• Journal of the Korean Society for Industrial and Applied Mathematics
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• 제25권4호
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• pp.296-311
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• 2021

Topological Data Analysis (TDA), a relatively new field of data analysis, has proved very useful in a variety of applications. The main persistence tool from TDA is persistent homology in which data structure is examined at many scales. Representations of persistent homology include persistence barcodes and persistence diagrams, both of which are not straightforward to reconcile with traditional machine learning algorithms as they are sets of intervals or multisets. The problem of faithfully representing barcodes and persistent diagrams has been pursued along two main avenues: kernel methods and vectorizations. One vectorization is the Betti sequence, or Betti curve, derived from the persistence barcode. While the Betti sequence has been used in classification problems in various applications, to our knowledge, the stability of the sequence has never before been discussed. In this paper we show that the Betti sequence is unstable under the 1-Wasserstein metric with regards to small perturbations in the barcode from which it is calculated. In addition, we propose a novel stabilized version of the Betti sequence based on the Gaussian smoothing seen in the Stable Persistence Bag of Words for persistent homology. We then introduce the normalized cumulative Betti sequence and provide numerical examples that support the main statement of the paper.

• Journal of Information Processing Systems
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• 제7권3호
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• pp.413-424
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• 2011

A variety of different metrics has been introduced to measure the similarity of two given sequences. These widely used metrics are ranging from spell correctors and categorizers to new sequence mining applications. Different metrics consider different aspects of sequences, but the essence of any sequence is extracted from the ordering of its elements. In this paper, we propose a novel sequence similarity measure that is based on all ordered pairs of one sequence and where a Hasse diagram is built in the other sequence. In contrast with existing approaches, the idea behind the proposed sequence similarity metric is to extract all ordering features to capture sequence properties. We designed a clustering problem to evaluate our sequence similarity metric. Experimental results showed the superiority of our proposed sequence similarity metric in maximizing the purity of clustering compared to metrics such as d2, Smith-Waterman, Levenshtein, and Needleman-Wunsch. The limitation of those methods originates from some neglected sequence features, which are considered in our proposed sequence similarity metric.

• 한국지능시스템학회논문지
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• 제22권2호
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• pp.181-186
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• 2012

최근 시간적으로 변화된 데이터에서 유사한 값의 움직임 즉 유사 패턴을 검색하는 연구가 활발히 진행되고 있다. 시간적으로 변화된 데이터는 시계열 데이터 (time series data) 또는 시퀀스 데이터(sequence data)로 분류되며 기존의 스칼라 값을 가지는 데이터와는 매우 다른 의미를 가진다. 본 논문에서 유사 시퀀스 검색은 시퀀스 데이터웨어하우스에서 값의 변화가 유사한 형태를 가지는 시퀀스들을 검색한다. 유사 시퀀스를 검색하기 위하여 본 논문에서는 먼저 시퀀스 원시 데이터에 이 산 푸리에 변환(DFT, Discrete Fourier Transform)을 적용하여 데이터를 변환한다. 변환된 데이터는 그 특성으로 인하여 유사 패턴의 검색에 적합하며 또 유사도를 비교할 때 일부분만 사용되므로 색인에 사용되는 속성의 개수를 줄이는 장점이 있다. 또 데이터웨어하우스 환경이므로 더 좋은 성능을 보일 수 있는 비트맵 색인 기법을 적용하였다. 시퀀스 데이터의 효율적인 검색을 위하여 영역 지정 검색 방법을 제안하고 효율적인 실행을 위한 비트맵을 활용한 다양한 조합의 색인을 생성하고, 질의 최적화기의 연산 비용을 비교하면서 효율적인 검색 연산을 위한 최저 비용의 색인을 선택하는 기법을 연구하였다.

• 한국정보처리학회:학술대회논문집
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• 한국정보처리학회 2023년도 춘계학술발표대회
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• pp.2-4
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• 2023

Sequence data plays an important role in the field of intelligence, especially for industrial control, traffic control and other aspects. Finding abnormal parts in sequence data has long been an application field of AI technology. In this paper, we propose an anomaly detection method for sequence data using a diffusion model. The diffusion model has two major advantages: interpretability derived from rigorous mathematical derivation and unrestricted selection of backbone models. This method uses the diffusion model to predict and reconstruct the sequence data, and then detects the abnormal part by comparing with the real data. This paper successfully verifies the feasibility of the diffusion model in the field of anomaly detection. We use the combination of MLP and diffusion model to generate data and compare the generated data with real data to detect anomalous points.

• Journal of the Korean Data and Information Science Society
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• 제17권2호
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• pp.569-579
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• 2006

Recently, the amount of genome sequence is increasing rapidly due to advanced computational techniques and experimental tools in the biological area. Sequence comparisons are very useful operations to predict the functions of the genes or proteins. However, it takes too much time to compare long sequence data and there are many research results for fast sequence comparisons. In this paper, we propose a hybrid grid system to improve the performance of the sequence comparisons based on the LanLinux system. Compared with conventional approaches, hybrid grid is easy to construct, maintain, and manage because there is no need to install SWs for every node. As a real experiment, we constructed an orthologous database for 89 prokaryotes just in a week under hybrid grid; note that it requires 33 weeks on a single computer.

• Genomics & Informatics
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• 제6권3호
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• pp.157-159
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• 2008

Multiple sequence alignment (MSA) is the most important step for many of biological sequence analyses, homology search, and protein structural assignments. However, large amount of data make biologists difficult to perform MSA analyses and it requires much computational time to align many sequences. Here, we have developed a simple and fast web alignment tool for aligning, editing, and visualizing large amount of sequence data. We used a cluster server installed ClustalW-MPI using web services and message passing interface (MPI). It also enables users to edit multiple sequence alignments for manual editing and to download the input data and results such as alignments and phylogenetic tree.

• 대한전자공학회논문지
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• 제12권2호
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• pp.1-10
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• 1975

본 논문은 사진데이타에 쉽게 적용할수있는 한 adaptive data compression 방법을 노표시하였다. 이웃 sample data 사이의 높은 correlation때문에 발생할 부호화 복잡성을 간편한 sample difference data로 대처하였으며, 자단의 statistical nonstationarity에 적응키 위해서 여덟가지 부호(code)로 구성된 code set중에서 최적부호를 선택토록 하였다. code erst는 두가지 등장부호와 여섯가지 보완형 Shannon-Fanro 부호로 되었다. difference data의 확률분포는 Laplacian model로, entropy의 확률분포는 Gaussian model대 하였다. 부호선별 Paranleter로서 entropy와 Pr[차이값=0]=Po를 비교하였다. 콤퓨타 실험결과 이 adaptive coding 방법으로 2대 1의 데이타 감축비를 얻었다. 이 방법은 fixed coding에 비해서 데이타 감축비와 부호화효율에서 약 10%와 15%의 이득을 주었다. 또한 도는 entropy보다 휠신 편리한 부호선별 parameter인 중시에 entropy 경우와 1% 내외의 좋은 결과를 얻을수 있음이 확인되었다. This paper presents an adaptive data compression algorithm for video data. The coling complexity due to the high correlation in the given data sequence is alleviated by coding the difference data, sequence rather than the data sequence itself. The adaptation to the nonstationary statistics of the data is confined within a code set, which consists of two constant length cades and six modified Shannon·Fano codes. lt is assumed that the probability distributions of tile difference data sequence and of the data entropy are Laplacian and Gaussion, respectively. The adaptive coding performance is compared for two code selection criteria: entropy and pr[difference value=0]=po. It is shown that data compression ratio 2 : 1 is achievable with the adaptive coding. The gain by the adaptive coding over the fixed coding is shown to be about 10% in compression ratio and 15% in code efficiency. In addition, po is found to he not only a convenient criterion for code selection, but also such efficient a parameter as to perform almost like entropy.

• ALGAE
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• 제26권3호
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• pp.229-235
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• 2011

Spliced leader (SL) trans-splicing is a mRNA processing mechanism in dinoflagellate nuclear genes. Although studies have identified a short, conserved dinoflagellate SL (dinoSL) sequence (22-nt) in their nuclear-encoded transcripts, whether the majority of nuclear-coded transcripts in dinoflagellates have the dinoSL sequence remains doubtful. In this study, we investigated dinoSL-containing gene transcripts using 454 pyrosequencing data (Cochlodinium polykrikoides, 93 K sequence reads, 31 Mb; Prorocentrum minimum, 773 K sequence reads, 291 Mb). After making comparisons and performing local BLAST searches, we identified dinoSL for one C. polykrikoides gene transcript and eight P. minimum gene transcripts. This showed transcripts containing the dinoSL sequence were markedly fewer in number than the total expressed sequence tag (EST) transcripts. In addition, we found no direct evidence to prove that most dinoflagellate nuclear-coded transcripts have this dinoSL sequence.

• 대한전기학회논문지:전력기술부문A
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• 제48권12호
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• pp.1554-1563
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• 1999

This paper presents the design of high speed processor for a sequence logic control using field programmable gate array(FPGA). The sequence logic controller is widely used for automating a variety of industrial plants. The FPGA designed by VHDL consists of program and data memory interface block, input and output block, instruction fetch and decoder block, register and ALU block, program counter block, debug control block respectively. Dedicated clock inputs in the FPGA were used for high speed execution, and also the program memory was separated from the data memory for high speed execution of the sequence instructions at 40 MHz clock. Therefore it was possible that sequence instructions could be operated at the same time during the instruction fetch cycle. In order to reduce the instruction decoding time and the interface time of the data memory interface, an instruction code size was implemented by 16 bits or 32 bits respectively. And the real time debug operation was implemented for easy debugging the designed processor. This FPGA was synthesized by pASIC 2 SpDE and Synplify-Lite synthesis tool of Quick Logic company. The final simulation for worst cases was successfully performed under a Verilog HDL simulation environment. And the FPGA programmed for an 84 pin PLCC package was applied to sequence control system with inputs and outputs of 256 points. The designed processor for the sequence logic was compared with the control system using the DSP(TM320C32-40MHz) and conventional PLC system. The designed processor for the sequence logic showed good performance.

• 한국지능정보시스템학회:학술대회논문집
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• 한국지능정보시스템학회 2004년도 추계학술대회
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• pp.221-229
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• 2004

Recently, there has been enormous growth in the amount of commercial and scientific data, such as protein sequences, retail transactions, and web-logs. Such datasets consist of sequence data that have an inherent sequential nature. However, only a few of the existing clustering algorithms consider sequentiality. This study presents a method for clustering such sequence datasets. The similarity between sequences must be decided before clustering the sequences. This study proposes a new similarity measure to compute the similarity between two sequences using a sequence element. Two clustering algorithms using the proposed similarity measure are proposed: a hierarchical clustering algorithm and a scalable clustering algorithm that uses sampling and a k-nearest neighbor method. Using a splice dataset and synthetic datasets, we show that the quality of clusters generated by our proposed clustering algorithms is better than that of clusters produced by traditional clustering algorithms.