ERIC A. BREIMER www.cs.rpi.edu/~breime Computer Science Department Rensselaer Polytechnic Institute 110 8th Street, Troy, NY 12180 h: 518 274-3185 w: 518 276-8265 breime@cs.rpi.edu RESEARCH INTERESTS Applied Learning Algorithms and Their Experimental Evaluation: Applying machine learning to design, improve, and discover algorithms.   Computational Biology: Building software systems for automatically improving algorithms for sequence comparison and alignment. TEACHING INTERESTS Core courses in the fundamentals of computer science, data structures and algorithms, database systems, computer organization and architecture, operating systems, programming languages, design and analysis of algorithms, and computability/automata theory   Special topic courses in machine learning and algorithms for computational biology. EDUCATION Ph.D. Computer Science Rensselaer Polytechnic Institute 2002 M.S. Computer Science Rensselaer Polytechnic Institute 2000 Dec B.S. Computer Science Binghamton University 1997 May A.S. Computer Science Dutchess Community College 1995 May HONORS & Founders Award for Academic Excellence, RPI 2000 AWARDS Magna Cum Laude, Binghamton University 1997 Dean's Scholar, Binghamton University 1995 Presidential Scholar, Dutchess Community College 1993 TEACHING Instructor Rensselaer Polytechnic Institute EXPERIENCE CSCI 2300: Data Structures and Algorithms Instructor for four semesters. Responsible for as many as four sections with 140 total students and four graduate teaching assistants. Developed substantial course content including syllabus, exams, programming projects, laboratory exercises, and extensive on-line material. Delivered over 100 lectures on topics such as object oriented programming, generic programming and the standard template library, discrete mathematics, algorithm analysis, abstract data types, and algorithms for trees and graphs. 2002 Spring 2000 Fall 2000 Spring 1999 Fall ITEC 1961: Introduction to Data Structures and Applications Responsible for two sections with 90 students total and two graduate teaching assistants. Developed substantial online lecture notes, delivered 28 lectures, and implemented studio format (50% lecture and 50% supervised activities). Developed syllabus and course content with an emphasis on applications and software development. 2001 Spring CSCI 1190: Beginning C Programming for Engineers Responsible for two sections with 50 students total and four undergraduate teaching assistants. Developed syllabus and lectures targeted towards teaching basic C programming to engineering students with little or no background in computer science. 2001 Fall Guest Lecturer Rensselaer Polytechnic Institute, Troy, NY 1997-Present CSCI 2500: Computer Organization 3 substitute lectures CSCI 6050: Computability and Complexity 2 substitute lectures CSCI 4260: Graph Theory 2 invited lectures CSCI 4020: Computer Algorithms 1 invited lecture While serving as a teaching assistant and research assistant, I was invited to present three special topic lectures and five substitute lectures. Teaching Assistant Rensselaer Polytechnic Institute, Troy, NY 1997 Fall CSCI 2500: Computer Organization Assisted in preparing and grading homework and exams, held regular office hours, and maintained MIPS assembly language simulator for testing and evaluating student projects. RESEARCH Research Assistant Rensselaer Polytechnic Institute EXPERIENCE Advisor: Mark K. Goldberg Studied research problems in the analysis of biological sequence data. Implemented a learning algorithm for the longest common subsequence problem. Co-designed a framework for learning input sensitive dynamic programming algorithms. Implemented SLIDE, a system which applies supervised learning and solution clustering to automatically enhance both the run time performance and solution quality of algorithms for computing local and multiple sequence alignment. 2001 Summer 2000 Summer 1999 Spring Research Intern T.J. Watson Research Center, IBM 1999 Summer Supervisors: Robert Farrell and Peter Fairweather Assisted in the design and implementation of a task-based, application-aware tutoring adjunct, a system that analyzes an operating systems event stream to detect application tasks and deliver context sensitive help. Research Assistant Rensselaer Polytechnic Institute 1998 Advisor: Mark K. Goldberg Rensselaer's Classroom in The Round Project: Investigated and tested instructional techniques for using collaborative classroom technologies. In cooperation with the psychology department, evaluated the effectiveness of technology in promoting collaborative learning. PUBLICATIONS Journal "On the Height of a Random Set of Points in a d-dimensional Unit Cube," Eric A. Breimer, Mark K. Goldberg, Brian Kolstad, Malik Magdon-Ismail, Journal of Experimental Mathematics, Vol. 10, No. 4, pp. 583-597, 2001. Refereed Conferences "A Supervised Learning Approach for Detecting Significant Local Alignments" Eric A. Breimer, Mark K. Goldberg International Conference on Research in Computational Molecular Biology (poster to appear) April 18-21, 2002, Washington DC. "Learning Significant Alignments: An Alternative to Normalized Local Alignment" Eric A. Breimer, Mark K. Goldberg International Symposium on Methodologies for Intelligent Systems (to appear) June 27-29, 2002, Lyon, France. "Experimental Evaluation of the Height of a Random Set of Points in a d-dimensional Cube," Eric A. Breimer, Mark K. Goldberg, Brian Kolstad, Malik Magdon-Ismail, Workshop on Algorithm Engineering and Experiments, January 5-7, 2001, Washington DC. "A Learning Algorithm for the Longest Common Subsequence Problem," Eric A. Breimer, Mark K. Goldberg, Darren T. Lim, Workshop on Algorithm Engineering and Experiments, January 7-8, 2000, San Francisco. "A Task-based Architecture for Application-aware Adjuncts," Robert Farrell, Peter Fairweather, Eric Breimer, International Conference on Intelligent User Interfaces, January 9-12, 2000, New Orleans. Technical Reports "Case Study of a Learning Algorithm for the Longest Common Subsequence Problem," Eric A. Breimer, Mark K. Goldberg, Computer Science Technical Report (RPI), 1998. "Exploring Collaborative Learning in Rensselaer's Classroom-in-the-Round," Robert F.Dugan, Eric A. Breimer, Darren T. Lim, Ephraim P. Glinert, Mark K. Goldberg, Computer Science Technical Report (RPI), 1998. PRESENTATIONS Invited Talk Rutgers University 2001 Nov 12 "SEAL: System for Enhancing Algorithms through Learning," DIMACS: Working Group on Computer-Generated Conjectures from Graph Theoretic and Chemical Databases I Conference Washington DC 2001 Jan 6 "Experimental Evaluation of the Height of a Random Set of Points in a d-dimensional Cube," Workshop on Algorithm Engineering and Experiments Conference San Francisco CA 2000 Jan 8 "A Learning Algorithm for the Longest Common Subsequence Problem," Workshop on Algorithm Engineering and Experiments OTHER Team Captain Intramural Basketball, RPI 2001 Fall ACTIVITIES Organized intramural basketball team for computer science department. Student Coordinator Faculty Search Committee, CS Dept., RPI 2000 Coordinated meetings between faculty candidates and graduate students. Contributor Student Survival Guide, CS Dept., RPI 1999-Present Contributed significant content and design to the Computer Science Department's On-line Graduate Student Survival Guide. http://www.cs.rpi.edu/guide Application Reviewer Admission Committee, CS Dept., RPI 1999-Present Reviewed and evaluated hundreds of graduate student applications. Peer Advisor Student Orientation, CS Dept., RPI 1998-Present Advised incoming graduates students on issues such as degree requirements, course offerings, and research opportunities. Computer Technician The Fresh Air Fund, New York, NY 1997 Summer Responsible for PC repair and maintenance, and instructional support for summer camp staff. Using MS Access implemented standard inventory and report system for camp operations center. 1996 Summer 1995 Summer Volunteer Firefighter Rombout Fire District, Fishkill, NY 1993-1996 Responded to over 300 alarms and completed over 200 hours of training, including hazardous materials, confined space rescue, and ladder operations.