• Journal of KIISE:Computer Systems and Theory
• /
• v.32 no.11_12
• /
• pp.598-607
• /
• 2005

We propose a new external-memory index data structure, the Suffix B-tree. The Suffix B-tree is a B-tree in which the key is a string like the String B-tree. While the node in the String B-tree is implemented with a Patricia trio, the node in the Suffix B-tree is implemented with an array. So the Suffix B-tree is simpler and easier to be Implemented than the String B-tree. Nevertheless, the branching algorithm of the Suffix B-tree is as efficient as that of the String B-tree. Consequently, the Suffix B-tree takes the same worst-case disk accesses as the String B-tree to solve the string matching problem, which is fundamental and important in the area of string algorithms.

• The KIPS Transactions:PartA
• /
• v.8A no.4
• /
• pp.509-516
• /
• 2001

As results of many genome projects, genomic sequences of many organisms are revealed. Various methods such as global alignment, local alignment are used to analyze the sequences of the organisms, and k -mer analysis is one of the methods for analyzing the genomic sequences. The k -mer analysis explores the frequencies of all k-mers or the symmetry of them where the k -mer is the sequenced base with the length of k. However, existing on-memory algorithms are not applicable to the k -mer analysis because a whole genomic sequence is usually a large text. Therefore, efficient data structures and algorithms are needed. String B-tree is a good data structure that supports external memory and fits into pattern matching. In this paper, we improve the string B-tree in order to efficiently apply the data structure to k -mer analysis, and the results of k -mer analysis for C. elegans and other 30 genomic sequences are shown. We present a visualization system which enables users to investigate the distribution and symmetry of the frequencies of all k -mers using CGR (Chaotic Game Representation). We also describe the method to find the signature which is the part of the sequence that is similar to the whole genomic sequence.

• Proceedings of the Korean Information Science Society Conference
• /
• 2001.04a
• /
• pp.748-750
• /
• 2001

최근 Human Genome Project(HGP)에서 사람의 염기 서열의 초안이 발표되었다. 생물체의 염기 서열을 분석하는 방법은 매우 많은데, 그 중 하나가 k-mer 분석이다. k-mer는 유전자의 염기 서열내의 길이가 k인 연속된 염기 서열이다. k-mer 분석은 염기서열이 가진 k-mer들의 빈도의 분포나 대칭성 등을 탐색하는 것이다. 그런데 유전자의 염기 서열은 대용량 텍스트이고 k가 줄 때 기존의 온메모리 알고리즘으로는 처리가 불가능하므로 효율적인 자료구조와 알고리즘이 필요하다. 본 논문에서는 패턴 일치(pattern matching)에 적합하고 외부 메모리를 지원하는 스트링 B-트리(string B-tree)를 이용한 k-mer 분석 방법을 제시하고, 그것을 구현하였으며 몇 가지 실험 결과에 대하여 기술한다.

• ETRI Journal
• /
• v.43 no.6
• /
• pp.1024-1037
• /
• 2021

Mining high utility itemsets (HUIs) from transaction databases considers such factors as the unit profit and quantity of purchased items. Two-phase tree-based algorithms transform a database into compressed tree structures and generate candidate patterns through a recursive pattern-growth procedure. This procedure requires a lot of memory and time to construct conditional pattern trees. To address this issue, this study employs two compressed tree structures, namely, Utility Count Tree and String Utility Tree, to enumerate valid patterns and thus promote fast utility computation. Furthermore, the study presents an algorithm called single-phase utility computation (SPUC) that leverages these two tree structures to mine HUIs in a single phase by incorporating novel pruning strategies. Experiments conducted on both real and synthetic datasets demonstrate the superior performance of SPUC compared with IHUP, UP-Growth, and UP-Growth+algorithms.

• The Transactions of the Korea Information Processing Society
• /
• v.6 no.6
• /
• pp.1458-1467
• /
• 1999

Existing index structures such as extendable hashing and B+-tree do not support partial string searches perfectly. The inverted file method and the signature file method that are used in the web retrieval engine also have problems that they do not provide partial string searches and suffer from serious retrieval performance degradation respectively. In this paper, we propose an efficient index method that supports partial string searches and achieves good retrieval performance. The proposed index method is based on the Inverted file structure. It constructs the index file with patterns that result from dividing terms by two syllables to support partial string searches. We analyze the characteristics of our proposed method through simulation experiments using wide range of parameter values. We analyze the derive analytic performance evaluation models of the existing inverted file method, signature file method and the proposed index method in terms of retrieval time and storage overhead. We show through performance comparison based on analytic models that the proposed method significantly improves retrieval performance over the existing method.

• The KIPS Transactions:PartA
• /
• v.9A no.3
• /
• pp.387-398
• /
• 2002

As whole genome sequences of many organisms have been revealed by small-scale genome projects, the intensive research on individual genes and their functions has been performed. However on-memory algorithms are inefficient to analysis of whole genome sequences, since the size of individual whole genome is from several million base pairs to hundreds billion base pairs. In order to effectively manipulate the huge sequence data, it is necessary to use the indexed data structure for external memory. In this paper, we introduce a workbench system for analysis and visualization of whole genome sequence using string B-tree that is suitable for analysis of huge data. This system consists of two parts : analysis query part and visualization part. Query system supports various transactions such as sequence search, k-occurrence, and k-mer analysis. Visualization system helps biological scientist to easily understand whole structure and specificity by many kinds of visualization such as whole genome sequence, annotation, CGR (Chaos Game Representation), k-mer, and RWP (Random Walk Plot). One can find the relations among organisms, predict the genes in a genome, and research on the function of junk DNA using our workbench.

• Proceedings of the Korea Information Processing Society Conference
• /
• 2006.11a
• /
• pp.357-360
• /
• 2006

범위 술어에 대한 문자열 선택도 추정은 해당 문자열 범위를 숫자 표현으로 변환 해야 하는 어려움이 있다. 하지만 문자열을 숫자 표현으로 변환할 경우 각각의 바이트에 대한 모든 경우의 수를 모두 고려해야 한다. 따라서 변환 시 문자열 뒷부분에 대한 정보를 고려할 수 없는 문제가 발생한다. 최근 연구되고 있는 부분 문자열에 대한 선택도 추정 방식을 적용할 경우 통계정보와 추정에 대한 연산이 증가되는 단점이 있다. 따라서 이는 범위 술어에 대한 추정만을 위해 사용하기에는 적합하지 않다. 따라서 이 논문에서는 B+ Tree 인덱스의 제한적인 통계정보만을 가지고 범위 술어에 대한 문자열 선택도를 추정하는 방법으로 알티베이스에 구현하였다.

• Wind and Structures
• /
• v.5 no.2_3_4
• /
• pp.291-300
• /
• 2002

An efficient large eddy simulation algorithm is used to compute surface pressure distributions on an eleven story (target) building on the NIST campus. Local meteorology, neighboring buildings, topography and large vegetation (trees) all play an important part in determining the flows and therefore the pressures experienced by the target. The wind profile imposed at the upstream surface of the computational domain follows a power law with an exponent representing a suburban terrain. This profile accounts for the flow retardation due to friction from the surface of the earth, but does not include fluctuations that would naturally occur in this flow. The effect of neighboring buildings on the time dependent surface pressures experienced by the target is examined. Comparison of the pressure fluctuations on the single target building alone with those on the target building in situ show that, owing to vortices shed by the upstream buildings, fluctuations are larger when such buildings are present. Even when buildings are lateral to or behind the target, the pressure disturbances generate significantly different flows around this building. A simple grid-free mathematical model of a tree is presented in which the trunk and the branches are each represented by a collection of spherical particles strung together like beads on a string. The drag from the tree, determined as the sum of the drags of the component particles, produces an oscillatory, spreading wake of slower fluid, suggesting that the behavior of trees as wind breakers can be modeled usefully.