Shun-Chuan Albert Chen

Personal Status: Permanent U.S. Resident Information Address: 3517 North Hills Dr. Apt Y303, Austin TX 78731 Phone: 1.512.297.0212 E-mail: [email protected]

Objective Searching for a Faculty/Postdoc Position in Computer Science and Engineering.

Education Ph.D. in Computer Sciences Expected 2009 winter University of Texas at Austin, Austin, TX Dissertation: ”Efficient Electrostatic Computation of Molecular Models”

M.S. in Computer Sciences May 2007 University of Texas at Austin, Austin, TX minor in Computational and Applied Mathematics

M.S. in Computer Science and Information Engineering June 2004 National Taiwan University, Taipei, Taiwan Thesis: ”Initial Studies on Chinese Spoken Document Analysis - Topic Segmentation, Title Gen- eration and Topic Organization”

B.S. in Computer Science and Information Engineering June 2002 National Taiwan University, Taipei, Taiwan Graduated with Phi Tau Phi Honor

Research My research interests mainly include developing and improving the core technologies for compre- Interests hensive computational modeling, simulation, analysis, and visualization of natural and synthetic phenomena, particularly in biomedical information.

Research BEM3D Jun 2005 - present Experience BEM3D is a platform for the efficient and accurate boundary element solution, evaluation and visual- ization. Compare to the current benchmark software, it decreases 20% of the average computational cost for solving partial differential equations. Several techniques I developed are applied in this project including • A parallel iterative linear solver implemented using the MPI interface.. • A library for numerically compute the singular integral over higher order surface discretization to reduce the number of elements with acceptable error tolerance • Preconditioning techniques to improve the rate of the convergence optimized with BLAS and LAPACK library. • This project is sponsored by National Institutes of Health (NIH).

PB-CFMM Jun 2005 - present PB-CFMM is a software package developed on the platform BEM3D for solving the Poisson- Boltzmann partial differential equation for rapid molecular electrostatic interaction. • A fast multipole method to speed up the calculation of the interaction between the far-away basis functions by grouping the sources that lie close together and treat them as a single source. This technique reduce the time complexity of the algorithm from O(N 2) to O(N), where N is the number of boundary elements. • This project is used in the protein docking package developed by the Scripps Research Institute and sponsored by National Institutes of Health (NIH). MolSurf package Jan 2006 - present MolSurf is a package for constructing molecular interfaces for the simulation of molecules. This is a team work which combines several working projects done by our lab members. The functions we developed include an efficient algorithm to generate high quality molecular surfaces, an octree-based level set contouring method to compute triangular/quadrilateral/tetrahedral/hexahedral meshes, a technique to improve the quality of a mesh, and a quality-guaranteed mesh decimation technique. This package is widely used by our collaborators including UCSD biochemistry lab and Scripps Research Institute. It is sponsored by National Institutes of Health (NIH).

Dynamic Box on Front Page Sep 2004 - May 2005 The project aimed to increase the utility of the front page by mining site access logs. We developed a caching algorithm to create a front page by selecting the important links of the website. The eventual goal of this technique is to provide links to web users while skipping over the in-between pages.

Chinese Broadcast News Retrieval System Sep 2002 - Sep 2003 The project is Chinese broadcast news retrieval system. Our lab developed a Chinese speech recog- nition technique for entering a query into the system. I developed a natural language processing algorithm, adaptive K nearest neighbor, to automatically summarize the transcribed spoken news into a readable title and a short summary. The spoken news is provided by our sponsor Central News Agency (CNA) in Taiwan and the final system is now working in CNA.

EVE: E-Vanguard for Emergency Sep 2001 - May 2002 This project is an embedded system to help the rescue and first-aid work in the present rescue operation. Several techniques are applied in this project. First, a Bluetooth networking system was designed for data and message transmission. Next, I developed a 8051 embedded system to control and monitor physical sensors, such as an oximeter and an electro-cardiograph provided with Bluetooth transmission for the injured. I also wrote a software on a wearable PDA for the rescue to communicate with each other and gather information from the 8051 physical monitoring system. A Windows application called a rescue command center is also developed for gathering the information from all the devices and commanding all the rescues through Bluetooth network system.

Selected ”Fast Molecular Poisson-Boltzmann Energy and Force Computation”, with Chandrajit Bajaj. work- Publications and ing paper. Scholarly Presentations ”Efficient and Accurate Higher-order Fast Multipole Boundary Element Method for Poisson Boltz- mann Electrostatics”, with Chandarjit Bajaj. UT ICES report 2009. Revised version submitted to SIAM Journal on Scientific Computing.

”Hierarchical Molecular Interfaces and Solvation Forces,” with Chandrajit Bajaj, Wenqi Zhao and Qin Zhang. SIAM/ACM Joint Conference on Geometric and Physical Modeling, San Francisco, CA, 2009. Revised version submitted to IEEE/ACM Transactions on Computational Biology and Bioinformatics.

”Protein Solvation Energies from 3D Electron Microscopy,” with Chandrajit Bajaj. 9th US National Congress on Computational Mechanics, San Francisco, CA, 2007.

”An Initial Prototype System for Chinese Spoken Document Understanding and Organization for Indexing/Browsing and Retrieval Applications,” with Lin-shan Lee, Shun-Chuan Chen, Yuan Ho, Jia-Fu Chen, Ming-Han Li, and Te-hsuan Li. International Symposium on Chinese Spoken Language Processing, pp. 329-332, Hong Kong, Dec. 2004.

”Active Learning for Story Segmentation of Spoken Documents,” In Proc. of the 2004 IEEE Inter- national Conference on Multimedia and Expo, Vol. 1, pp. 607-610, Taipei, Taiwan, Jun. 2004. ”Automatic Title Generation for Chinese Spoken Documents Using an Adaptive K Nearest-Neighbor Approach,” with Lin-shan Lee. In Proc. of Eurospeech 2003, pp. 2813-2816, Sep. 2003, Geneva, Switzerland.

”Cross Domain Chinese Speech Understanding and Answering Based on Name-Entity Extraction,” with Yun-Tien Lee and Lin-shan Lee. In Proc. of Eurospeech 2003, pp. 2821-2824, Sep. 2003, Geneva, Switzerland.

”Automatic Title Generation for Chinese Spoken Documents Considering the Special Structure of the Language,” with Lin-shan Lee. In Proc. of Eurospeech 2003, pp. 2325-2328, Sep. 2003, Geneva, Switzerland.

”Why is the Special Structure of the Language Important for Chinese Spoken Language Processing? Examples on Spoken Document Retrieval, Segmentation and Summarization,” with Lin-shan Lee, Yuan Ho, Jia-fu Chen. In Proc. of Eurospeech 2003, pp. 49-52, Sep. 2003, Geneva, Switzerland.

”E-Vanguard for Emergency - A Wireless System for Rescue and Healthcare,” with Hsuan-Wei Chen, Ang Lee, Kuo-Hao Chao, Yu-Cheng Huang and Feipei Lai. Healthcom 2003, pp. 29-35, Jun. 2003, Santa Monica, USA.

Skills • Programming Languages: C/C++, Java, Delphi, Intel 80x86 Assembly, Perl, Python, LaTex, MATLAB, C#, SQL, QT • Platforms: Linux, Microsoft Windows XP/2000/NT/Vista, Mac OS X, UNIX • Languages: English (fluent), Chinese Mandarin (native), Japanese (basic) • GRE: 2360 (V 760 Q 800 A 800)

Academic Research Assistant, University of Texas at Austin Jun 2007 - present Experience Advisor: Dr. Chandrajit Bajaj Research Areas: Computational biology, distributed scientific computing, geometric modeling and data visualization.

Teaching Assistant, University of Texas at Austin Sep 2004 - May 2007 CS383D: Numerical Analysis: Interpolation, Approximation, Quadrature, and Differential Equations (CS graduate course). CS 371p: Objected-Oriented Programming (CS undergraduate courses). CS 313e: Elements of Computer and Programming (CS undergraduate courses).

Research Assistant, National Taiwan University, Taiwan Sep 2002 - Jun 2004 Advisor: Dr. Lin-shan Lee Research Areas: speech recognition, information retrieval and multimedia systems.

Graduate Large-scale Data Mining, Machine Learning, Artificial Intelligence, Algorithms: Techniques and Coursework Theory, Theory of Computation, Distributed Computing, Numerical Treatment of Differential Equa- tions, Numerical Analysis: Interpolation, Approximation, Quadrature, and Differential Equations, Computer Graphics, Computer Animation, Computer Vision Systems, Multi-scale Bio-Modeling and Visualization, Geometric Modeling and Visualization

Honors And SIAM Student Travel Awards, 2009 Awards USNCCM9 Graduate Student Fellowship, 2007 Phi Tau Phi Scholastic Honor, 2002 (top 5% of class) Presidential Award, National Taiwan University, Taiwan, June 2002 (top 5% of class) Pan Wen-Yuan Foundation Scholarship 2001 Memberships and • Leader of University Summer CS Camp, National Taiwan University 2001 Activities • Activity Division Head of National Taiwan University CS Student Association, 2000-2001 • Members of IEEE, ACM, SIAM, IACM, USACM

References • Dr. Chandrajit Bajaj Professor of Computer Sciences Computational Applied Mathematics Chair in Visualization Director of Center for Computational Visualization University of Texas at Austin Email: [email protected] Phone: 1.512.481.8870 • Dr. Lexing Ying Assistant Professor of Mathematics and Institute for Computational Engineering and Sciences University of Texas at Austin Email: [email protected] Phone: 1.512.471.3149 • Dr. Yongjie Jessica Zhang Assistant Professor of Mechanical Engineering Carnegie Mellon University Email: [email protected] Phone: 1.412.268.5332 • Dr. Zeyun Yu Assistant Professor of Computer Science University of Wisconsin-Milwaukee Email: [email protected] Phone: 1.414.229.2960