• Journal of the Korea Institute of Information and Communication Engineering
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• v.10 no.12
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• pp.2187-2192
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• 2006

This paper presents a method of constructing the universal multiple processing element unit(UMPEU) by De Bruijn Graph. The second method is as following. First, we propose transformation operators in order to construct the De Bruijn UMPEU using properties of graph. Second, we construct the transformation table of De Bruijn graph using above transformation operators. Finally we construct the De Bruijn graph using transformation table. The proposed UMPEU be able to construct the De Bruijn graph for any prime number and integer value of finite fields. Also the UMPEU is applied to fault-tolerant computing system, pipeline class. parallel processing network, switching function and its circuits.

• Proceedings of the IEEK Conference
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• 2002.07b
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• pp.959-962
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• 2002

This paper presents a method of constructing the universal multiple processing element unit(UMPEU) based on De Bruijn Graph. The proposed method is as following. Firstly we propose transformation operators in order to construct the De Bruijn graph using properties of graph. Secondly we construct the transformation table of De Bruijn graph using above transformation operators. Finally we construct the De Bruijn graph using transformation table. The proposed UMPEU is capable of constructing the De Bruijn geraph for any prime number and integer value of finite fields. Also the UMPEU is applied to fault-tolerant computing system, pipeline class, parallel processing network, switching function and its circuits.

• Proceedings of the Korea Multimedia Society Conference
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• 2002.11b
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• pp.587-592
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• 2002

본 논문에서는 De Bruijn 그래프에 기초한 다중처리기구성의 한 가지 방법을 제안하였다. 제안한 방법에서는 유한체상의 수학적 성질과 그래프의 성질을 사용하여 변환연산자를 제한하였으며, 이들 변환연산자를 이용하여 De Bruijn 그래프의 변환표를 도출하였다. 그리고, 이 변환표로부터 유한체상의 De Bruijn 그래프를 도출하였다. 제안한 다중처리기는 유한체상의 임의의 소수와 양의 정수에 대해 구성할 수 있으며 고장허용컴퓨팅시스템, 파이프라인 시스템, 병렬처리 네트워크, 스위칭 함수와 이의 회로, 차세대 디지털논리시스템 및 컴퓨터구조 중의 하나인 다치디지털논리시스템 등에 적용할 수 있으리라 전망된다.

• Journal of Communications and Networks
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• v.6 no.1
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• pp.46-59
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• 2004

In this paper, we present two algorithms for efficiently aggregating link state information needed for quality-of-service (QoS) routing. In these algorithms, each edge node in a group is mapped onto a node of a shufflenet or a node of a de Bruijn graph. By this mapping, the number of links for which state information is maintained becomes aN (a is an integer, N is the number of edge nodes) which is significantly smaller than N2 in the full-mesh approach. Our algorithms also can support asymmetric link state parameters which are common in practice, while many previous algorithms such as the spanning tree approach can be applied only to networks with symmetric link state parameters. Experimental results show that the performance of our shufflenet algorithm is close to that of the full-mesh approach in terms of the accuracy of bandwidth and delay information, with only a much smaller amount of information. On the other hand, although it is not as good as the shufflenet approach, the de Bruijn algorithm also performs far better than the star approach which is one of the most widely accepted schemes. The de Bruijn algorithm needs smaller computational complexity than most previous algorithms for asymmetric networks, including the shufflenet algorithm.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.29 no.11B
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• pp.946-955
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• 2004

It is shown that the do Bruijn graph (dBG) can be used as an architecture for interconnection network and a suitable structure for parallel computation. Recent works have classified dBG based routing algorithms into shortest path routing and fault tolerant routing but investigation into fault free shortest path (FFSP) on dBG has been non-existent. In addition, as the size of the network increase, more faults are to be expected and therefore shortest path dBG algorithms in fault free mode may not be suitable routing algorithms for real interconnection networks, which contain several failures. Furthermore, long fault free path may lead to high traffic, high delay time and low throughput. In this paper we investigate routing algorithms in the condition of existing failure, based on the Bidirectional do Bruijn graph (BdBG). Two FFSP routing algorithms are proposed. Then, the performances of the two algorithms are analyzed in terms of mean path lengths and discrete set mean sizes. Our study shows that the proposed algorithms can be one of the candidates for routing in real interconnection networks based on dBG.

• Journal of Microbiology and Biotechnology
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• v.32 no.2
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• pp.149-159
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• 2022

Cancers of the lung and liver are the top 10 leading causes of cancer death worldwide. Thus, it is essential to identify the genes specifically expressed in these two cancer types to develop new therapeutics. Although many messenger RNA (mRNA) sequencing data related to these cancer cells are available due to the advancement of next-generation sequencing (NGS) technologies, optimized data processing methods need to be developed to identify the novel cancer-specific genes. Here, we conducted an analytical comparison between Bowtie2, a Burrows-Wheeler transform-based alignment tool, and Kallisto, which adopts pseudo alignment based on a transcriptome de Bruijn graph using mRNA sequencing data on normal cells and lung/liver cancer tissues. Before using cancer data, simulated mRNA sequencing reads were generated, and the high Transcripts Per Million (TPM) values were compared. mRNA sequencing reads data on lung/liver cancer cells were also extracted and quantified. While Kallisto could directly give the output in TPM values, Bowtie2 provided the counts. Thus, TPM values were calculated by processing the Sequence Alignment Map (SAM) file in R using package Rsubread and subsequently in python. The analysis of the simulated sequencing data revealed that Kallisto could detect more transcripts and had a higher overlap over Bowtie2. The evaluation of these two data processing methods using the known lung cancer biomarkers concludes that in standard settings without any dedicated quality control, Kallisto is more effective at producing faster and more accurate results than Bowtie2. Such conclusions were also drawn and confirmed with the known biomarkers specific to liver cancer.

• Proceedings of the IEEK Conference
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• 2002.07c
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• pp.1371-1374
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• 2002

This paper compares four network con-figurations for using as the logical topology in multi- hop wavelength division multiplexing (WDM) networks. The regular network configurations studied in this paper axe ShuffleNet, de Bruijn graph, hypercube, and Man-hattan street network. Instead of using the weight mean hop distance of node placement problem for comparing optimum logical topology, we introduce a new objective function that includes h and the network cost. It can be seen that the network cost strongly depends on the logical topology selected for the implementation of the network. The objective of this paper is to find an optimum logical topology for WDM networks that gives low as well as low network cost.

• Communications of the Korean Mathematical Society
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• v.32 no.2
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• pp.435-445
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• 2017

Let D be a directed graph with p vertices and q arcs. A vertex out-magic total labeling is a bijection f from $V(D){\cup}A(D){\rightarrow}\{1,2,{\ldots},p+q\}$ with the property that for every $v{\in}V(D)$, $f(v)+\sum_{u{\in}O(v)}f((v,u))=k$, for some constant k. Such a labeling is called a V-super vertex out-magic total labeling (V-SVOMT labeling) if $f(V(D))=\{1,2,3,{\ldots},p\}$. A digraph D is called a V-super vertex out-magic total digraph (V-SVOMT digraph) if D admits a V-SVOMT labeling. In this paper, we provide a method to find the most vital nodes in a network by introducing the above labeling and we study the basic properties of such labelings for digraphs. In particular, we completely solve the problem of finding V-SVOMT labeling of generalized de Bruijn digraphs which are used in the interconnection network topologies.