Yusu Wang Assistant Professor Computer Science and Engineering The Ohio State University 487 Dreese Lab 2015 Neil Ave. �� Columbus, Ohio 43210 Phone: (614) 292-1309 Fax : (614) 292-2911 yusu at cse dot ohio-state dot edu

Brief Bio.

I obtained my M.S and Ph.D degree from Duke Univ., and B.S. degree from Tsinghua Univ. Before joining OSU, I was a post-doctoral researcher at Geometric Computing lab in Stanford Univ. from 2004-2005. I received DOE (Dept. of Energy) Career award in 2006, and NSF (National Science Foundation) Career award in 2008. I am currently on the editorial board of Journal of Computational Geometry (JoCG).

Research Interest

• Shape analysis and visualization, computational geometry, computational topology, and bioinformatics.
• My research is currently supported by NSF and DOE.

I am looking for students interested in shape analysis, geometric computing, visualization, algorithms, and computational biology. I recruit both students who want to work in theory (geometric computing and computational topology) and in application fields (bioinformatics, visualization, and graphics).

Software:

Our group has developed several software packages.

• Smolign [web-server]: A complete software suite to compare multiple protein structures. It uses a novel method to extract and align spatial motifs from protein structures.
• EPO [web-server]: An Enhanced Partial-Order Graph algorithm for comparing multiple (possibly high dimensional) curves. It aims at capturing low level of similarity.
• LFM-Pro [download]: A tool for detecting significant local structural sites in proteins.
• Mol-Viz [web-server]: This is the outcome of our summer-2007 R2 project by two undergraduate students, under my supervision. It is a simple web server allowing the visualization of molecular structures and geometric descriptor functions defined on them (e.g, the atomic-density function). We will graduately add more types of descriptor functions, and morph this server into a versatile visualization tool for multiple quantities defined on molecules.

Publications

• Book Chapters

Visual Analysis of Biomolecular surfaces
with V. Natarajan, P. Koehl, and B. Hamann. In L. Linsen, H. Hagen, and B. Hamann (editors), Mathematical Methods for Visualization in Medicine and Life Sciences..
Springer Verlag, Mathematics and Visualization, 237--256, 2008. [ pdf ]

• Journal Publications

An enhanced partial order curve comparison algorithm and its application to analyzing protein folding trajectories
with H. Sun and H. Ferhatosmanoglu. BMC BioInformatics 2008, 9 : 344. [web-server] [pdf ]

Approximating Nearest Neighbor Among Triangles in Convex Position
Information Processing Letters. To appear, 2008. [ pdf ]

Hausdorff distance under translation for points and balls
with P. K. Agarwal, S. Har-Peled, and M. Sharir. ACM Trans. Alg. To appear, 2008. [ pdf ]

Towards Unsupervised Segmentation of Semi-rigid Low-resolution Molecular Surfaces
with L. J. Guibas. Algorithmica. 48 (4): 433--448 (Aug. 2007). [ pdf ]

Placement-Proximity-Based Voltage Island Grouping under Performance Requirement
with H. Wu, M. Wong, and I. Liu. IEEE Trans. Computer-Aided Design. 26 (7): 1256--1269 (July 2007). [ pdf ]

LFM-Pro: A Tool for Detecting Significant Local Structural Sites in Proteins
with A. Sacan, O. Ozturk and H. Ferhatosmanoglu. BioInformatics. 23 (6): 709--716 (Mar. 2007). [ pdf ]

Efficient Algorithms for Contact-map Overlap Problem
with P. K. Agarwal and N. Mustafa. J. Comput. Biology (JCB) . 14 (2): 131--143 (Mar. 2007). [ pdf ]

A Two-Dimensional Kinetic Triangulation with Near-Quadratic Topological Changes
with P. K. Agarwal and H. Yu. Discrete and Computational Geometry (DCG) 36 (4): 573--592 (Dec. 2006). [ pdf ]

Extreme Elevation on a 2-Manifold
with P. K. Agarwal, H. Edelsbrunner, and J. Harer. Discrete and Computational Geometry (DCG). 36 (4): 553--572 (Dec. 2006). [ pdf ]

Segmenting molecular surfaces
with V. Natarajan, P. Bremer, V. Pascucci and B. Hamann. Computer Aided Geometric Design (CAGD). 23: 495--509 (June 2006). [ pdf ]

Near-linear time approximation algorithms for curve simplification in two and three-dimensions
with P. K. Agarwal, S. Har-Peled, and N. Mustafa. Algorithmica. 42(3/4): 203--221 (2005). [ pdf ]

Shape fitting with outliers
with S. Har-Peled. SIAM J. Comput. 33(2): 269--285 (2004). [ pdf ]

Computing the writhing number of a polygonal knot
with P. K. Agarwal and H. Edelsbrunner. Discrete and Computational Geometry (DCG) 32(1): 37--53 (2004). [ pdf ]

• Conference Publications

Convergence, Stability, and Discrete Approximation of Laplace Spectra
with T. K. Dey and P. Rajan. ACM-SIAM Symposium on Discrete Algorithms (SODA), 2010, To appear. [pdf]

Approximating Gradients for Meshes and Point Clouds via Diffusion Metric
with C. Luo and I. Safa. Eurographics Symposium on Geometric Processing (SGP) , 2009, To apeear. [pdf]

Integral Estimation from Point Cloud in d-Dimensional Space: A Geometric View
with C. Luo and J. Sun. ACM Symposium on Computational Geometry (SOCG) , 2009, To apeear. [pdf]

Constructing Laplace Operator from Point Clouds in R^d
with M. Belkin and J. Sun. ACM-SIAM Symposium on Discrete Algorithms (SODA), 2009, 1031--1040. [pdf] [code (by J. Sun) ]

Exact Partial Curve Matching under the Frechet Distance
ACM-SIAM Symposium on Discrete Algorithms (SODA), 2009, 645--654. [Original-version]
with K. Buchin and M. Buchin, [ !! Improved-version !!]

Distributed Roadmap Aided Routing in Sensor Networks
with Z. Zheng, K. Fan, and P. Sinha. IEEE MASS 2008, 347--352. [pdf]

Discrete Laplace Operator for Meshed Surfaces
with M. Belkin and J. Sun. ACM SOCG 2008, To appear. [pdf ] [code (by J. Sun) ]

An Enhanced Partial Order Curve Comparison over Multiple Protein Folding Trajectories
with H. Sun, H. Ferhatosmanoglu, and M. Ota, Proc. Intl. Conf. Computational Systems Bioinformatics, 2007, 299--310.

Relations Between Two Common Types of Rectangular Tiling
Proc. Intl. Symp. Algorithms and Computation, LNCS 4288, Springer-Verlag, 2006, 193--202.

Frechet Distances for Curves, Revisited
with B. Aronov, S. Har-Peled, C. Kauner and C. Wenk, ESA 2006, 52--63.

Towards Unsupervised Segmentation of Semi-rigid Low-resolution Molecular Surfaces
with L. J. Guibas. GMP 2006, 129--142.

Distance-sensitive routing and information brokerage in sensor networks
with S. Funke, L. J. Guibas and A. Nguyen. DOCSS 2006, 234--251.

Post-placement voltage island generation under performance requirement
with H. Wu, I. Liu, and M. D. F. Wong, ICCAD 2005, 309--316

Low bounds for sparse geometric spanners
with P. K. Agarwal and P. Yin, SODA 2005, 670--671

Coarse and reliable geometric alignment for protein docking
with P. K. Agarwal, P. Brown, H. Edelsbrunner and J. Rudolph, PSB 2005, 66--77

A 2D kinetic triangulation with near-quadratic topological changes
with P. K. Agarwal and H. Yu, SOCG 2004, 180--189

Extreme elevation on a 2-manifold
with P. K. Agarwal, H. Edelsbrunner and J. Harer, SOCG 2004, 357--365

Hausdorff distance under translation for points and balls
with P. K. Agarwal, S. Har-Peled and M. Sharir, SOCG 2003, 282--291

Shape fitting with outliers
with S. Har-Peled, SOCG 2003, 29--38

Near-linear time approximation algorithms for curve simplification
with P. K. Agarwal, S. Har-Peled, and N. Mustafa, ESA 2002, 29--41

Computing the writhing number of a polygonal knot
with P. K. Agarwal and H. Edelsbrunner, SODA 2002, 791--799

Occlusion culling for fast walkthrough in urban areas
with P. K. Agarwal and S. Har-Peled, EuroGraphics 2001.

• Tech-Reports and Submitted

Approximating Loops in a Shortest Homology Basis from Point Data
with T. K. Dey and J. Sun. Manuscript, 2009. [pdf]

Measuring Similarity between Curves on 2-Manifolds via Minimum Deformation Area
Manuscript, 2008. [pdf]

Exact Algorithm for Partial Curve Matching via the Frechet Distance
Tech Report OSU-CISRC-9/08-TR48, 2008. [ pdf]
Note: The result is then improved in the SODA'09 paper above.

Approximating Nearest Neighbor Among Triangles in Convex Position
Tech Report OSU-CISRC-5/07-TR41, 2007

Partial Curve Matching under the Frechet Distance
with S. Har-Peled. Manuscript [ pdf ]

Awards

• NSF Career Award, 2008
• DOE Career Award, 2006
• Best PhD Dissertation Award, CS Dept, Duke, 2004

Current Teaching

Winter 2009: CSE788: Geometric and Topological Algorithms: Theory and Applications

Spring 2009: CSE625: Automata ad Formal Languages

Links

CV: [PDF]

Personal: Little Sasha [dir]