Department Accomplishments

NIH Awards the Prestigious R01 Grant to Dr. Singh

The National Institutes of Health has awarded one of its most prestigious research grants to a team of investigators from SFSU and UCSF. Dr. Singh is one of the three joint-principal investigators (PIs) of this grant. This research will combine algorithmic research by Dr. Singh's lab with techniques from high-throughput screening and Parasitology to develop novel ways of drug screening against the disease Schistosomiasis, which inflicts a large number of people across the world.


This is the first time in the history of SFSU that a faculty member has competed for and received the NIH-R01 grant. With this award Dr. Singh also joins a very select group of computer scientists across the country who hold simultaneous PI-ship on the NSF CAREER grant (given to the most promising your scientists by the National Science Foundation) and the NIH R01 grant. Enquiries for further information about this research/grant should be directed to Dr. Singh.


Dr. Singh Receives the CSUPERB Entrepreneurial Joint Venture Grant

Dr. Rahul Singh has received the Entrepreneurial Joint Venture grant from the California State University Program for Education and Research in Biotechnology As part of this grant, Dr. Singh's lab will develop algorithms for analyzing the phenome of parasites that lead to many of the most widespread parasitic diseases of mankind. Enquiries for further information about this research/grant should be directed to Dr. Singh.


CS Department Students Win Top Prizes at 2009 COSE Student Project Showcase

We are proud to announce that students from the Computer Science Department won top prizes in the Graduate Physical Science Division of the College of Science and Engineering's (COSE) Student Project Showcase competition held at SFSU on 4/24/09. Of the four graduate students from the department that entered, three placed. They are:

  • First Prize: “Directional Mean Shift”, student: M. Kafai, Advisor: Prof. K. Okada
  • Second Prize (Shared): "XMAS: Experiential Visualization, Mining, and Analysis of Time-Series Microarray Experiments; Student B. Dalziel"; Advisors: Profs R. Singh, H. Yang
  • Fifth Prize: “Automated Image-Based Phenotypic Screening of Multi-Cellular Pathogens for High-Throughput Drug Discovery


Dr. Petkovic Receives Distinguished Faculty of the Year Award

Professor Petkovic awarded Office of International Programs's 2009 Distinguished Faculty of the Year for his contributions in the field of international education...more


Stanford Bioengineering and SFSU CS Awarded NIH Grant

The Stanford Bioengineering team, led by Prof. Russ Altman, Stanford Bioengineering Department, and SFSU team (Profs. Petkovic, Hsu, Buturovic and CCLS Research Programmer M. Wong) were awarded NIH grant titled "Annotating Functional Sites in 3D Biological Structures." The San Francisco State University team will be working on Software Engineering aspects, applications of machine learning and on performance enhancements using modern GPU processors. The grant is funded for 5 years.

Grant abstract is at the link below:


Dr. Okada to Present Seminar

Dr. Okada has been invited to present a seminar on "Robust Medical Image Analysis using the Mean Shift Framework" for Computer Science Colloquia on May 2008 at University of Bonn, Germany. More details can be found here.


Dr. Okada Presents Tutorial

Dr. Okada has presented an invited tutorial titled "Mean Shift: From Theory to Applications" for the IPSJ Computer Vision and Image Media Workshop held at Kanazawa, Japan on March 2008. More details can be found here.


Dr. Okada to Present Seminar

Dr. Okada has been invited to present a seminar on "Mean Shift Framework for Robust Analysis of Lung Nodules in CT Scans" for the 4th International Seminar on Primordial Knowledge Model on January 2008 at Kyoto University, Japan. More details can be found here.


A team led by Dr. Kazunori Okada wins the best poster honorable mention award at SPIE Medical Imaging Conference

The paper titled “Segmentation of Large Periapical Lesions toward Dental Computer-Aided Diagnosis in Cone-Beam CT Scans” by Steve Rysavy (CS grad student), Arturo Flores (CS grad student), Reyes Enciso (external collaborator, USC School of Dentistry), and Kazunori Okada (CS department) has been awarded an honorable mention for the best poster award at SPIE Medical Imaging Conference at San Diego 2008. SPIE Medical Imaging is one of the major international conferences in this field and our paper was selected among more than 100 posters presented. This paper describes our research work, co-funded by the Center for Computing for Life Science (CCLS) and CSU Program for Education and Research in Biotechnology (CSUPERB), toward applying algorithmically advanced computational tools to solve clinically-significant real-world problems in the field of dentistry.


Interactive Music Project of Prof. W. Hsu covered in a new book on Electronic Music

The new Cambridge Companion to Electronic Music (eds. Nick Collins and Julio d'Escrivan, Cambridge University Press) has a section on Dr. Hsu's music improvisation systems that integrate timbral information. 

For more information:


The CS Department is happy to announce funding of the following CCLS mini grant proposals for Fall 07 to CS Faculty

  • H. Yang, CS Department: Characterize the Evolutionary Nature of Protein Folding Trajectories in Space-Time
  • J. Dujmovic, CS Department: Evaluation of Medical Conditions Using the LSP Method
  • H. Yang, CS Department: Nutritional Genomics--Stage II: Mining the Educational Needs for Nutrition Practitioners in Nutritional Genomics
  • K. Okada, CS Department: Facial Expression Analysis for Comparative Studies of Autism in Human and Nonhuman Primates
  • R. Singh, CS Department: Analyzing Protein-Protein Interaction Networks by Spectral Clustering-based Graph Analysis


Dr. Kazunori Okada has been awarded a five-year federal grant from U.S. Dept of Education

Dr. Kazunori Okada has been awarded a five-year federal grant from U.S. Dept of Education, Office of Special Education & Rehabilitative Services, titled "Restructuring the Level 1 Credential Program to Prepare Highly Qualified Teachers to Teach Students with High Incidence Disabilities in Culturally Diverse Urban Public Schools using the Response to intervention (RTI) Model" (total $448,882). As a co-PI, Dr. Okada will collaborate with a team of expert investigators from SFSU School of Education, Dr. Sue Courey (PI) and Dr. Pamela LePage (co-PI).

Within this context over the duration of this grant, Dr. Okada's work will involve:

  1. developing an on-line Curriculum-Based Measurement (CBM) System for current and graduating students to use for progress monitoring in their classrooms,
  2. developing an on-line system for creating lesson plans that align with Individualized Education Plan (IEP) goals and that provides links to evidence-based instructional strategies and interventions,
  3. developing dynamic on-line portfolio system to examine credential students' pedagogical and content area competence.


Prof. Levine participates at First Armtech Congress in San Francisco

In July, Dr. Levine participated in the ArmTech Congress '07 ( where he co-authored a paper “Engineering Programs at the American University of Armenia: Preparing the Future Leaders of Armenian Technology” and participated with industry leaders in the Software Industry Panel on "How can Armenia Harness the Power of the Software Industry to Accelerate the Growth of Its High Tech Industries?"


Prof. Ilmi Yoon wins prize at NetSCi conference

The paper titled “Diversity and Complexity of Ecosystems: Exploring Balance and Imbalance in Nature” by Prof. Ilmi Yoon (CS Department) and Neo Martinez (Biology Department) has been chosen as the 2nd place winner in the NetSci Visualizing Network Dynamics Competition at NetSci Conference


Click here for more information


CS Department students and faculty win prizes at COSE Science Fair

First place for graduate project in physical sciences: 

MACE: A Simple Algorithm for Lossless Compression of Microarray Images without Spot Segmentation 

Robert Bierman, Faculty: Dr. R. Singh


Third price in graduate category, physical sciences: 

Prediction of protein-ligand interactions using geometric models of active sites

Joanna Lipinski (Biology), Carla Webster (Biology), Faculty: Dr. Rahul Singh


Honorable mention in graduate category, physical sciences: 

Novel Bayesian Network Evaluation Algorithm for Discovering Gene Regulatory Pathways from Microarray Data 

Arturo Flores, Lala Motlhabi (Biology), Rocco Varela, Elinor Velasquez, Faculty Advisors: Frank Bayliss (Biology), Hui Yang, Ilmi Yoon, Staff Advisor: Mike Wong (Center for Computing for Life Sciences)


Honorable mention in undergraduate category, physical sciences: 

Vision-Based detection of Visually Dissimilar Objects 

Taeil Goh, Ryan West, Faculty: Dr. Kaz Okada

Click here for more information


Dr. Levine initiates project to bridge the digital divide in the Caucasus Region

Dr. Levine is bringing the equivalent of the Iraqi Virtual Science Library project to Armenia and the surrounding region. Sun Microsystems is developing the Iraqi Virtual Science Library project. ( and (


This infrastructure would facilitate the research of scientists by providing access to digital libraries, as well as other digitized library resources in a convenient manner. The project will be housed at American University of Armenia (AUA), which is affiliated with the University of California. Digital library resources will be aggregated to provide convenient access to the researchers at schools and the Academy of Sciences in Armenia, Dr. Levine is approaching major scientific societies to encourage them to address the "digital divide" by providing their paid subscription services at a greatly reduced rate in support of this project.


Prof. Hsu's Interactive Improvisation System at LAM 2006 (December)

Prof. Hsu gave a talk, "Modeling Mood and Interaction in Automatic Improvisation", at the Live Algorithms for Music conference in London, December 2006. His automatic improvisation system participated in two concerts, improvising with saxophonists John Butcher and Evan Parker. For more information:


Outstanding Thesis/Project Awards for 2006


CS Department established a yearly Outstanding Culminating Thesis/Project Award to be given to up to 5 CS Department Thesis/Projects, upon nomination by the CS Faculty and review by the award committee. I am delighted to inform you that the CS Department awarded five Outstanding Thesis/Project Awards for 2006. We congratulate the students and their advising faculty. The recipients and their advisors are (in alphabetical order of the students):


Jensen Galan Advisor: Prof. M. Murphy

Caching TCP Options With Syn_coockies. in the Linux 2.6 kernel


Ya-Wen Hsu Advisor: Prof. R. Singh

Exploring Alternative Strategies for Presentation of Results of Web Search


Yan Liu Advisor: Prof. M. Murphy

Web Services Joins using ER Design Tool XML Databus


Preeti Malik Advisor Prof. R. Singh

FreeFlowDB - Drug Database and Analysis Tools


Jun Murakawa Advisor: Prof. Ilmi Yoon

Parts, Image, and Sketch based 3D Modeling Method


Dr. Rahul Singh receives NSF Faculty Early Career Development Grant (January 2007)

Dr. Rahul Singh has received the prestigious NSF CAREER grant for his research. The CAREER is the NSF's most prestigious award for junior faculty members. Established in 1995, the CAREER program aims at recognizing and supporting the early career-development activities of those teacher-scholars who are most likely to become the academic leaders of the 21st century. Title of the grant is " Designing Systems for Molecular Query-Retrieval and Molecular Informatics."


Prof. Singh's research focuses on three challenges:

(1) Designing techniques for representation and similarity-based matching of molecules,

(2) Development of indexing strategies for molecular query-retrieval,


(3) Designing knowledge environments for discovery of therapeutics. The specific research innovations include design of standard coordinate systems to represent highly complex molecular surfaces, developing efficient information matching and retrieval techniques for comparing molecules, and design of integrated information management of molecular structures and biological properties including the development of user-data interaction techniques and algorithms for context supportive access to meta-knowledge.


Prof. Okada is awarded for CSUPERB Faculty Seed Grant


Prof. Okada is awarded for CSUPERB Faculty Seed Grant for his proposal, Computer-Assisted Image Analysis for Differential Diagnosis in Dentistry. The award of $13,500 is granted for advancing endodontic dentisitry by automating the CT image-based diagnotic processes with advanced segmentation techniques developed originally for general medical imaging purpose.


Four grants awarded by Microsoft Research in Bay Area

We are happy to announce that four grants were awarded to us by Microsoft Research in Bay Area. We are grateful for Microsoft’s support.

"Managing and Mining Protein Folding Data", PI. Prof. H. Yang from Computer Science 

“Serious Games for Nursing Education – Prototype and Evaluation" , PI Prof. D. Petkovic from Computer Science with co-PIs Prof. J. F de Leon from School of Nursing and Prof. J. Veeder from Design and Industry Department

Discovery and Analysis of User Information Goals and Usage in a Scientific Website  "  PI Prof. R. Singh from Computer Science

"Parts, Image, and Sketch based 3D Modeling Method for Domain Experts", PI Prof. I. Yoon from Computer Science


CS Students Receive Top Awards in the College of Science and Engineering Project Showcase


Students from the CS department received the top awards at the 2006 graduate project showcase organized by the SFSU College of Science and Engineering. Entries from the department competed in the Physical Sciences section. 


Elinor Velasquez and Emmanuel Yera took first prize for their research, "Structural Querying in Molecular Databases." This research focuses on structural similarity searching for small molecules and holds significant importance for pharmaceutical drug discovery. This research is being conducted under the guidance of Dr. Rahul Singh. 

Ya-Wen Hsu and Naureen Moon took second prize for their research, "Multiple-Perspective Interactive Web Search." This research develops a novel paradigm for user-information interaction in web-search. This research is also being conducted under the guidance of Dr. Rahul Singh. 

Jun Murakawa and Tracie Hong took fourth prize for their research, "Parts, Image, and Sketch based 3D modeling Method." This research develops a novel and intuitive modeling system using 2D images and simple user sketches. This system allows novice users to easily construct 3D models with domain knowledge. This research is being conducted under the guidance of Dr. Ilmi Yoon 

Further information on these projects can be obtained from the web-page of Dr. Singh's research group: or Dr. Yoon's research page:


Two CS Faculty Members Receive the SFSU Presidential Scholar Award

Dr. Arno Puder and Dr. Rahul Singh of the Computer Science department have been named among the recipients of the SFSU Presidential Scholar Award for the 2006 - 2007 academic year. The presidential award is the highest award at SFSU given in recognition of research excellence to tenure-track faculty. Usually, only 10 are given each year for the whole SFSU. 


Dr. Puder joined SFSU in Fall 2002. His research interests include middleware, ubiquitous computing, and applications in sensor networks. 


Dr. Singh joined the faculty at SFSU in the fall semester of 2004. His research interests lie in the areas of Computational Drug Discovery, Bioinformatics, and Multimedia Systems.


Dr. Levine assists in initiating open source medical records project.

Dr. Barry Levine (who also serves as the Computer & Information Science program Director at American University of Armenia <>), and lecturer/Sourcio CEO <>, Hovhannes Avoyan, have initiated the project "Electronic/Medical Records (EMR)". This project is sponsored by Sun Microsystems, which provides logistical and financial support. "EMR" will offer healthcare providers, hospitals, polyclinics, diagnostic centers a comprehensive, web-based solution to effectively automate vital processes within the practice, improve information sharing, customer service, reporting and other functions. More information on the project may be found at


Dr. Levine is leading the Voluntary Accelerated Removal project at SFSU.

SFSU graduate students are developing the web site which we are hosting at:

The Voluntary Accelerated Removal (VAR) program is a joint effort of the Northwest Public Power Association and San Francisco State University to reduce the use of polychlorinated biphenyls (PCBs) in electrical equipment and promote the remediation of sites where such PCBs have been released. Utilities and non-utilities that own electrical equipment containing PCBs are invited to join the VAR effort. As VAR partners track their activities, they can apply for recognition to the US Protection Agency for their leadership as environmental stewards as they support the following international initiatives to reduce PCB use and potential releases:

   * The 1996 North Regional Action Plans for PCBs

   * The 1997 Binational Toxic Strategy

   * The Stockholm Convention on Persistent Organic Pollutants.


Our netBEAMS project (joint work with Agilent Technologies and Sun Microsystems) received Duke's Choice Award at JavaOne in July 2005.

NetBEAMS project deals with developing sensor array networks for Bay Area water monitoring.

Read more about this exciting development here: SFSU's Unique Collaboration with Tech Industry Wins JavaOne Award.

The NetBEAMS WWW site is

The PI for the project is Prof. Arno Puder, with co-PI Prof. D. Petkovic.

This is an example of how we plan to involve our students in exciting work in a real R&D setting, as well as help them establish links to local high tech companies.


NSF Faculty Early Career Development Grant Awarded.

Dr. Edward Lank has been awarded an NSF Grant under the Faculty Early Career Development (CAREER) Program. It is a Foundation-wide activity that offers the National Science Foundation's most prestigious awards in support of the early career-development activities of those teacher-scholars who are most likely to become the academic leaders of the 21st century.



"Inferring User Intention in Pen Systems" is the title and focus of his grant. This grant seeks to characterize the opportunity to add intelligence to pen/stylus interfaces. Its goal is to study the empirical effectiveness and develop the underlying principles involved in designing interfaces that infer aspects of the user's intent. To do this, this grant intends to develop new mathematical models of human motion with pen/stylus devices, apply characteristics of human vision to the analysis of content, develop algorithms to apply these models in interfaces, and implement prototype applications that test these models. It advocates the understanding and management of uncertainty in inferring user intention. Finally, it explores the mental models developed by users, seeking ways to compare the perception they have of the behavior of applications, and to characterize the appropriate use of intelligence in pen/stylus interfaces.


Program for Graduate-Level Academic Exchange Between San Francisco State University and The University of Applied Sciences, Fulda, Germany

We have established a formal bilateral exchange between the Computer Science Departments of San Francisco State University and the University of Applied Sciences in Fulda. This is the first bilateral agreement within the College of Science and Engineering (COSE). The exchange will be sponsored at SFSU by the Computer Science Department and will have the following features:


SFSU CS graduate students will take specified classes at the University of Applied Sciences and these will be counted as electives in their graduate program. Courses will be taught in English and will be in subject areas such as electronic business and multimedia systems.

Graduate students from the University of Applied Sciences will take specified graduate and undergraduate courses in the CS Department that may be counted toward completion of their home degree. Courses will be in subject areas such as distributed systems and multimedia systems.


This agreement has been spearheaded by Prof. A. Puder from SFSU Computer Science Department and Prof. R. Todtenhoefer from Fulda University.


Students interested to participate in this exchange please contact Prof. Puder directly.

Professor Dujmovic received an invitation to give an invited talk at the International EUFORUSE conference in June 2005 in Belgrade


Professor Jozo Dujmovic received the invitation to give an invited talk at the International EUFORUSE conference in June 2005 in Belgrade. The aim of EUROFUSE is to bring together researchers and practitioners applying fuzzy set techniques in operations research and related fields. After successful editions on Planning and Scheduling (Mons, 2000), Preference Modeling and Applications (Granada, 2001) Information Systems (Varenna, 2002), and Data and Knowledge Engineering (Warszawa, 2004), the coordinators have chosen to dedicate the 2005 conference to Fuzzy Systems in Optimization. EUROFUSE celebrates this year its 30th anniversary.


Collaborative art/technology project at Catharine Clark Gallery

Professor Bill Hsu worked on software control for Matt Heckert's kinetic sculptures. The "Rotification" exhibit was on view at Catharine Clark Gallery in San Francisco, 1/20/05 through 2/26/05. See for details.


Professor Buturovic releases open-source software for machine learning

In November 2004, Professor Buturovic released an open-source machine learning program PCP (Pattern Classification Program). The program runs on Linux operating system and implements a number of popular machine learning algorithms and methods, such as k-means clustering, Fisher's linear discriminant, linear classifiers, k-nearest neighbors, neural networks, Support Vector Machine algorithm, committee learning, cross-validation etc. PCP is available at


SFSU Presidential Scholar Award.


Dr. Edward Lank has been awarded a Presidential Leave for the Professional Development of Probationary Faculty. This award will allow Dr. Lank to spend the Fall 2005 semester engaged in research and collaboration with colleagues, and to continue to develop his active research program.


SFSU Wins Sensor Network Research Grant.

Joint SFSU Computer Science, SFSU Electrical Engineering, the Romberg Tiburon Center for Environmental Studies and the Java Distributed Data Acquisition and Control Community (JDDAC), has been awarded a $ 64,000 grant for work in sensor networks. 

The grant titled: "NetBEAMS - Building a Large Scale Sensor Network of Bay Environmental Assessment and Monitoring Stations", is funded by Agilent Labs, and will be partially matched with in-kind benefits from Sun Microsystems. Agilent Labs and Sun Microsystems are both corporate members of the JDDAC Community. 

The goal of this project will be to investigate sensor networks in the real-life scenario of monitoring water conditions in the San Francisco Bay . In conjunction with the Engineering Department, the Romberg Tiburon Center at SFSU, and their corporate partners, the CS Department will build up a prototype wireless sensor network to monitor and collect information gathered from sensor arrays positioned throughout the San Francisco Bay . This project will make use of the JDDAC infrastructure developed by Agilent Labs, as well as other technologies from Agilent Labs and Sun Microsystems. 

Main contact is Prof. Puder (PI). RTC participant is Prof. Garfield, EE participant is Prof. Cooklev.


Invited presentation by Professor Petkovic in the SPIE conference.

Professor D. Petkovic will give an invited talk titled "Visual Information Systems: Lessons for its Future" at the upcoming SPIE Conference in San Jose, January 2005. 


Invited talk by Professor Singh at the University of Minnesota.

Professor Rahul Singh gave an invited presentation at the department of Electrical and Computer Engineering, University of Minnesota , in the Twin Cities on November 18 2004 . Professor Singh's talk covered various computational abstractions used for molecular representation and their implications for query-retrieval in molecular databases. Further details are available at the Electrical and Computer Engineering website of the University of Minnesota : 


Invited presentation by Professor Dujmovic in Denmark on the LSP method.

In September 2004, the Aalborg University in Denmark invited Professor Dujmovic to present his LSP method for evaluation, optimization, and comparison of complex systems. Some of lectures were offered to the general public at the university, and some to graduate students in the information retrieval area. Previously, Professor Dujmovic was invited to present the LSP method at two universities in Argentina; his students have published more than 10 papers based on the LSP method, and one of them defended their Ph.D. thesis using the LSP method to model the quality of web sites. 


CSUPERB Funds Research

The California State University Program for Education and Research in Biotechnology (CSUPERB) announced funding for research being conducted by Professor Rahul Singh in the area of query-retrieval of molecules from structural databases. Professor Singh has been awarded $10,000 to support his research in this area. 


Computer Music from SFSU in Concert!

Professor William Hsu gave a workshop/performance with John Butcher on Timbre-aware interactive computer music system at Kraakgeluiden Werkplaats, Amsterdam , 11/20-22/2004. 


Computer Science Professor Receives Best Paper Award

Professor Rahul Singh received the best paper award for systems biology and bioinformatics at the Systemics, Cybernetics, and Informatics Conference 2004 (SCI 2004) in Orlando , Florida . The paper by Dr. Singh titled "Issues in Computational Modeling of Molecular Structure-Property Relationships in Real-World Settings" analyzes the challenges faced by existing algorithmic approaches for modeling molecular structure-property relationships. The paper proposes alternate approaches to address such problems using a novel characterization of the molecular structural space and machine learning formulation. This research was conducted by Professor Singh while he was at the Georgia Institute of Technology. His current research focuses on further development of these ideas. 


Computer Science Department to collaborate with American University of Armenia on joint projects

In August 2003, the presidents of American University of Armenia (AUA) and San Francisco State University signed a Memorandum of Understanding (MOU) to enable the two institutions to pursue joint endeavors and enhance educational and research cooperation between their students, faculty and staff. The MOU was initiated by Professor Dr. Barry Levine, who also directs the AUA Computer and Information Science (CIS) program. The goal of the MOU is to brand the CSD at SFSU and CIS program at AUA as leaders in the study of offshore software development issues through collaborative projects and curricula involving students and faculty at both institutions. In addition, we hope to introduce novel software engineering courses at both institutions that address issues in collaborative project management. The collaborations will be enhanced via the development of distance education offerings originating from both schools. The provision of distance education and the study of its efficacy in the context of severe bandwidth constraints are of interest to many countries in the developing world. AUA also maintains affiliations with Johns Hopkins University, UCLA, and UC Berkeley.