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PubMine: An Ontology-Based Text Mining System for Deducing Relationships among Biological Entities

  • Kim, Tae-Kyung;Oh, Jeong-Su;Ko, Gun-Hwan;Cho, Wan-Sup;Hou, Bo-Kyeng;Lee, Sang-Hyuk
    • Interdisciplinary Bio Central
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    • v.3 no.2
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    • pp.7.1-7.6
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    • 2011
  • Background: Published manuscripts are the main source of biological knowledge. Since the manual examination is almost impossible due to the huge volume of literature data (approximately 19 million abstracts in PubMed), intelligent text mining systems are of great utility for knowledge discovery. However, most of current text mining tools have limited applicability because of i) providing abstract-based search rather than sentence-based search, ii) improper use or lack of ontology terms, iii) the design to be used for specific subjects, or iv) slow response time that hampers web services and real time applications. Results: We introduce an advanced text mining system called PubMine that supports intelligent knowledge discovery based on diverse bio-ontologies. PubMine improves query accuracy and flexibility with advanced search capabilities of fuzzy search, wildcard search, proximity search, range search, and the Boolean combinations. Furthermore, PubMine allows users to extract multi-dimensional relationships between genes, diseases, and chemical compounds by using OLAP (On-Line Analytical Processing) techniques. The HUGO gene symbols and the MeSH ontology for diseases, chemical compounds, and anatomy have been included in the current version of PubMine, which is freely available at http://pubmine.kobic.re.kr. Conclusions: PubMine is a unique bio-text mining system that provides flexible searches and analysis of biological entity relationships. We believe that PubMine would serve as a key bioinformatics utility due to its rapid response to enable web services for community and to the flexibility to accommodate general ontology.

Real-Time Indexing Performance Optimization of Search Platform Based on Big Data Cluster (빅데이터 클러스터 기반 검색 플랫폼의 실시간 인덱싱 성능 최적화)

  • Nayeon Keum;Dongchul Park
    • Journal of Platform Technology
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    • v.11 no.6
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    • pp.89-105
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    • 2023
  • With the development of information technology, most of the information has been converted into digital information, leading to the Big Data era. The demand for search platform has increased to enhance accessibility and usability of information in the databases. Big data search software platforms consist of two main components: (1) an indexing component to generate and store data indices for a fast and efficient data search and (2) a searching component to look up the given data fast. As an amount of data has explosively increased, data indexing performance has become a key performance bottleneck of big data search platforms. Though many companies adopted big data search platforms, relatively little research has been made to improve indexing performance. This research study employs Elasticsearch platform, one of the most famous enterprise big data search platforms, and builds physical clusters of 3 nodes to investigate optimal indexing performance configurations. Our comprehensive experiments and studies demonstrate that the proposed optimal Elasticsearch configuration achieves high indexing performance by an average of 3.13 times.

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Design and Implementation of Information Retrieval System Based on Ontology Using Semantic Web (시맨틱 웹을 이용한 온톨로지 기반의 정보검색 시스템 설계 및 구현)

  • Seo, Woo-Jin;Rhyu, Kyeong-Taek
    • Journal of Digital Convergence
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    • v.17 no.1
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    • pp.209-217
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    • 2019
  • In this paper, the purpose of this paper is to lay the foundation for the search system by using and building an online search engine suitable for the search domain and enabling search, conversion, integration and sharing of information. It is to use the ontology to infer hierarchical relationships, deduce objects based on that layer, and extract attributes to search areas that are relevant to the data that the user wants. In order to search for information in this way, the information search system was implemented by entering key words related to 'qualifications'. The implemented system arranged the meaning and relationship of each attribute online so that the general public can search information quickly, easily, and accurately. In addition, the implementation results were compared with two different search engines. Comparable search engines are Naver and Daum, the two major search engines. The search engine of this study, which was built using an ontology suitable for the search domain to perform searches using the semantic web, was evaluated to have excellent results. However, it is thought that a more formalized online location is necessary to increase the accuracy and reliability of search engines and to include more comprehensive categories of search terms.

A Semantics-based Video Retrieval System using Annotation and Feature (주석 및 특징을 이용한 의미기반 비디오 검색 시스템)

  • 이종희
    • Journal of the Institute of Electronics Engineers of Korea CI
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    • v.41 no.4
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    • pp.95-102
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    • 2004
  • In order to process video data effectively, it is required that the content information of video data is loaded in database and semantic-based retrieval method can be available for various query of users. Currently existent contents-based video retrieval systems search by single method such as annotation-based or feature-based retrieval, and show low search efficiency md requires many efforts of system administrator or annotator because of imperfect automatic processing. In this paper, we propose semantics-based video retrieval system which support semantic retrieval of various users by feature-based retrieval and annotation-based retrieval of massive video data. By user's fundamental query and selection of image for key frame that extracted from query, the agent gives the detail shape for annotation of extracted key frame. Also, key frame selected by user become query image and searches the most similar key frame through feature based retrieval method and optimized comparison area extracting that propose. Therefore, we propose the system that can heighten retrieval efficiency of video data through semantics-based retrieval.

A Semantic-based Video Retrieval System using Design of Automatic Annotation Update and Categorizing (자동 주석 갱신 및 카테고라이징 기법을 이용한 의미기반 동영상 검색 시스템)

  • 김정재;이창수;이종희;전문석
    • Journal of the Korea Computer Industry Society
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    • v.5 no.2
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    • pp.203-216
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    • 2004
  • In order to process video data effectively, it is required that the content information of video data is loaded in database and semantic- based retrieval method can be available for various query of users. Currently existent contents-based video retrieval systems search by single method such as annotation-based or feature-based retrieval, and show low search efficiency and requires many efforts of system administrator or annotator form less perfect automatic processing. In this paper, we propose semantic-based video retrieval system which support semantic retrieval of various users by feature-based retrieval and annotation-based retrieval of massive video data. By user's fundamental query and selection of image for key frame that extracted from query, the agent gives the detail shape for annotation of extracted key frame. Also, key frame selected by user become query image and searches the most similar key frame through feature based retrieval method that propose. Therefore, we design the system that can heighten retrieval efficiency of video data through semantic-based retrieval.

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A Semantic-based Video Retrieval System Using the Automatic Indexing Agent (자동 인덱싱 에이전트를 이용한 의미기반 비디오 검색 시스템)

  • Kim Sam-Keun;Lee Jong-Hee;Yoon Sun-Hee;Lee Keun-Soo;Seo Jeong-Min
    • Journal of Korea Multimedia Society
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    • v.9 no.1
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    • pp.127-137
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    • 2006
  • In order to process video data effectively, it is required that the content information of video data is loaded in database and semantic- based retrieval method can be available for various query of users. Currently existent contents-based video retrieval systems search by single method such as annotation-based or feature-based retrieval, and show low search efficiency and requires many efforts of system administrator or annotator form less perfect automatic processing. In this paper, we propose semantic-based video retrieval system which support semantic retrieval of various users by feature-based retrieval and annotation-based retrieval of massive video data. By user's fundamental query and selection of image for key frame that extracted from query, the automatic indexing agent gives the detail shape for annotation of extracted key frame. Also, key frame selected by user become query image and searches the most similar key frame through feature based retrieval method that propose. Therefore, we propose the system that can heighten retrieval efficiency of video data through semantic-based retrieval.

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Effect of Node Size on the Performance of the B+-tree on Flash Memory (플래시 메모리 상에서 B+-트리 노드 크기 증가에 따른 성능 평가)

  • Park, Dong-Joo;Choi, Hae-Gi
    • The KIPS Transactions:PartA
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    • v.15A no.6
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    • pp.325-334
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    • 2008
  • Flash memory is widely used as a storage medium for mobile devices such as cell phones, MP3 players, PDA's due to its tiny size, low power consumption and shock resistant characteristics. Additionally, some computer manufacturers try to replace hard-disk drives used in Laptops or personal computers with flash memory. More recently, there are some literatures on developing a flash memory-aware $B^+$-tree index for an efficient key-based search in the flash memory storage system. They focus on minimizing the number of "overwrites" resulting from inserting or deleting a sequence of key values to/from the $B^+$-tree. However, in addition to this factor, the size of a physical page allocated to a node can affect the maintenance cost of the $B^+$-tree. In this paper, with diverse experiments, we compare and analyze the costs of construction and search of the $B^+$-tree and the space requirement on flash memory as the node size increases. We also provide sorting-based or non-sorting-based algorithms to be used when inserting a key value into the node and suggest an header structure of the index node for searching a given key inside it efficiently.

An Encryption Algorithm Based on DES or Composition Hangul Syllables (DES에 기반한 조합형 한글 암호 알고리즘)

  • 박근수
    • Journal of the Korea Institute of Information Security & Cryptology
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    • v.9 no.3
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    • pp.63-74
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    • 1999
  • In this paper we present a Hangul Encryption Algorithm (HEA) which encrypts composition Hangul syllables into composition Hangul syllables using the non-linear structure of Hangul. Since ciphertexts generated by HEA are displayable characters HEA can be used in applications such as Privacy Enhanced mail (PEM) where ciphertexts should be displayable characters. HEA is based on DES and it can be shown that HEA is as safe as DES against the exhaustive key search differential cryptanalysis and linear cryptanalysis. HEA also has randomness of phonemes of ciphertexts and satisfies plaintext-ciphetext avalanche effect and key-ciphertext avalanche effect.

Classification method for failure modes of RC columns based on key characteristic parameters

  • Yu, Bo;Yu, Zecheng;Li, Qiming;Li, Bing
    • Structural Engineering and Mechanics
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    • v.84 no.1
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    • pp.1-16
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    • 2022
  • An efficient and accurate classification method for failure modes of reinforced concrete (RC) columns was proposed based on key characteristic parameters. The weight coefficients of seven characteristic parameters for failure modes of RC columns were determined first based on the support vector machine-recursive feature elimination. Then key characteristic parameters for classifying flexure, flexure-shear and shear failure modes of RC columns were selected respectively. Subsequently, a support vector machine with key characteristic parameters (SVM-K) was proposed to classify three types of failure modes of RC columns. The optimal parameters of SVM-K were determined by using the ten-fold cross-validation and the grid-search algorithm based on 270 sets of available experimental data. Results indicate that the proposed SVM-K has high overall accuracy, recall and precision (e.g., accuracy>95%, recall>90%, precision>90%), which means that the proposed SVM-K has superior performance for classification of failure modes of RC columns. Based on the selected key characteristic parameters for different types of failure modes of RC columns, the accuracy of SVM-K is improved and the decision function of SVM-K is simplified by reducing the dimensions and number of support vectors.

A Study on the Effects of Search Language on Web Searching Behavior: Focused on the Differences of Web Searching Pattern (검색 언어가 웹 정보검색행위에 미치는 영향에 관한 연구 - 웹 정보검색행위의 양상 차이를 중심으로 -)

  • Byun, Jeayeon
    • Journal of the Korean Society for Library and Information Science
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    • v.52 no.3
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    • pp.289-334
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    • 2018
  • Even though information in many languages other than English is quickly increasing, English is still playing the role of the lingua franca and being accounted for the largest proportion on the web. Therefore, it is necessary to investigate the key features and differences between "information searching behavior using mother tongue as a search language" and "information searching behavior using English as a search language" of users who are non-mother tongue speakers of English to acquire more diverse and abundant information. This study conducted the experiment on the web searching which is applied in concurrent think-aloud method to examine the information searching behavior and the cognitive process in Korean search and English search through the twenty-four undergraduate students at a private university in South Korea. Based on the qualitative data, this study applied the frequency analysis to web search pattern under search language. As a result, it is active, aggressive and independent information searching behavior in Korean search, while information searching behavior in English search is passive, submissive and dependent. In Korean search, the main features are the query formulation by extract and combine the terms from various sources such as users, tasks and system, the search range adjustment in diverse level, the smooth filtering of the item selection in search engine results pages, the exploration and comparison of many items and the browsing of the overall contents of web pages. Whereas, in English search, the main features are the query formulation by the terms principally extracted from task, the search range adjustment in limitative level, the item selection by rely on the relevance between the items such as categories or links, the repetitive exploring on same item, the browsing of partial contents of web pages and the frequent use of language support tools like dictionaries or translators.