• Title/Summary/Keyword: scale-space filtering

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CNVDAT: A Copy Number Variation Detection and Analysis Tool for Next-generation Sequencing Data (CNVDAT : 차세대 시퀀싱 데이터를 위한 유전체 단위 반복 변이 검출 및 분석 도구)

  • Kang, Inho;Kong, Jinhwa;Shin, JaeMoon;Lee, UnJoo;Yoon, Jeehee
    • Journal of KIISE:Databases
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    • v.41 no.4
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    • pp.249-255
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    • 2014
  • Copy number variations(CNVs) are a recently recognized class of human structural variations and are associated with a variety of human diseases, including cancer. To find important cancer genes, researchers identify novel CNVs in patients with a particular cancer and analyze large amounts of genomic and clinical data. We present a tool called CNVDAT which is able to detect CNVs from NGS data and systematically analyze the genomic and clinical data associated with variations. CNVDAT consists of two modules, CNV Detection Engine and Sequence Analyser. CNV Detection Engine extracts CNVs by using the multi-resolution system of scale-space filtering, enabling the detection of the types and the exact locations of CNVs of all sizes even when the coverage level of read data is low. Sequence Analyser is a user-friendly program to view and compare variation regions between tumor and matched normal samples. It also provides a complete analysis function of refGene and OMIM data and makes it possible to discover CNV-gene-phenotype relationships. CNVDAT source code is freely available from http://dblab.hallym.ac.kr/CNVDAT/.

Learning Material Bookmarking Service based on Collective Intelligence (집단지성 기반 학습자료 북마킹 서비스 시스템)

  • Jang, Jincheul;Jung, Sukhwan;Lee, Seulki;Jung, Chihoon;Yoon, Wan Chul;Yi, Mun Yong
    • Journal of Intelligence and Information Systems
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    • v.20 no.2
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    • pp.179-192
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    • 2014
  • Keeping in line with the recent changes in the information technology environment, the online learning environment that supports multiple users' participation such as MOOC (Massive Open Online Courses) has become important. One of the largest professional associations in Information Technology, IEEE Computer Society, announced that "Supporting New Learning Styles" is a crucial trend in 2014. Popular MOOC services, CourseRa and edX, have continued to build active learning environment with a large number of lectures accessible anywhere using smart devices, and have been used by an increasing number of users. In addition, collaborative web services (e.g., blogs and Wikipedia) also support the creation of various user-uploaded learning materials, resulting in a vast amount of new lectures and learning materials being created every day in the online space. However, it is difficult for an online educational system to keep a learner' motivation as learning occurs remotely, with limited capability to share knowledge among the learners. Thus, it is essential to understand which materials are needed for each learner and how to motivate learners to actively participate in online learning system. To overcome these issues, leveraging the constructivism theory and collective intelligence, we have developed a social bookmarking system called WeStudy, which supports learning material sharing among the users and provides personalized learning material recommendations. Constructivism theory argues that knowledge is being constructed while learners interact with the world. Collective intelligence can be separated into two types: (1) collaborative collective intelligence, which can be built on the basis of direct collaboration among the participants (e.g., Wikipedia), and (2) integrative collective intelligence, which produces new forms of knowledge by combining independent and distributed information through highly advanced technologies and algorithms (e.g., Google PageRank, Recommender systems). Recommender system, one of the examples of integrative collective intelligence, is to utilize online activities of the users and recommend what users may be interested in. Our system included both collaborative collective intelligence functions and integrative collective intelligence functions. We analyzed well-known Web services based on collective intelligence such as Wikipedia, Slideshare, and Videolectures to identify main design factors that support collective intelligence. Based on this analysis, in addition to sharing online resources through social bookmarking, we selected three essential functions for our system: 1) multimodal visualization of learning materials through two forms (e.g., list and graph), 2) personalized recommendation of learning materials, and 3) explicit designation of learners of their interest. After developing web-based WeStudy system, we conducted usability testing through the heuristic evaluation method that included seven heuristic indices: features and functionality, cognitive page, navigation, search and filtering, control and feedback, forms, context and text. We recruited 10 experts who majored in Human Computer Interaction and worked in the same field, and requested both quantitative and qualitative evaluation of the system. The evaluation results show that, relative to the other functions evaluated, the list/graph page produced higher scores on all indices except for contexts & text. In case of contexts & text, learning material page produced the best score, compared with the other functions. In general, the explicit designation of learners of their interests, one of the distinctive functions, received lower scores on all usability indices because of its unfamiliar functionality to the users. In summary, the evaluation results show that our system has achieved high usability with good performance with some minor issues, which need to be fully addressed before the public release of the system to large-scale users. The study findings provide practical guidelines for the design and development of various systems that utilize collective intelligence.