Numerical Characterization of DNA Sequence Based on Dinucleotides

Sequence comparison is a primary technique for the analysis of DNA sequences. In order to make quantitative comparisons, one devises mathematical descriptors that capture the essence of the base composition and distribution of the sequence. Alignment methods and graphical techniques (where each sequence is represented by a curve in high-dimension Euclidean space) have been used popularly for a long time. In this contribution we will introduce a new nongraphical and nonalignment approach based on the frequencies of the dinucleotide XY in DNA sequences. The most important feature of this method is that it not only identifies adjacent XY pairs but also nonadjacent XY ones where X and Y are separated by some number of nucleotides. This methodology preserves information in DNA sequence that is ignored by other methods. We test our method on the coding regions of exon-1 of β–globin for 11 species, and the utility of this new method is demonstrated

“Follow the Leader”: A Centrality Guided Clustering and Its Application to Social Network Analysis

Within graph theory and network analysis, centrality of a vertex measures the relative importance of a vertex within a graph. The centrality plays key role in network analysis and has been widely studied using different methods. Inspired by the idea of vertex centrality, a novel centrality guided clustering (CGC) is proposed in this paper. Different from traditional clustering methods which usually choose the initial center of a cluster randomly, the CGC clustering algorithm starts from a “LEADER”—a vertex with the highest centrality score—and a new “member” is added into the same cluster as the “LEADER” when some criterion is satisfied. The CGC algorithm also supports overlapping membership. Experiments on three benchmark social network data sets are presented and the results indicate that the proposed CGC algorithm works well in social network clustering

Defensive Alliances in Signed Networks

The analysis of (social) networks and multi-agent systems is a central theme in Artificial Intelligence. Some line of research deals with finding groups of agents that could work together to achieve a certain goal. To this end, different notions of so-called clusters or communities have been introduced in the literature of graphs and networks. Among these, defensive alliance is a kind of quantitative group structure. However, all studies on the alliance so for have ignored one aspect that is central to the formation of alliances on a very intuitive level, assuming that the agents are preconditioned concerning their attitude towards other agents: they prefer to be in some group (alliance) together with the agents they like, so that they are happy to help each other towards their common aim, possibly then working against the agents outside of their group that they dislike. Signed networks were introduced in the psychology literature to model liking and disliking between agents, generalizing graphs in a natural way. Hence, we propose the novel notion of a defensive alliance in the context of signed networks. We then investigate several natural algorithmic questions related to this notion. These, and also combinatorial findings, connect our notion to that of correlation clustering, which is a well-established idea of finding groups of agents within a signed network. Also, we introduce a new structural parameter for signed graphs, signed neighborhood diversity snd, and exhibit a parameterized algorithm that finds a smallest defensive alliance in a signed graph

A Novel Model for DNA Sequence Similarity Analysis Based on Graph Theory

Determination of sequence similarity is one of the major steps in computational phylogenetic studies. As we know, during evolutionary history, not only DNA mutations for individual nucleotide but also subsequent rearrangements occurred. It has been one of major tasks of computational biologists to develop novel mathematical descriptors for similarity analysis such that various mutation phenomena information would be involved simultaneously. In this paper, different from traditional methods (eg, nucleotide frequency, geometric representations) as bases for construction of mathematical descriptors, we construct novel mathematical descriptors based on graph theory. In particular, for each DNA sequence, we will set up a weighted directed graph. The adjacency matrix of the directed graph will be used to induce a representative vector for DNA sequence. This new approach measures similarity based on both ordering and frequency of nucleotides so that much more information is involved. As an application, the method is tested on a set of 0.9-kb mtDNA sequences of twelve different primate species. All output phylogenetic trees with various distance estimations have the same topology, and are generally consistent with the reported results from early studies, which proves the new method\u27s efficiency; we also test the new method on a simulated data set, which shows our new method performs better than traditional global alignment method when subsequent rearrangements happen frequently during evolutionary history

“Follow the Leader”: A Centrality Guided Clustering and Its Application to Social Network Analysis

Within graph theory and network analysis, centrality of a vertex measures the relative importance of a vertex within a graph. The centrality plays key role in network analysis and has been widely studied using different methods. Inspired by the idea of vertex centrality, a novel centrality guided clustering (CGC) is proposed in this paper. Different from traditional clustering methods which usually choose the initial center of a cluster randomly, the CGC clustering algorithm starts from a “LEADER”—a vertex with the highest centrality score—and a new “member” is added into the same cluster as the “LEADER” when some criterion is satisfied. The CGC algorithm also supports overlapping membership. Experiments on three benchmark social network data sets are presented and the results indicate that the proposed CGC algorithm works well in social network clustering

Autonomous Navigation and Configuration of Integrated Access Backhauling for UAV Base Station Using Reinforcement Learning

Fast and reliable connectivity is essential to enhancing situational awareness and operational efficiency for public safety mission-critical (MC) users. In emergency or disaster circumstances, where existing cellular network coverage and capacity may not be available to meet MC communication demands, deployable-network-based solutions such as cells-on-wheels/wings can be utilized swiftly to ensure reliable connection for MC users. In this paper, we consider a scenario where a macro base station (BS) is destroyed due to a natural disaster and an unmanned aerial vehicle carrying BS (UAV-BS) is set up to provide temporary coverage for users in the disaster area. The UAV-BS is integrated into the mobile network using the 5G integrated access and backhaul (IAB) technology. We propose a framework and signalling procedure for applying machine learning to this use case. A deep reinforcement learning algorithm is designed to jointly optimize the access and backhaul antenna tilt as well as the three-dimensional location of the UAV-BS in order to best serve the on-ground MC users while maintaining a good backhaul connection. Our result shows that the proposed algorithm can autonomously navigate and configure the UAV-BS to improve the throughput and reduce the drop rate of MC users.Comment: This work has been submitted to the IEEE for possible publication. Copyright may be transferred without notice, after which this version may no longer be accessibl

Dismantling networks abruptly by tree decomposition

Dismantling a network by removing the minimum vertices is a challenging problem in complex networks. While most existing methods focus on efficiency, they overlook the importance of abruptness during the dismantling process. Gradual changes in the largest connected component size can alert the target and render the attack ineffective. To overcome this issue, we propose a new dismantling method based on tree decomposition and a new metric quantifying the abruptness of the dismantling process. Our method involves applying tree decomposition to the network using the min fill-in method, identifying the most critical edge in the decomposed tree, and removing the vertices contained in the edge. Experimental results on eight real networks demonstrate that our proposed method significantly outperforms classical methods in abruptness and efficiency

Assessing cyber-user awareness of an emerging infectious disease: evidence from human infections with avian influenza A H7N9 in Zhejiang, China

Objectives: The aim of this study was to assess cyber-user awareness of human infections with avian influenza A H7N9 in Zhejiang, China. Methods: Daily Baidu index values were compared for different keywords, different periods (epidemic and non-epidemic), different levels of epidemic publicity (whether new cases were publicized), and different cities (divided into high, medium, low, and zero groups according to the number of cases). Furthermore, the correlation between the daily Baidu index values and the daily number of new cases was analyzed. Results: Three epidemic periods (periods A/C/E) and three non-epidemic periods (periods B/D/F) were identified from April 2013 to May 2015 according to the curves of daily new cases. Each epidemic period was followed by a non-epidemic period. Baidu index values using ‘H7N9’ as a keyword were higher than the values using the keyword ‘fx1’ (avian influenza in Chinese) in earlier periods, but the situation reversed in later periods. Index values for ‘H7N9’ in the epidemic periods were higher than in the non-epidemic periods. In the first epidemic period (period A), the Baidu index values for ‘H7N9’ showed no difference between the different levels of epidemic publicity and had no correlation with the daily number of new cases. The index values in cities without reported cases showed no difference from the values recorded in the medium and low groups. However, a difference and a correlation were found in a later epidemic period. Conclusions: The Baidu index would be a useful tool for assessing cyber-user awareness of an emerging infectious disease

A Novel Model for DNA Sequence Similarity Analysis Based on Graph Theory

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