-degenerated graph is at most Δ(G) + 2.

Keywords: total colorings, the total chromatic number, 3-degenerated, CLAW-FREE

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Authors: Aqeela Ashraf, Muhammad Imran, Tahir Yaqub, Muhammad Tayyab, Yung Fu Chang

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For the identification of bovine mastitic pathogen, an economical, rapid and sensitive molecular diagnostic assay is developed by PCR multiplexing of gene and pathogenic species specific DNA sequences. The multiplex PCR assay is developed for detecting nine important bacterial pathogens causing mastitis Worldwide. The bacterial species selected for this study are Streptococcus agalactiae, Streptococcus dysagalactiae, Streptococcus uberis, Staphylococcus aureus, Escherichia coli, Staphylococcus haemolyticus, Staphylococcus chromogenes Mycoplasma bovis and Staphylococcus epidermidis. A single reaction assay was developed and validated by 27 reference strains and further tested on 276 bacterial strains obtained from culturing mastitic milk. The multiplex PCR assay developed here is further evaluated by applying directly on genomic DNA isolated from 200 mastitic milk samples. It is compared with bacterial culturing method and proved to be more sensitive, rapid, economical and can specifically identify 9 bacterial pathogens in a single reaction. It has detected the pathogens in few culture negative mastitic samples. Recognition of disease is the foundation of disease control and prevention. This assay can be very helpful for maintaining the udder health and milk monitoring.

Keywords: multiplex PCR, bacteria, mastitis, milk

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Authors: Mostafa Gamal, Hoda K. Mohamed, Islam El-Maddah, Ali Hamdi

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In recent years, many digital documents on the web have been created due to the rapid growth of ’social applications’ communities or ’Data-intensive applications’. The evolution of online-based multimedia data poses new challenges in storing and querying large amounts of data for online recommender systems. Graph data models have been shown to be more efficient than relational data models for processing complex data. This paper will explain the key differences between graph and relational databases, their strengths and weaknesses, and why using graph databases is the best technology for building a realtime recommendation system. Also, The paper will discuss several similarity metrics algorithms that can be used to compute a similarity score of pairs of nodes based on their neighbourhoods or their properties. Finally, the paper will discover how NLP strategies offer the premise to improve the accuracy and coverage of realtime recommendations by extracting the information from the stored unstructured knowledge, which makes up the bulk of the world’s data to enrich the graph database with this information. As the size and number of data items are increasing rapidly, the proposed system should meet current and future needs.

Keywords: graph databases, NLP, recommendation systems, similarity metrics

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Authors: Roya Khajepour, Alireza B. Novinzadeh

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In this paper, the spherical robot is modeled using the Band-Graph approach. This breed of robots is typically employed in expedition missions to unknown territories. Its motion mechanism is based on convection of a fluid in a set of three donut vessels, arranged orthogonally in space. This robot is a non-linear, non-holonomic system. This paper utilizes the Band-Graph technique to derive the torque generation mechanism in a spherical robot. Eventually, this paper describes the motion of a sphere due to the exerted torque components.

Keywords: spherical robot, Band-Graph, modeling, torque

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