PAVEL KUKSA

Research Interests

• Machine learning, algorithms, data mining, pattern recognition, sequence analysis, bioinformatics, computer vision

Education

•  Ph.D.—Computer Science, Fall 2005-present
  Rutgers University, NJ
  
  •  GPA: 4.00
  •  Projected Graduation Date: Sept. 2010
•  M.Sc.—Computer Science, 2004
  Bauman Moscow State Technical University, Moscow, Russia
  •  GPA: 5.00/5.00
    
•  B.Sc.—Computer Engineering, 2002)
  Bauman Moscow State Technical University, Moscow, Russia
  
  •  GPA: 4.96/5.00
    

Technical Skills

•  Programming Languages:
  
  • Proficient in C/C++, Java, Matlab, Pascal, JavaScript, Assembly
    
  • Familiar with Python, Lua, Perl, SQL, Lisp, Prolog, VBScript, VBA, VHDL, R
    
• Tools and Systems:
  
  • Matlab, Eclipse, WebSphere
    
  • Web development: HTML, XHTML, CSS, XML, Dreamweaver
    
• Operating Systems: Linux (Fedora, Red Hat, Ubuntu, ASP), Windows 9x/2000/XP/2003
  

Research and Industry Experience

• Research assistant—Rutgers University
  2005-present
  
  • Discriminative learning, string algorithms, large-scale learning, semi-supervised learning
    
  • Kernel methods and algorithms for general sequence classification: DNA barcoding, remote homology prediction, text categorization, etc.
    
  • Natural language processing
    
  • Clustering and classification of video motion sequences and audio data
    
• Research Assistant—NEC Laboratories America, Princeton, NJ
  May 2009 – August 2009
  
  • Semi-supervised large-scale learning for bioNLP (natural language processing for
    bio-medical literature). Supervisor: Dr. Yanjun Qi
    
• Research Assistant—NEC Laboratories America, Princeton, NJ
  May 2008 – August 2008
  
  • Unified Architecture for Natural Language Processing, multi-task learning with deep
    architectures. Supervisor: Dr. Jason Weston
    
• Software Engineer—Mobile Business Systems
  2003–2005
  

Teaching Experience

• Teaching Assistant—Rutgers University
  2005–2009
  
  • Graduate courses: CS530 "Principles of AI", CS535 "Pattern Recognition", CS536 "Machine
    Learning"
    
  • Undegraduate courses: CS440 "Introduction to Artificial Intelligence", CS206 "Discrete
    Structures II", CS170 "Computer Applications in Business"
    
• Lecturer/Instructor—BMSTU
  2002
  
  •  "Systems Modeling"
    

Selected Publications

• Pavel Kuksa, Yanjun Qi.Semi-Supervised Bio-Named Entity Recognition with Word-Codebook Learning. In SDM, 2010.
• Pavel Kuksa, Pai-Hsi Huang, and Vladimir Pavlovic. Scalable algorithms for string kernels with inexact matching. In NIPS, Spotlight Presentation, 2008.
• Pavel Kuksa, Pai-Hsi Huang, and Vladimir Pavlovic. Fast protein homology and fold detection with sparse spatial sample kernels. In ICPR, Oral presentation, 2008.
• Pavel Kuksa, Pai-Hsi Huang, Vladimir Pavlovic. Efficient use of unlabeled data for protein sequence classification. BMC Bioinformatics, 2009.
• Pavel Kuksa and Vladimir Pavlovic. Fast kernel methods for SVM sequence classifiers. In WABI, pages 228–239, 2007.
• Yanjun Qi, Pavel Kuksa, Ronan Collobert, Koray Kavukcuoglu, Jason Weston. Semi-Supervised Sequence Labeling with Self-Learned Feature. In ICDM (regular paper), 2009.

Invited talks

• String kernel-based Species Identification Using DNA Barcodes. Joint Molecular Biosciences Symposium, Feb. 2008.
• Kernel Methods for DNA Barcoding. Rutgers Bioinformatics meeting, Nov. 10, 2006
  

Honors and Awards

• DIMACS Graduate Award, 2009/2010
• DIMACS Graduate Student Award, 2008/2009
• Graduate Fellowship, Rutgers University, 2005-2007
• President of Russia’s Award, 2003-2004
• University Scientific Board Scholarship, BMSTU, 2002-2003
• Academic Excellence Award, BMSTU, 2001-2002
• M.Sc. with Honors, 2004
• B.Sc. with Honors, 2002
  

Professional Activities

• Reviewer for CVPR, ICML, ICPR, BMC Bioinformatics, Neural Networks
• Co-organizer, Yahoo Machine Learning seminar series, 2009
• Secretary, Rutgers Compute Science Graduate Student Society, 2007–2008
• Treasurer, Rutgers Computer Science Graduate Student Society, 2006–2007
• Secretary, Rutgers Bioinformatics Club, 2006–2007
• Member of IEEE, 2005–present
  

References

Prof. Vladimir Pavlovic,     Dept. of Computer Science,     Rutgers University,     vladimir@cs.rutgers.edu	Prof. Casimir Kulikowski,     Dept. of Computer Science,     Rutgers University,     kulikows@cs.rutgers.edu	Prof. Muthu Muthukrishnan,     Dept. of Computer Science,     Rutgers University,     muthu@cs.rutgers.edu
Dr. Yanjun Qi,     Machine Learning Department,     NEC Laboratories America,     yanjun@nec-labs.com	Dr. Jason Weston,     Google Research     Google, NY     jaseweston@gmail.com

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