Overview of Graduate Program
at CS SFSU
Fall 2007
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 important
• 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 Department
• 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 wireless
• 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 development.
• 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
Some new initiatives motivated
by strong needs
• MS CS with business concentration (in
plan)
• MS CS with art/media/games concentration
(in plan)
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
• Jobs are plenty
• SW Engineering voted best job by Money
magazine
BUT
– New skills are needed
Computer Scientist of the future
• Knowledge of technical material (up to date)
• Knowledge of some specific domains (financials,
biotech, games…)
• Project and teamwork skills
• Verbal and written communication and
presentation skills
• Ability to work in a global and open SW
environment
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, tools)
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 conferences
• 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/grad_program.html
• Graduate page http://cs.sfsu.edu/grad/graduate.html
• 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_sequence.html
• Graduate seminar series requirement
http://cs.sfsu.edu/news/Fall-2004-Pernet-Requirments.html
• Internships – new polices on 893 (practicum) – important
for foreign students http://cs.sfsu.edu/forms/student%20forms/893694%20Course%20Requirments.pdf
More…
• All steps in preparing culminating project forms
http://cs.sfsu.edu/forms/aboutculminatingproject.html
• Culminating experience
http://cs.sfsu.edu/grad/new_grad_culminating_req.html
• How to write culminating project report
http://cs.sfsu.edu/grad/writing_cpr.html
• For new grads
http://www.cs.sfsu.edu/grad/new_grad_helpnotes.html
• Cheating and plagiarism
http://www.cs.sfsu.edu/plagarism.html
• International program – Fulda, Germany
http://cs.sfsu.edu/news/SFSUFulda.htm
Graduate seminar (formerly
Pernet)
• Brings outstanding speakers from academia an
industry. Every Wednesdays 5:30 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
• Early two seminars by Prof. D. Petkovic: about
graduate program and about department research
• http://www.cs.sfsu.edu/news/Fall-2004-Pernet-Requirments.html
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 5:30 in TH 331
• Should attend Chair’s 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
AND letter signed by student about the rules (NEW).
http://cs.sfsu.edu/forms/student%20forms/opt_cpt_letter_instructions.html
• 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
Foreign students – CSC 893
• CSC 893 allows you to get visa for summer jobs – 1 unit,
up to three times
• Summer internships are very important!
• Report written at the beginning and end (check CS WWW)
http://www.cs.sfsu.edu/forms/student%20forms/893694%20Course%20Requirments.pdf
• Three 893s can not be used as elective
• Those who are offered to continue work in Fall semester
need special approval from Chair:
– Employer agreement to offer only up to 20 H/week work (e-mail
from employer sent to Chair)
– GPA > 3.5
– Chair approval
– Approval done on semester by semester basis
Practical training – foreign
students
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Must have GPA > 3
Must not delay graduation
Thesis practical training will be harder to justify
Post-completion practical training can start only when the
thesis is 90% or more completed AND when students signs
the letter stating he/she understand the rules about
finishing the thesis
• Starting work under practical training before graduation is
not advisable and not good for you!
• New process:
– http://www.cs.sfsu.edu/forms/student%20forms/opt_cpt_letter_inst
ructions.html
Foreign students- OPT stuff
• Jobs are plenty and grads need money –
understood!
• To get OPT permit takes 2-3 months
• However, no OPT letter will be issued unless the
work on the culminating experience (including the
writing part) is 90% or more done.
• The above will be conformed by e-mail of advisor
to Chair AND by student signing the letter stating
that no thesis defense can be scheduled unless
culminating experience report is done
Update on Written English
proficiency SCI 614
• Level One: The Computer Science Department will
strictly enforce the University Policy that all students must
satisfy English Level I prior to filing their GAP. Computer
Science students can satisfy the English Level I
requirement by a grade of PASS on the GET, or by a grade
of PASS in SCI 614 (or CHS 514 with the approval of a
CS Graduate Advisor). Please note that if English Level I
is not satisfied by the end of the second term of study,
completion of the MS degree in four semesters is unlikely.
The Computer Science department recommends that
entering graduate students take the GET exam immediately
prior to entry into the program, then enroll in SCI 614
during their first term of study, as necessary.
• Take SCI 614 NOW (class has room)
Welcome foreign students!
• Learn about USA: customs, culture, geography
• Bay Area is one of the bets areas in USA:
geographically, culturally, for education and
technology
• Get internships with local industry
• Visit places, talk to [people
• Learn English (reading, writing)
• Have fun!
Check new schedule
(note: tentative Spring 08 schedule
also posted)
• http://www.cs.sfsu.edu/schedule.html
• New courses
872 Pattern Analysis and Machine Intelligence
Prerequisite: grades of C or better in CSC 510 and CSC 520 or
consent of instructor.
Foundation of pattern analysis and machine intelligence. Artificial
intelligence: agent, logic, search. Machine learning: Bayesian
classification. Neural network: simulated annealing. Imaging:
image segmentation, object recognition.
New courses
• 831 Multiplayer Game Development
– Prerequisite: CSC 413 or consent of instructor.
– Computer graphics and network characteristics
of multiplayer games. Design and development
of a game as a team project. Paired with CSC
631. Students who have completed 631 may not
take 831 for credit
New courses
• CSC 440 Programming Cafe (will be
renumbered as 6XX)
– Prerequisites: CSC 413 with grade C or better
or consent of instructor.
– Extensive programming practice to advance
programming skills and processes; pair
programming exercises; code review techniques
and practice.
Other stuff
• CSC 858 “Biology for CS” is now is prereq for
“Bioinformatics Computing”
• Please consider taking CSC 858 – great material,
great instructor - Prof. S. Weize
• Policy on cheating and plagiarism will be strictly
enforced – (students are getting inventive…)
– http://www.cs.sfsu.edu/plagarism.html
Cluster Computing
• New 40 node DELL Cluster operational in CCLS
http://ccls.lab.sfsu.edu/bin/view/Cluster/DellPowerEdgeCl
uster
• For projects in computational biology and life sciences
• For education (distributed and parallel computing, data
mining…)
Next Graduate Seminar
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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 experience
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@cs.sfsu.edu
Outline
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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 experience
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_req.html
• 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 conferences
– 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
schedules
http://www.cs.sfsu.edu/forms/aboutculminatingproject.html
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.html
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
http://cs.sfsu.edu/ccls/index.html
• 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
http://www.cs.sfsu.edu/techreports/ce_list.html
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: http://cs.sfsu.edu/techreports/ce_list.html
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 work
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/culminatingexperience.htm
• 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
life
• 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 career
• 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/student%20forms/prep_oral_presentations.htm
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, Petkovic
• DB Tools, Multimedia databases: Profs. Murphy, Singh, Petkovic
• Bioinformatics: Prof. Singh
• Visualization/Graphics: Profs. Yoon, Okada
• WWW Applications, Community applications: Prof. Levine
• Performance: Prof. Dujmovic
• WWW info retrieval, WWW 2.0: Profs. Singh, Wong
• Algorithms, compilers, WWW search: Profs. Wong, Dujmovic
• 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
Goal: Develop computing as a new way
(in addition to Biology and Chemistry) to
reason about the complexity of life
Projects
-Develop techniques for query-retrieval of
molecules
- Predicting pharmaceutically-important
molecular properties
- Drug-discovery information storage, retrieval, and
interactions (currently being used at UCSF)
-Tandem Mass Spectrometry-based de-novo
protein sequencing
- Microarray compression, storage, and analysis
Multimedia Systems
Goal: Make storage, querying, and interactions
across multiple-media easier than across single
media
Projects
-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 group’s web page: http://tintin.sfsu.edu
Data Mining
• Dr. Hui Yang (TH966, huiyang@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 Genomics
• 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
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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 Theory)
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Joined Computer Science Department at SFSU in 1985
Visiting Scientist at Lawrence Berkeley Labs, Data Management Group, 19871992
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
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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 enhancements
• 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.html
Projects in computer music / audio
• Performance measurement / characterization of
real-time audio applications
• Toolkit / workbench for psychoacoustic
measurements
• Exploration of novel interface devices for realtime music / audio applications
Bill Hsu’s homepage:
http://userwww.sfsu.edu/~whsu/
Dr. Okada: Projects & Interests
• New Funded Projects
– Computer-aided Diagnosis for Dentistry (CCLS, CSUPERB)
• 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
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Statistical Pattern recognition
Computer vision
Machine learning
Neural Network
Artificial intelligence
Dr. Okada: Why & How to Join
• Why?
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Preparation for PhD studies and R&D jobs
Mentoring on AI / Machine Learning / Computer Vision
Coaching the art of publications
External summer internships at Siemens
 Funded research opportunities
• How to join
 New course on AI / Neural Network / Machine Learning
 Appointment via email: kazokada@sfsu.edu. TH911
 http://organic.usc.edu:8376/~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.ivsl.org/)
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 Server)
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.
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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.
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Sample topics :
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* Internet gadget management
* RSS feed management
* Personalized web page
* Dynamic web content
* Centralized file sharing software system