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Overview of Graduate Program at CS SFSU February 2007


A lot of research, projects and publications. www.cs.sfsu.edu. Trends in Software Development ... Recommended sequence of study, selection of concentration ... – PowerPoint PPT presentation

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Title: Overview of Graduate Program at CS SFSU February 2007

Overview of Graduate Program at CS SFSU February
  • Prof. D. Petkovic

Welcome graduate students!
  • MS degree becoming a key for advancement
  • Ability to work with geographically dispersed
    teams and multidisciplinary teams is increasingly
  • Combination of general CS skills, domain depth
    and soft skills is critical
  • Welcome foreign students
  • Jobs are good!

CS Department mission
  • Goals to be the best in CSU and world famous in
    selected areas of Computer Science
  • Prepare students for careers in industry
  • Prepare students for further graduate study
  • CS WWW site www.cs.sfsu.edu
  • Visit CS WWW site often and read office e-mail
  • We offer BS and MS in CS
  • About 500 undergrads, about 120 grads
  • Most students have MS as terminal degree, and
    there are some going for Ph.D.

About CS Department
  • Blends top notch instructions with research
  • Very high quality research for CSU standards, at
    the level of top schools
  • Second NSF CAREER grant won (Prof. R. Singh)
    outstanding accomplishment for faculty and the
  • A lot of research, projects and publications
  • www.cs.sfsu.edu

Trends in Software Development
  • Global development of computer software through
    international cooperation and outsourcing are the
    main characteristics of current and future
    software engineering development process
  • Increased emphasis on building SW from components
    and services developed globally
  • Everything is getting connected with WWW and
  • Critical need for making systems easy to use, on
    time and budget, and with adequate performance,
    with geographically dispersed teams
  • Open source software community is another example
    of global collaborative approach to SW
  • New areas games, sensor networks, biotech,
    personal devices…

Computing and Life Sciences
  • Biotechnology, bioinformatics and related
    applications are considered next frontiers for
    computer science, both technically and in terms
    of business opportunities
  • Bay Area is one of the world centers of
    bioinformatics and bio technology
  • SFSU has outstanding programs related to biology
    and chemistry/biochemistry and skills and
    interests from Math
  • Every major university is having or will have
    programs in this area
  • Increased focus by funding agencies, government,
    politicians and university executives
  • Strong interest among students and faculty
  • ? SFSU Center for Computing for Life Sciences

Motivation for updating the curricula
  • ACM study on SW outsourcing and globalisation
    specifically mentions the need to train SE
    students in so called soft skills, teamwork,
    communication, SE process organization and issues
    related to globalisation
  • Aspray W., Mayadas F., Vardi M.Y., Editors
    Globalisation and Offshoring of Software, A
    Report of the ACM Job Migration Task Force, ACM
    2006, http//www.acm.org/globalizationreport/

  • Jobs are plenty
  • SW Engineering voted best job by Money magazine
  • http//money.cnn.com/magazines/moneymag/bestjobs/
  • BUT
  • New skills are needed

Computer Scientist of the future
  • Knowledge of technical material (up to date)
  • Knowledge of some specific domains (finacials,
    biotech, games…)
  • Project and teamwork skills
  • Verbal and written communication and presentation
  • Ability to work in a global and open SW

Recent changes in SFSU MS program
  • 2 new concentrations started in 2004 SW
    Engineering and Computing for Life Sciences (old
    program basically a third, general concentration)
  • More multidisciplinary projects especially in the
    area of Computing for Life Sciences
  • More research and involvement of students in
    research and publications
  • More individual and team projects, with written
    and oral components
  • Projects and internships with local industry
  • Practicum option for foreign students
  • Center for Computing for Life Sciences
    established (projects, theses, research, space,

Program description
  • 3 concentration, but basically a MS CS degree
  • Concentrations General. SW Engineering,
    Computing for Life Sciences
  • Same core and same electives
  • Concentrations differ by concentration core and
    thesis/CE (culminating experience) topic
  • 30-33 units (extra 3 for practicum option for
    foreign students)
  • http//cs.sfsu.edu/grad/grad_program.html

Thesis and Culminating project
  • Mandatory
  • Why thesis?
  • Forces students to do independent work and
    complete a substantial project or scientific work
  • Requires writing and presentation skills also
  • Sets you apart from those who have not done it
  • Enables you to publish papers and go to
  • Enables CS department to do research and attract
    top notch faculty important for you too
  • Makes our school much more fun

Center for Computing for Life Sciences (CCLS)
  • CCLS is an official multidisciplinary SFSU Center
    for addressing problems in broad area of
    Computing for Life Sciences such as
    bioinformatics, imaging, collaborative tools, UI,
    visualization, databases, computational biology
    and chemistry, applications in drug discovery,
    collaborative tools, algorithms etc.
  • Goal is to develop CCLS into signature marquee
    program of SFSU
  • CCLS is joint collaboration between Computer
    Science, Biology, Chemistry and Biochemistry,
    Math, Physics and Astronomy
  • http//www.cs.sfsu.edu/ccls/index.html

Important stuff
  • Visit WWW site and read e-mail
  • Program description http//www.cs.sfsu.edu/grad/gr
  • Graduate page http//cs.sfsu.edu/grad/graduate.htm
  • Check new schedule http//cs.sfsu.edu/schedules/07
  • Importance of early advising. New students MUST
    see advisor http//cs.sfsu.edu/advising.html
  • Recommended sequence of study, selection of
    concentration second semester finding the
    advisor http//cs.sfsu.edu/grad/grad_recom_sequenc
  • Graduate seminar series requirement
  • Internships new polices on 893 (practicum)
    important for foreign students http//cs.sfsu.edu/

  • All steps in preparing culminating project forms
  • Culminating experience http//cs.sfsu.edu/grad/new
  • How to write culminating project report
  • For new grads http//www.cs.sfsu.edu/grad/new_grad
  • Cheating and plagiarism http//www.cs.sfsu.edu/pla
  • International program Fulda, Germany

Graduate seminar (formerly Pernet)
  • Brings outstanding speakers from academia an
    industry. Every Wednesdays 530 in TH 331.
    Exposes students to great topics and great
    speakers, helps give ideas for projects and jobs
  • Each graduate student must attend all seminars in
    one Semester
  • First two seminars by Prof. D. Petkovic about
    graduate program and about department research
  • Starts 02/07/07
  • http//www.cs.sfsu.edu/news/Fall-2004-Pernet-Requi

Advising - NEW
  • Must see advisor upon start of the program
  • Must attend first Graduate Seminar during the
    first term (CS Chair will overview grad program)
    Wednesdays 530 in TH 331
  • Should attend Chairs welcome group meeting at
    the beginning of each semester
  • Get timely advising as often as you need
  • Those planning for Ph. D. program see CS Chair
    in the first semester
  • Advising page http//cs.sfsu.edu/advising.html

Welcome foreign students!
  • Keep GPA and class load above the minimum -
    Overall GPA 3.0, class load 9 units
  • New practicum option Max 3 one unit 893 can be
    taken that do not count toward electives and
    allow you permit to work outside of SFSU. Mostly
    for Summer work. Total units in MS program are
    then are 33
  • Post completion training allowed only when thesis
    is more than 90 complete, need confirmation by
    the advisor. http//cs.sfsu.edu/forms/student20fo
  • Conditional graduate students should chose CR/NC
    option for conditional courses where possible in
    case they get NC they do go on probation but do
    not lose work permit. Department will enforce
    conditions but this gives us greater flexibility

Practical training foreign students
  • Must have GPA gt 3
  • Must not delay graduation
  • Thesis practical training will be harder to
  • Post-completion practical training can start only
    when the thesis is 90 or more completed
  • Starting work under practical training before
    graduation is not advisable and not good for you!
  • New process
  • http//www.cs.sfsu.edu/forms/student20forms/opt_c

Welcome foreign students!
  • Learn about USA customs, culture, geography
  • Bay Area is one of the bets areas in USA
    geographically, culturally, for education and
  • Get internships with local industry
  • Visit places, talk to people
  • Learn English (reading, writing)
  • Have fun!

Check new schedule
  • http//cs.sfsu.edu/schedules/07/sp07.htm
  • New courses
  • CSC 869 Data Mining
  • CSC 870 Comp. Geometry (with Math Department)
  • Help in writing Culminating Experience Reports
  • http//www.cs.sfsu.edu/grad/writing_cpr.html

Other stuff
  • Biology for CS is now is prereq for
    Bioinformatics Computing
  • Policy on cheating and plagiarism will be
    strictly enforced (students are getting
  • http//www.cs.sfsu.edu/plagarism.html

Cluster Computing
  • New 40 node DELL Cluster operational in CCLS
  • For projects in computational biology and life
  • For education (distributed and parallel
    computing, data mining…)

Next Graduate Seminar
  • What is culminating experience
  • Why is it good for you
  • Formal requirements and paperwork
  • How to find the project and advisor
  • What is good research/project for culminating
  • How to do it?
  • How to write the Culminating Experience Report
  • How to prepare oral presentation
  • Overview of research in CS Department and CCLS

Graduate Seminar Series How to complete
Culminating Experience and have fun doing it
  • Prof. D. Petkovic
  • Chair, CS Department, SFSU
  • dpetkovic_at_cs.sfsu.edu

  • What is culminating experience
  • Why is it good for you
  • Formal requirements and paperwork
  • How to find the project and advisor
  • What is good research/project for culminating
  • How to do it?
  • How to write the Culminating Experience Report
  • How to prepare oral presentation
  • Overview of research in CS Department and CCLS

Culminating Experience
  • Thesis (CSC 898) vs. Project (CSC 895)
  • http//www.cs.sfsu.edu/grad/new_grad_culminating_r
  • One or two semesters prep (897 or 899) and one
    semester thesis or project write-up and
    completion (898 or 895)
  • Those going for Ph. D. advised to take two
    semester prep and more advanced culminating
    experience, with external publications

Why is Culminating Experience good for you
  • It is Mandatory
  • Why?
  • Forces students to do independent work and
    complete a substantial project or scientific work
  • Requires writing and presentation skills also
  • Sets you apart from those who have not done it
  • Enables you to publish papers and go to
  • Prepares you for jobs and Ph.D. studies
  • Enables CS Department to do research and attract
    top notch faculty important for you too
  • Makes our school much more fun

Formal requirements and paperwork
  • Please follow the process and observe the
  • http//www.cs.sfsu.edu/forms/aboutculminatingproje
  • By this time you should already get an advisor!
    Start in second semester
  • Follow the suggested course of study
  • http//www.cs.sfsu.edu/grad/grad_recom_sequence.ht

For Foreign Students
  • When doing 895 or 898 make sure you check for
    reduced load with OIP
  • Post completion practical training will NOT be
    approved until 95 of the thesis or project work
    is completed (need e-mail from the advisor)
    this is for your protection
  • If 895 or 898 not completed, you get an RP, which
    is OK for visa issues.

How to find advisor and project
  • Check CS WWW site for faculty pages and their
    work http//www.cs.sfsu.edu/People/people.html
  • Check CS accomplishments and published papers to
    get an idea what work is going on and who is
    doing it, then talk to them
  • http//cs.sfsu.edu/RecentAccomplishments.htm
  • http//cs.sfsu.edu/externalpubs/2004pubs.htm
  • Attend Graduate Seminar Series and other seminars
    at SFSU
  • Check CCLS page for current projects
  • Do your own research for topics (WWW, friends,
    technical press)
  • Take the course form the professors teaching your
    favorite topics favorite professor
  • Ask professors, meet with the Chair
  • Check previous theses and projects

What is good research for culminating experience
  • Novel algorithm solving something useful
  • New user interface or visualization
  • New application (use of complex machine vision,
    AI, visualization, search…)
  • Substantial SW project (complex WWW site, useful
    application etc.)
  • Data management and analysis system for some
    application (e.g. drug development)
  • Performance study (networking, search, storage,
    cluster computing)
  • Computing for life sciences intersection of CS
    and biology and chemistry
  • ……………..
  • In all cases one has to prove the usefulness
    theoretically, experimentally, user studies etc.
    whichever applies
  • Culminating experience examples

How to do the research
  • Requires independence, focus and follow up
  • Understanding of the problem
  • Literature review (what did others do)
  • Design, analysis, prototyping
  • Experiments
  • Implementation
  • Writing
  • It requires much more independence then class
  • It is student responsibility to follow up, not
    the instructor!

Project Proposal
  • Submitted as part of your culminating experience
    package ? Needed for enrolling into 895
  • http//www.sfsu.edu/7Egradstdy/culminating-experi
  • It is a contract between you and advisor on
    what you want to do, scope, methods, tools used
    etc. Has to be approved by the advisor.
  • Suggested Content Motivation, planned approach,
    benefits of the approach, method/tools to be
    used, reverences PLUS milestones and schedule
    (the best you can) for exact outline check with
    your advisor
  • About 5-8 pages

How to write culminating experience report
  • There is some structure
  • http//cs.sfsu.edu/grad/writing_cpr.html
  • Usual length about 60-70 pages (no code)
  • Code on a CD
  • Requires time
  • Expect multiple iterations with the instructor
  • It becomes your portfolio for the rest of your
  • Make every attempt possible to write a scientific
    paper form this (must for those going to Ph. D).

How to prepare oral presentation
  • Being able to present well is critical for your
  • Culminating experience presentation plan to talk
    30 min. Count 1 slide 2 min.
  • Test the presentation on the very same laptop you
    will use
  • Get feedback from advisor
  • Do early motivation and demo, then details
  • Talk to the audience, not the screen
  • Practice for time and delivery
  • Resources
  • http//cs.sfsu.edu/forms/student20forms/prep_oral

Overview of research and CS Department and CCLS
  • CS Department check papers, faculty pages
  • http//cs.sfsu.edu/externalpubs/2004pubs.htm
  • http//cs.sfsu.edu/People/people.html
  • CCLS Check projects
  • http//cs.sfsu.edu/ccls/projandgrants.htm
  • Some highlights follow ?

Some project ideas/people
  • DB/UI/Applications in biology and bioinformatics
    and CLS area Profs. Singh, Yoon, Okada, Yang,
  • DB Tools, Multimedia databases Profs. Murphy,
    Singh, Petkovic
  • Bioinformatics Prof. Singh
  • Visualization/Graphics Profs. Yoon, Okada
  • WWW Applications, Community applications Prof.
  • Performance Prof. Dujmovic
  • WWW info retrieval, WWW 2.0 Profs. Singh, Wong
  • Algorithms, compilers, WWW search Profs. Wong,
  • Distributed Systems, Open Source Prof. Puder
  • Multimedia, sound, music Profs. Hsu, Singh
  • Games Profs. Yoon, Okada
  • AI, Computer Vision Prof. Okada
  • Data Mining Prof. Yang

Research Thrusts and Initiatives
  • Rahul Singh

Current Research Projects
Computing in Life-Sciences
Multimedia Systems
Goal Develop computing as a new way (in addition
to Biology and Chemistry) to reason about the
complexity of life
Goal Make storage, querying, and
interactions across multiple-media easier than
across single media
  • Develop techniques for query-retrieval of
  • molecules
  • - Predicting pharmaceutically-important
  • molecular properties
  • Drug-discovery information storage, retrieval,
  • interactions (currently being used at UCSF)
  • Tandem Mass Spectrometry-based de-novo
  • protein sequencing
  • - Microarray compression, storage, and analysis
  • Development of unified multimedia data models
  • Application of unified-modeling in personal
  • information management
  • - New UI-paradigms for interacting with media
  • Multimodal Web-Usability Analysis
  • Linguistic Models for Image Retrieval
  • Multimodal Biological Information Search and
  • Exploration
  • - IR across multiple media

Details available at my research groups web
page http//tintin.sfsu.edu
Data Mining
  • Dr. Hui Yang (TH966, huiyang_at_cs.sfsu.edu)
  • http//cose-stor.sfsu.edu/huiyang
  • Main research projects
  • Protein structural analysis
  • Gene expression analysis of the human
    maternal-fetal interface
  • Educational needs assessment in Nutritional
  • Student research assistant needed now!
  • Main task web applications design development
  • Key skills HTML, XML, JaveScript, PHP, and
    web-based MySql data manipulation

Prof. Marguerite Murphy
  • BS Electrical Engineering/Computer Science, UC
    Berkeley (1980)
  • Software Programmer/Analyst, Intel Systems Corp.
    (Summer 1981)
  • MS Computer Science, UC Berkeley (1982)
  • PhD Computer Science, UC Berkeley (1985)
  • Project Advisor Prof. Michael Stonebraker
  • Thesis Area Database Systems
  • Minor fields Statistics and IEOR (Queueing
  • Joined Computer Science Department at SFSU in
  • Visiting Scientist at Lawrence Berkeley Labs,
    Data Management Group, 1987-1992
  • Research Consultant at Hewlet Packard Labs, DB
    Technology Department, 1990
  • Tenured at SFSU in 1991 and promoted to Full
    Professor in 1994

Prof. Marguerite Murphy
  • Home Page https//dbsgrad.sfsu.edu/mmurphy
  • Current Areas of Instruction/Research
  • Database Systems
  • Computer Networks/Internetworks
  • Bioinformatic/Scientific Data Management
  • Multimedia Systems
  • Educational Software Development

Prof. Marguerite Murphy
  • Recent Student Projects
  • 75 culminating experience projects completed
    since my home web site came up in 2000 (and many
    more were completed prior to that time!)
  • Student Projects Web Site
  • https//dbsgrad.sfsu.edu/mmurphy/Research.htm
  • most topics have follow up projects available,
    and many projects have web sites with links on
    the page above
  • Recommended preparatory coursework for doing
    project work under my supervision CSC 730/875
    and/or CSC 845

Bill Hsu research summary
  • Areas and related courses
  • Computer architecture and performance
  • CSc 656 Computer organization
  • CSc 846 Systems architecture
  • CSc 856 Advanced computer architecture
  • Computer music/audio
  • CSc 637/737 Software for computer music
  • CSc 837 Advanced sound synthesis

  • Projects in computer architecture / performance
    mostly involve benchmarking, CPU-level and
    system-level measurements
  • Select interesting application domain, measure
    hardware resource consumption, explore
  • Build tools for performance measurement
  • Recent examples
  • Chahal
  • http//cs.sfsu.edu/techreports/05/TR-05-25.htm
  • Mariadassou
  • http//cs.sfsu.edu/techreports/04/summer/TR-04-31

  • Projects in computer music / audio
  • Performance measurement / characterization of
    real-time audio applications
  • Toolkit / workbench for psychoacoustic
  • Exploration of novel interface devices for
    real-time music / audio applications
  • Bill Hsus homepage
  • http//userwww.sfsu.edu/whsu/

Dr. Okada Projects Interests
  • New Funded Projects
  • Computer-aided Diagnosis for Dentistry (CCLS,
  • Data segmentation and classification
  • Collaboration with a team at Univ. So. Cal.
  • Interactive Intelligent Computing (CCLS, SFSU)
  • Fusion HCI and Pattern Recognition
  • Web-based collaboration tool
  • 3D biomedical data visualization annotation
  • Computer Vision (SFSU)
  • Face and object recognition
  • Interests
  • Statistical Pattern recognition
  • Computer vision
  • Machine learning
  • Neural Network
  • Artificial intelligence

Dr. Okada Why How to Join
  • Why?
  • Preparation for PhD studies and RD jobs
  • Mentoring on AI / Machine Learning / Computer
  • Coaching the art of publications
  • External summer internships at Siemens
  • Funded research opportunities
  • How to join
  • New course on AI / Neural Network / Machine
  • Appointment via email kazokada_at_sfsu.edu. TH911
  • http//organic.usc.edu8376/kazunori/

Projects with Prof. Levine (Open Source Based)
Learning Management Systems
  • Develop tools for popular systems
  • Ilearn (Moodle)
  • Sakai

Iraqi Virtual Science Library Project (https//www
  • Infrastructure to provide server-based access to
    aggregated digital library resources
  • Currently being ported to Armenia
  • Need students interested in developing modules to
    enhance use
  • Java-based (Java Server Faces, Sun Application

Requirements to Work with Dr. Levine
  • Complete CSC 868 with good grade
  • Enroll in CSC 899/895

Prof. Wong
  • Design and implement Web 2.0 applications.
  • Web 2.0 refers to second generation of
    Web-based services such as
  • Google (e.g. Google Map and My Google), Flickr,
    and YouTube.
  • A Web 2.0 application typically uses the
    technologies including JavaScript,
  • AJAX, RSS data, APIs and XML. Using these
    technologies, it is possible
  • to create powerful, dynamic and real-time
    interactive web applications
  • fast and relatively inexpensive.
  • Sample topics
  • Internet gadget management
  • RSS feed management
  • Personalized web page
  • Dynamic web content
  • Centralized file sharing software system
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