Personal Information

• Name: LEE, Woei-Jyh (Adam)
• Professional email address: adamlee at umiacs.umd.edu
• Personal email addresses: adamlee at cs.umd.edu or lee7666 at cs.nyu.edu or adam at csie.ntu.edu.tw

Research Interests

• Bioinformatics, Computational Biology and Systems Biology
• Genomics and Genetics
• Information Integration, Data Management and Mining
• Systems Simulation and Performance Evaluation
• Parallel Computing and Distributed Systems

Education

• 9/00 - present: Ph.D. candidate

Department of Computer Science
College of Computer, Mathematical and Physical Sciences
University of Maryland, College Park, Maryland
 
• 9/96 - 1/98: Master of Science

Department of Computer Science
Courant Institute of Mathematical Sciences
Graduate School of Arts and Science
New York University, New York
 
• 10/89 - 6/93: Bachelor of Science in Engineering

Department of Computer Science & Information Engineering
National Taiwan University, Taiwan

Publications

Journals

• W.-J. Lee, L. Raschid, H. Sayyadi, P. Srinivasan, "Exploiting ontology structure and patterns of annotation to mine significant associations between pairs of controlled vocabulary terms," Lecture Notes in Bioinformatics / Lecture Notes in Computer Science, Vol.5109, pp.44-60, June 2008
• W.-J. Lee, L. Raschid, P. Srinivasan, N. Shah, D. Rubin, N. Noy, "Using annotations from controlled vocabularies to find meaning associations," Lecture Notes in Bioinformatics / Lecture Notes in Computer Science, Vol.4544, pp.247-263, June 2007
• A. L.H. Chow, L. Golubchik, J. C.S. Lui, W.-J. Lee, "Multi-path streaming: optimization of load distribution," Performance Evaluation, Vol.62, pp.417-438, October 2005
• C.-H. Tai, W.-J. Lee, J. J. Vincent, B. Lee, "Evaluation of domain prediction in CASP6," Proteins: Structure, Function, and Bioinformatics, Vol.61, Sup.7, pp.183-192, September 2005
• D. Liang, P. Chung, Y. Huang, C. Kintala, W.-J. Lee, T. K. Tsai, and C.-Y. Wang, "NT-SwiFT: Software implemented Fault Tolerance on Windows NT," The Journal of Systems and Software, Vol.71, No.1-2, pp.127-141, April 2004
• L. Golubchik, J. C.S. Lui, T. F. Tung, A. L.H. Chow, W.-J. Lee, G. Franceschinis, and C. Anglano, "Multi-path continuous media streaming: what are the benefits?" Performance Evaluation, Vol.49, pp.429-449, September 2002
• M. Bearden, S. Garg, and W.-J. Lee, "Integrating goal specification in Policy-Based Management," Lecture Notes in Computer Science, Vol.1995, pp.153-170, January 2001

Conferences and Workshops

• W.-J. Lee, L. Raschid, H. Sayyadi, P. Srinivasan, "Exploiting ontology structure and patterns of annotation to mine significant associations between pairs of controlled vocabulary terms," The 5th International Workshop on Data Integration in the Life Sciences (DILS 2008), June 2008
• L. Raschid, P. Srinivasan, W.-J. Lee, "A framework for discovering associations from the annotated biological web (prototype)," The 17th Annual Workshop on Information Technologies and Systems (WITS 2007), December 2007
• W.-J. Lee, L. Raschid, P. Srinivasan, N. Shah, D. Rubin, N. Noy, "Using annotations from controlled vocabularies to find meaning associations," The 4th International Workshop on Data Integration in the Life Sciences (DILS 2007), June 2007
• L. Raschid, Y. Wu, W.-J. Lee, M.-E. Vidal, P. Tsaparas, P. Srinivasan, A. K. Sehgal, "Ranking target objects of navigational queries," The 8th ACM International Workshop on Web Information and Data Management (WIDM 2006), November 2006
• A. Lash, W.-J. Lee, L. Raschid, "A methodology to enhance the semantics of links between PubMed publications and markers in the human genome," The 5th IEEE Symposium on Bioinformatics and Bioengineering (BIBE 2005), pp.185-192, October 2005
• A. L.H. Chow, L. Golubchik, J. C.S. Lui, W.-J. Lee, "Multi-path streaming: optimization and load distribution," International Symposium on Computer Performance Modeling, Measurement and Evaluation (Performance 2005), October 2005
• X. Wu, W.-J. Lee, C.-W. Tseng, "ESTmapper: efficiently aligning DNA sequences to genomes," The 4th IEEE International Workshop on High Performance Computational Biology (HiCOMB 2005), p.196a, April 2005
• B. Abdouni, W. C. Cheng, A. L.H. Chow, L. Golubchik, W.-J. Lee, J. C.S. Lui, "Multi-path streaming: optimization and evaluation," The 12th Annual Multimedia Computing and Networking (MMCN 2005), pp.216-227, January 2005
• L. Golubchik, J. C.S. Lui, T. F. Tung, A. L.H. Chow, W.-J. Lee, G. Franceschinis, C. Anglano, "Multi-path continuous media streaming: what are the benefits?" International Symposium on Computer Performance Modeling, Measurement and Evaluation (Performance 2002), September 2002
• M. Bearden, S. Garg, W.-J. Lee, "Integrating goal specification in Policy-Based Management," Policies for Distributed Systems and Networks, International Workshop (Policy 2001), January 2001
• M. Bearden, S. Garg, W.-J. Lee, A. van Moorsel, "User-centric QoS policies, or saying what and how (Work-in-Progress Report)," International Workshop on Distributed Systems Operation and Management (DSOM 2000), December 2000
• P. Chung, W.-J. Lee, J. Shih, S. Yajnik, Y. Huang, "Fault-injection experiments for distributed objects," International Symposium on Distributed Objects and Application (DOA'99), pp.88-97, September 1999
• P. Chung, W.-J. Lee, Y. Huang, D. Liang, C.-Y. Wang, "Winckp: a transparent checkpointing and rollback recovery tool for Windows NT applications," The 29th IEEE Annual International Symposium on Fault-Tolerant Computing (FTCS-29), pp.220-223, June 1999
• Y.-M. Wang, W.-J. Lee, "COMERA: COM Extensible Remoting Architecture," The 4th USENIX Conference on Object-Oriented Technologies and Systems (COOTS'98), pp.79-88, April 1998
• Y.-M. Wang, O. P. Damani, W.-J. Lee, "Reliability and availability issues in Distributed Component Object Model (DCOM)," The 4th International Workshop on Community Networking (CN4'97), pp.59-63, September 1997

Posters

• W.-J. Lee, "A framework for discovering associations from the annotated biological web," The 1st Annual EITC Workshop on Bioinformatics and Biomedical Research (EITC-Bio 2008), June 2008
• W.-J. Lee, L. Raschid, P. Srinivasan, "A framework for discovering associations from the annotated biological web," UMD Bioscience Research & Technology Review Day, November 2007
• W.-J. Lee, L. Raschid, P. Srinivasan, "Mining meaningful associations from annotations in life science data resources," The 4th NIH National Graduate Student Research Festival (2007 NGSRF), October 2007
• L. Raschid, P. Srinivasan, W.-J. Lee, "A framework for discovering associations from the annotated biological web," The National Science Foundation Symposium on Next Generation of Data Mining and Cyber-Enabled Discovery for Innovation (NGDM 2007), October 2007
• W.-J. Lee, L. Raschid, P. Srinivasan, "Using GO and MeSH annotations to find meaningful associations," The 4th International Workshop on Data Integration in the Life Sciences (DILS 2007), June 2007
• W.-J. Lee, L. Raschid, M.-E. Vidal, "A generic, flexible and scalable methodology to enhance the semantics of links in life science data resources," UMD Bioscience Research & Technology Review Day, November 2006
• W.-J. Lee, L. Raschid, M.-E. Vidal, "A generic, flexible and scalable methodology to enhance the semantics of links in life science data resources," The 9th Annual Conference on Computational Genomics (CG 2006), October 2006
• W.-J. Lee, C.-H. Tai, B. Lee, "Evaluation of protein domain parsing and boundary prediction," NIH Research Festival, October 2006
• W.-J. Lee, L. Raschid, A. Lash, "A methodology to enhance the semantics of links: using links between PubMed abstracts and markers in the human genome as an example," UMD Bioscience Research & Technology Review Day, November 2005
• W.-J. Lee, L. Raschid, A. Lash, "A methodology to enhance the semantics of links: using links between PubMed abstracts and markers in the human genome as an example," The 2nd Biennial DB/IR Day, Best Poster Awards, October 2005
• X. Wu, W.-J. Lee, C.-W. Tseng, K. Brown, "A comparison of tandem mass spectrometry techniques for protein identification," UMD Bioscience Research & Technology Review Day, November 2004
• X. Wu, W.-J. Lee, C.-W. Tseng, "ESTmapper: efficiently mapping DNA sequences to genomes," UMD Bioscience Research & Technology Review Day, November 2004
• X. Wu, W.-J. Lee, D. Gupta, C.-W. Tseng, "ESTmapper: efficiently clustering EST sequences using genome maps," The 8th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2004), pp.87-88, March 2004

Technical Reports and Research Briefings

• L. Raschid, W.-J. Lee, P. Srinivasan, D. L. Rubin, N. Shah, "Using annotations from controlled vocabularies to find patterns in Life Science Links," University of Maryland, CHIDS Research Briefings, Vol.2, Iss.1A, pp.1-4, Spring 2007
• W.-J. Lee, L. Raschid, P. Srinivasan, D. L. Rubin, N. Shah, "Using annotations from controlled vocabularies to find patterns in Life Science Links," University of Maryland, Technical Report CS-TR-4862 (UMIACS-TR-2007-15), March 2007
• W.-J. Lee, L. Raschid, M.-E. Vidal, "A generic, flexible and scalable methodology to enhance the semantics of links in life science data resources," University of Maryland, Technical Report CS-TR-4809 (UMIACS-TR-2006-29), June 2006
• X. Wu, W.-J. Lee D. Gupta, C.-W. Tseng, "ESTmapper: efficiently clustering EST sequences using genome maps," University of Maryland, Technical Report CS-TR-4575 (UMIACS-TR-2004-20), April 2004
• B. Abdouni, W. C. Cheng, A. L.H. Chow, L. Golubchik, W.-J. Lee, J. C.S. Lui, "Multi-path streaming: optimization and evaluation," University of Southern California, Technical Report CS-04-815 (IMSC-04-001), 2004

Research Experiences

• 6/04 - present: Research Assistant, Department of Computer Science, University of Maryland, College Park, Maryland
• LSLink, designed and developed a generic, flexible and scalable methodology to enhance the semantics of links in life sciences data resources
• a flexible and scalable system that consolidates information and annotation extraction, link generation and labeling
• a generic semantic model that uses a three-layer architecture to specify the life sciences web, which includes a domain ontology to describe the data entries as well as a controlled vocabulary that describes the relationships captured by the links
• a declarative protocol workflow that implements finite state automata to formalize the methodology which can perform the extraction, generation, labeling and mining tasks
• an extensible framework for discovering potentially meaningful and not already well known associations from the annotated life sciences web
• a scalable query language that integrates domain ontologies and controlled vocabularies to explore the enhanced links, and to reason new implicit properties of the links from the knowledge encoded in the domain ontologies and controlled vocabularies
• BioFast: efficient and seamless life science data management; components include
  • BIP, assisted to design a modular bioinformatics pipeline to create a system for the storage and analysis of various types of biological sequence data
  • BioNavigation, designed and established a relational database on IBM DB2 to sample five NCBI sources and their interconnected links to support biological queries and visualization of query results
• assisted to compare tandem mass spectrometry techniques for protein identification, including SEQUEST, X!Tandem and OMSSA
• ESTmapper, assisted to build suffix trees for the genomic sequences, searched long common substrings between each EST and the genomic trees, located the gapped matching regions for each EST, and clustered ESTs with overlapped matching regions
• UM-BLAST, assisted to build a wrapper which is capable of selecting the proper combination of NCBI BLAST, mpiBLAST and BLAST++ to achieve better performance based on the size of the sequence database and the length of query sequences


• 6/02 - 6/03: Visiting Scholar, Integrated Media Systems Center, University of Southern California, California
 
• Multi-Path Continuous Media Streaming, studied and evaluated the benefits of using multiple paths to deliver continuous media over best-effort wide-area networks


• 3/98 - 8/00: Member of Technical Staff, Network Software Research, Bell Laboratories, Lucent Technologies, New Jersey
 
• Gallifrey, policy-based enterprise services management
• NT-SwiFT (software implemented fault tolerance for Windows NT): components include
• Watchd for process and machine failures detection and recovery
• Winckp for transparent checkpoint of application state, logging/replaying of windows messages
• One-IP for IP packet dispatching and re-routing
• REPL for on-line file replication
• Libft for process checkpoint and communication message logging/replaying
• DCOM-SwiFT (software implemented fault tolerance for DCOM applications)
• Fault Injection Experiments, performed a threading model comparison of DCOM and CORBA (IONA's MT-Orbix)


• 9/97 - 1/98: Independent Researcher, Advanced Laboratory in Computer Science, New York University, New York
 
• FlakeNet, designed and implemented a replicated state machine on top of a pseudo network, in which servers or clients might die and messages might be dropped or reordered
• Paralleled VRP (Vehicle Routing Problem), assisted to use Persistent Linda to parallelize the algorithm


• 5/97 - 12/97: Student Intern, Communication Information Systems Research, AT&T Labs, AT&T, New Jersey
 
• Designed architectural supports for QoS (quality of service) and QoFT (quality of fault tolerance) on DCOM
• InterCOM, exploited and enhanced the interception mechanisms and extensible architecture of DCOM for supporting scalability, load balancing, and fault tolerance
• COMERA (COM Extensible Remoting Architecture), designed a truly componentized remoting architecture to provide extensibility and flexibility


• 5/97 - 8/97: Independent Researcher, Information Technology Projects, New York University and Morgan Stanley, New York
 
• WebPerf Measurement Engine, established the SSL socket connection to analyze the performance of Morgan Stanley Dean Witter's secure web server


• 9/91 - 6/93: Independent Researcher, Communications & Multimedia Laboratory, National Taiwan University, Taiwan
 
• Multimedia Authoring System, implemented a system parsing simple Visual Basic source codes and translating into C source codes, which could be compiled and run on MS-Windows
• LD Online Panel, implemented a GUI controlling a large disc player through RS-232 and TARGA interfaces on MS-Windows

Teaching Experiences

• 8/03 - 6/04: Teaching Assistant, Department of Computer Science, University of Maryland, College Park, Maryland
 
• CMSC723/LING645 Introduction to Computational Linguistics: responsible for holding office hours and newsgroup, grading homework and projects
• CMSC434 Introduction to Human-Computer Interaction: responsible for holding office hours, grading homework and projects
• CMSC114 Computer Science I, responsible for holding office hours, implementing and grading projects


• 8/00 - 6/02: Teaching Assistant, Department of Computer Science, University of Maryland, College Park, Maryland
 
• CMSC420 Data Structures: responsible for holding office hours, answering e-mails and newsgroup messages, grading homework and projects


• 9/95 - 8/96: Lecturer, MiTAC Computer Education School and Gjun Information School, Taiwan
 
• Taught webpage designs, Internet software, web server management and Windows applications


• 6/95 - 8/96: Lecturer, Center of Excellence for Research in Computer Systems, National Science Council, Taiwan
 
• Taught Java programming

Work Experiences

• 4/96 - 7/96: Project Leader, 1996 Computers and Communications Exposition for Children, Taiwan
 
• Used Superscape's VRT authoring software to build a 3D virtual reality model collecting the web pages, which were good for children to play and learn


• 10/95 - 6/96: Organizer, 1996 National Conference to the Achievement of the Computer Related Area, Taiwan
 
• Authorized by government, to invite the experts from academy, research organizations and industrial laboratories to review and evaluate the budget of the fiscal year


• 6/95 - 8/96: Assistant, Center of Excellence for Research in Computer Systems, National Science Council, Taiwan
 
• Redesigned the network, built up an education center with 48 PCs with Internet connection


• 10/93 - 6/95: Network Manager, Armed Forces Reserves Mobilization Management School, Taiwan
 
• Designed, set up and maintained a campus-wide distance learning system using Novell NetWare system on 31 PCs


• 1/91 - 3/93: Leader, Software Development Students Group, National Taiwan University, Taiwan
 
• NTU Campus Service System, designed and developed a user-friendly multimedia touring system using C++ (sponsored by Dean of Student Affairs)
• NTU Enrollment Query System, designed and developed an interface for students to look up the course information and print out all matched schedules using dBase IV and Clipper (sponsored by Dean of Academic Affairs)

Invited Talks

• "Mining associations in the annotated biomedical web," PIR Seminar, June 30, 2008
• "A framework for discovering associations from the annotated biological web," NCBI CBB Seminar, March 13, 2008
• "A framework for discovering associations from the annotated biological web," UMD CBCB Seminar Series, February 14, 2008
• "Using annotations from controlled vocabularies to find meaningful associations," UMD CBCB Seminar Series, April 19, 2007
• "Using annotations from controlled vocabularies to find patterns in life science links," NTU CSIE Seminar, March 30, 2007
• "Using annotations from controlled vocabularies to find patterns in life science links," NCU CSIE Seminar, March 28, 2007
• "Enhancing the semantics of links in life science data resources," UMD CBCB Seminar Series, May 4, 2006
• "A methodology to enhance the semantics of links: using links between PubMed abstracts and markers in the human genome as an example," NCBI CBB Seminar, November 1, 2005
• "A methodology to enhance the semantics of links between PubMed publications and markers in the human genome," UMD CBCB Seminar Series, October 12, 2005

Patents

• "METHOD AND APPARATUS FOR USE IN SPECIFYING AND INSURING SERVICE-LEVEL QUALITY OF SERVICE IN COMPUTER NETWORKS," U.S. Patent No. 6,871,233, March 22, 2005
• "METHOD AND APPARATUS FOR USE IN SPECIFYING AND INSURING POLICIES FOR MANAGEMENT OF COMPUTER NETWORKS," U.S. Patent No. 6,732,168, May 4, 2004

Honors

• 8/00 - 8/02: Merit-based Fellowship Award, University of Maryland, Maryland
• 2/93: Foreign Visiting Students, Keio University, Tokyo, JAPAN

Professional Memberships

• 6/02 - present: Student Member, Association for Computing Machinery (ACM)
• 6/02 - present: Student Member, Institute of Electrical and Electronics Engineers (IEEE)
• 4/04 - present: Student Member, International Society for Computational Biology (ISCB)
• 2/06 - present: Member, International Society of Engineers (ISENG)
• 4/98 - 4/01: Member, USENIX Association

Computer Skills

• Platform: Mac OS X, RedHat Linux, SuSE Linux, Sun Solaris, SunOS, Microsoft Windows, MS-DOS
• Language: Java, C++/C, Perl, XML, HTML/XHTML, CGI, JavaScript, JSP, SQL, C Shell Scripts, Pascal, Ada95, Lisp, Prolog, ML, Clipper
• Others: MATLAB/Simulink, OpenGL, Network Simulator (ns-2), CSIM 18, DCOM/ActiveX, system administration (Solaris, Linux, Windows), database administration (IBM DB2, Oracle, MySQL)

Adam Lee, 26 August 2008