Shengyin Gu


     I am currently a Ph.D. student in the department of Computer Science, UC-Davis. I work closely with Professor Nina Amenta, Professor Bernd Hamann, Professor Patrice Koehl from UCD and scientist Inna Dubchak from Ernest Orlando Lawrence Berkeley National Laboratory (LBNL). Before I came to UCD, I received my B.S. degree for double majors in computer science and economics from Rutgers University.

     I am currently interested in computer graphics, visualization and computational geometry.

Resume:
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Research Projects:

   Molecular Docking. Molecules, such as proteins, DNA, RNA and drugs, function when they dock onto other molecules. Experimental discovery of docking information is currently inefficient and high cost. Many research has been done to predict binding sites and orientations in rigid and flexible docking, however the current tools available still require both speedup and improvement of accuracy. We approach protein docking problem by using geometric and computer vision related methods as well as including physical and chemical properties of molecules.

(Left: Comparison of Tryspin (green) with bovine tyspin inhibitor (blue) at atomic resolution (left) and in the reduced model (each sphere represents a pseudo-atom in the reduced model. Courtesy of Jacob University).

   Geometric Representation of Proteins. (Abstract) The amino acid sequence of a protein is the key to understanding its structure and ultimately its function in the cell. This paper addresses the fundamental issue of encoding amino acid in ways that the visualization of protein sequences facilitate the decoding of its information content. We show that a featured-based representation in a three dimensional space provides an adequate representation from which the folding class of a protein as well as its domain content can be predicted.

Gu, S., Poch, O., Hamann B., Koehl, P., A Geometric Representation of of Protein Sequences, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp 135-142, 2007. http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=4413047
   TreeQ-Vista: An interactive Tree Visualization Tool with Functional Annotation Query Capabilities. (Abstract) We describe a general multiplatform exploratory tool called TreeQ-Vista, designed for presenting functional annotations in a phylogenetic context. Traits, such as phenotypic and genomic properties, are interactively queried from a user-provided relational database with a user-friendly interface which provides a set of tools for users with or without SQL knowledge. The query results are projected onto a phylogenetic tree and can be displayed in multiple color groups. A rich set of browsing, grouping and query tools are provided to facilitate trait exploration, comparison and analysis.

Gu, S., Anderson, I., Kunin, V., Cipriano, M.J., Minovitsky, S., Weber, G.H., Amenta, N., Hamann, B. and Dubchak, I.L. (2007), TreeQ-VISTA: an interactive tree visualization tool with functional annotation query capabilities, Bioinformatics 23(6), Oxford University Press, pp. 764-766. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/6/764

   Retro-deformation of fossils. (Abstract) We consider a problem in which we want to restore the bilateral symmetry of an object which has been deformed by compression. This problem arises in paleontology, where symmetric fossils are deformed by the compression of the rocks in which they are embedded. Our input is a user-selected set of point-pairs on the deformed object, which are assumed to be mirror-images on the original symmetric object, with some added noise. We give a closed-form solution to one variant of the problem, and we show examples using this solution.

(under revision) Amenta, N., Kazhdan, M., Gu, S., Wiley, D., Motani, R., Hamann, B., Symmetry Restoration by stretching.

Retro-deformation is a part of a broader project called Evolutionary Morphing.

Graphics and Visualization Class Projects:

­­­­­­­­ MemViz is a visualization tool of memory graph. A memory graph is a footprint of memory for a program. Each node is created for an allocated memory location and directed edges are created for memory pointers. Memory graph evolves in different stages of a running program. It can be helpful to debugging, code optimization, security improvement etc. of a program.
   Multi-class segmentation of medical data using SVM. In the world of medical image analysis, segmentation methods are important and necessary. Automatic segmentation methods outperform traditional segmentation methods which utilizes human judgment, in ways that computer methods are more consistent, reliable and many times faster; however they require human expertise at the refinement stage after automatic procedure. I implemented a modified support vector machine (SVM) and analyzed its performance for multi-class segmentation.
   First Person Shooter Game. A first person shooter (FPS) game was created by using a simple game engine I wrote. The engine is organized by scene graph. It supports quake 3 level maps, several 3D model formats, animations of characters, user control key board events, sounds effects. It implements hierarchical transformation, hierarchical bounding volumes, texturing, lighting, level of details (or LOD) and view frustum culling.
   Volume Rending. I implemented several interpolation methods in a volume render. The visual results were compared and analyzed.