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CS3230R: Design and Analysis of Algorithms (R)
Spring 2014
R Section for CS3230R of Fall 2013, Spring 2014
(Leong Hon Wai and Ken Sung Wing Kin)

Course Web-Site

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LATEST UPDATE

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Course Instructors:

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Course Information:

• Course Info Presentation Slides () -- [here (pdf)]

• Project Deliverables -- [ here (txt)] (Project Software and Report)

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CS3230R Talk Series

• 06-Feb (W4) -- "Overview of Community Detection Methods", Davin Choo -- | slide
• 13-Feb (W5) -- "Community Detection II, CS3230R Guidelines", by Hon Wai -- | slide
• 20-Feb (W6) -- "Choosing your Specific Topic", discussion led by Hon Wai

• Break

• 06-Mar (W7) -- Update Meeting, led by Hon Wai
• 13-Mar (W8) -- Davin and WenBo (Testing and Test-Data) -- | Davin's slides | WenBo's slides
• 20-Mar (W9) -- YuJian, Darius -- | Darius's slides
• 27-Mar (W10) -- ShuZhi, Duy -- | ShuZhi's slides | Duy's slides
• 03-Apr (W11) -- Eugene Lim | Eugene's slides
• 10-Apr (W12) -- Wu Lifu, Naomi Leow,

• 17-Apr (W13) -- Tang YiXuan, Davin?, WenBo?

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Test Data for Community Detection Algorithms (compiled by Wei WenBo, Thanks!)

• CS3230R-Famous-Graphs (zip)
• CS3230R-Random-Graphs (zip)

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Possible Project Topics:

• From LeongHW (Fall 2013, Spring 2014):
  • 1. algorithms for detecting communities in large sparse graphs.
  • 2. algorithms for finding conserved frequent k-mers in DNA sequences.

    Reference:
    1. Santo Fortunato, "Community detection in graphs," Physics Reports, Volume 486, Issues 3-5, Feb 2010, pp.75-174.
    | Link | local-copy |
    (or you can also Google "community detection in large graphs").

    2. Please contact me (LeongHW) for details of this problem.

• From Ken Sung (Fall 2013):
  • I don't have any specific problems for the students.
    Most likely, I will just ask to implement algorithms related to phylogenetic tree or date compression.
    Depend on the progress of the students, they can generate some new ideas.

  • References:
    1) Jesper Jansson, Chuanqi Shen, Wing-Kin Sung: Improved Algorithms for Constructing Consensus Trees. SODA 2013: 1800-1813
    2) Deorowicz, S.; Danek, A. & Grabowski, S. "Genome compression: a novel approach for large collections". Bioinformatics 2013

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Student List (those who took CS3230 Fall 2013):

• "LI Zhaoxian" , (Consensus Tree [Ken Sung])
• "Naomi LEOW" , (community detection [K-means])
• "TANG Yixuan" , (community detection [MCL and random walks])
• "WANG TaiNing" , (compression [Ken Sung])
• "WEI Wenbo" , (community detection [Girvan-Newman])
• "WU LiFu" , (k-mers)
• "YAO Yujian" , (community detection [appl to study]) -
• "YU Shuzhi" , (community detection [Hierarchical method])

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Student List (those taking CS3230 Spring 2014):

• "Darius FOO Tsien Wei" , (LR parser [self])
• "LIM Hong Hui Eugene" , (community detection [Clique Percolation])

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Student List (others):

• "NGUYEN Truong Duy" (community detection [Infomap and MCL])
• "Davin CHOO" , (community detection [Modularity optimization])

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Some General Readings:

• COMPULSORY: Read this first! -- Cattywampus? -- An inspiring article.

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Past Announcements (reverse chrono order):

• 20-Mar-2014 (W9): Talk by YAO YuJian and Darius Foo
  • ShuZhi to chair the session.
  • Prof Leong away on conference in Japan -- | NII-Shonan-Meeting #45
    "Towards the Ground Truths: Exact Algorithms for Bioinformatics Research"

• 13-Mar-2014 (W8) Talk on Testing and Test-Data
  • Testing and Comparison Metrics -- Davin Choo
  • Test Data & its Generation -- Wu WenBo

• 27-Feb-2014 (Break) -- No meeting during the Mid-Sememster Break

• 20-Feb-2014 (W6) -- Finalizing all projects, by Hon Wai

• 13-Feb-2014 (W5) -- Second Talk in Series, by Hon Wai

• 06-Feb-2014 (W4) -- CS3230R Talk Series (first one today)
  • First talk will be "Overview of Community Detection Methods"
  • Time: Thursday, 12nn -- 1pm
  • Venue: MR5 (COM1-Level 1)

• 28-Jan-2014 (W3) -- No meeting, CNY Eve

• 21-Jan-2014 (W2) -- First Meeting -- Your projects selected?
  • I have finally got all the answers to your project choices;
  • Apparently "community detection" is very popular.
  • So, a meeting (later this week) is probably a good idea to get started.
  • Look out for my email on timing and details. Will post here when finalized.

• 13-Jan-2014 -- CS3230R site linked to CS3230 (Spring 2014)
  • I have set up the course web-page.
  • Email has gone out to students from Fall 2013 who indicated interest and to those in Spring 2014 who has already contacted us to ask about CS3230R.

• 07-Jan-2014 -- Course website set up
  • Basic info on CS3230R online. More to come soon.

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