1. Overview of Graduate Program at CS SFSU Fall 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.eduwww.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. Some new initiatives motivated by strong needs MS CS with business concentration (in plan) MS CS with art/media/games concentration (in plan)

8. 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/

9. Jobs Jobs are plenty SW Engineering voted best job by Money magazine BUT –New skills are needed

10. 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

11. 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)

12. 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

13. 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

14. 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.htmlhttp://www.cs.sfsu.edu/ccls/index.html

15. Important stuff Visit WWW site and read e-mail Program description http://www.cs.sfsu.edu/grad/grad_program.html http://www.cs.sfsu.edu/grad/grad_program.html Graduate page http://cs.sfsu.edu/grad/graduate.htmlhttp://cs.sfsu.edu/grad/graduate.html Importance of early advising. New students MUST see advisor http://cs.sfsu.edu/advising.htmlhttp://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 http://cs.sfsu.edu/grad/grad_recom_sequence.html Graduate seminar series requirement http://cs.sfsu.edu/news/Fall-2004-Pernet-Requirments.html 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 http://cs.sfsu.edu/forms/student%20forms/893- 694%20Course%20Requirments.pdf

16. More… All steps in preparing culminating project forms http://cs.sfsu.edu/forms/aboutculminatingproject.html http://cs.sfsu.edu/forms/aboutculminatingproject.html Culminating experience http://cs.sfsu.edu/grad/new_grad_culminating_req.html http://cs.sfsu.edu/grad/new_grad_culminating_req.html How to write culminating project report http://cs.sfsu.edu/grad/writing_cpr.html http://cs.sfsu.edu/grad/writing_cpr.html For new grads http://www.cs.sfsu.edu/grad/new_grad_helpnotes.html http://www.cs.sfsu.edu/grad/new_grad_helpnotes.html Cheating and plagiarism http://www.cs.sfsu.edu/plagarism.html http://www.cs.sfsu.edu/plagarism.html International program – Fulda, Germany http://cs.sfsu.edu/news/SFSUFulda.htm http://cs.sfsu.edu/news/SFSUFulda.htm

17. 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

18. 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 http://cs.sfsu.edu/advising.html

19. 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 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

20. 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/893- 694%20Course%20Requirments.pdf http://www.cs.sfsu.edu/forms/student%20forms/893- 694%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

21. 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 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.htmlhttp://www.cs.sfsu.edu/forms/student%20forms/opt_cpt_letter_inst ructions.html

22. 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

23. 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)

24. 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!

25. 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.

26. 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

27. 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.

28. 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.htmlhttp://www.cs.sfsu.edu/plagarism.html

29. Cluster Computing New 40 node DELL Cluster operational in CCLS http://ccls.lab.sfsu.edu/bin/view/Cluster/DellPowerEdgeCl uster 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…)

30. 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

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

32. 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

33. 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

34. 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

35. 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

36. 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.

37. How to find advisor and project Check CS WWW site for faculty pages and their work http://www.cs.sfsu.edu/People/people.html 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 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 http://www.cs.sfsu.edu/techreports/ce_list.html

38. 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 http://cs.sfsu.edu/techreports/ce_list.html

39. 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!

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

41. 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).

42. 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

43. 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 

44. 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

45. Research Thrusts and Initiatives Rahul Singh

46. 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, 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 Projects Details available at my research group’s web page: http://tintin.sfsu.edu

47. Data Mining Dr. Hui Yang (TH966, huiyang@cs.sfsu.edu)huiyang@cs.sfsu.edu –http://cose-stor.sfsu.edu/~huiyanghttp://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

48. 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

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

50. 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

51. 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

52. 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

53. 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/

54. 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

55. 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/

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

57. Learning Management Systems Develop tools for popular systems: Ilearn (Moodle) Sakai

58. 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)

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

60. 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