Overview of Graduate Program at CS SFSU February 2007

1. Overview of Graduate Program at CS SFSUFebruary 2007 Prof. D. Petkovic

2. 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!

3. 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.

4. 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

5. 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…

6. 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

7. 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/

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

9. 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 skills • Ability to work in a global and open SW environment

10. 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)

11. 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

12. 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

13. 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

14. 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 • Check new schedule http://cs.sfsu.edu/schedules/07/sp07.htm • 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/893-694%20Course%20Requirments.pdf

15. 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

16. 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 • 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-Requirments.html

17. 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

18. 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/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

19. Practical training – foreign students • 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 • 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_instructions.html

20. 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!

21. 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

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

23. Cluster Computing • New 40 node DELL Cluster operational in CCLS http://ccls.lab.sfsu.edu/bin/view/Cluster/DellPowerEdgeCluster • For projects in computational biology and life sciences • For education (distributed and parallel computing, data mining…)

24. 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 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

25. Graduate Seminar Series:How to complete Culminating Experience and have fun doing it Prof. D. Petkovic Chair, CS Department, SFSU dpetkovic@cs.sfsu.edu

26. Outline • 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

27. 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

28. 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

29. 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

30. 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.

31. 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

32. 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

33. 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!

34. Project Proposal • Submitted as part of your culminating experience package  Needed for enrolling into 895 • http://www.sfsu.edu/%7Egradstdy/culminating-experience.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

35. 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).

36. 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

37. 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 

38. 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

39. Research Thrusts and Initiatives Rahul Singh

40. Current Research Projects Multimedia Systems Computing in Life-Sciences 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 Projects 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 • 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

41. 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

42. 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 Theory) • Joined Computer Science Department at SFSU in 1985 • 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

43. 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

44. 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

45. 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

46. 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

47. Projects in computer music / audio • Performance measurement / characterization of real-time audio applications • Toolkit / workbench for psychoacoustic measurements • Exploration of novel interface devices for real-time music / audio applications Bill Hsu’s homepage: http://userwww.sfsu.edu/~whsu/

48. 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 • Statistical Pattern recognition • Computer vision • Machine learning • Neural Network • Artificial intelligence

49. Dr. Okada: Why & How to Join • Why? • 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/

50. Projects with Prof. Levine(Open Source Based)