Yusu Wang Associate 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).

News:

• We are organizing an AMS (American Math Society)-sponsored MRC summer conference on Discrete and Computational Geometry, to be held in Snowbird, Utah, in June 2012. Math (or math-oriented) PhD students within +/- 2 years of graduation are welcome to apply. The deadline of application is March 1, 2012. See the [website] for more details.
  

Research Interest

• Computational geometry and topology, Geometric data / shape analysis, Geometric computing, and Computational biology.
• My research is currently supported by NSF and DOE.

Software:

Our group has developed several software packages.

• NEW!

  Ayla [web-page]: A collaborative visual analytic platform which produces a 2D-terrain metaphor for researchers to visualize and explore the high-dimensinoal molecular simulation data. (Developed by W. Harvey) See a youtube video describing the tool [here], and also an image of the interface on the right and [here].

• 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

Reeb Graphs: Approximation and Persistence
with T. K. Dey. Discrete and Computational Geometry 2012. To appear. [pdf]

Feature-preserving reconstruction of singular surfaces
with T. K. Dey, X. Ge, Q. Que, I. Safa, and L. Wang. Computer Graphics Forum (special issue from SGP 2012), 31 (5), 1787--1796. 2012. [pdf]

Eigen-deformation of 3D models.
with T. K. Dey and P. Ranjan. The Visual Computer 28 (6--8): 585--595, 2012. [video]

Feature-aware streamline generation of planar vector fields via topological methods.
with C. Luo and I. Safa. Computers and Graphics 36(6): 754--766, 2012.

Approximating Cycles in a Shortest Basis of the First Homology Group from Point Data
with T. K. Dey and J. Sun. Inverse Problems 2012. To appear. [full-version][software by O. Busaryev]

Smolign: A Spatial Motifs Based Protein Multiple Structural Alignment Method
with H. Sun, A. Sacan and H. Ferhatosmanoglu. IEEE//ACM Transactions on Computational Biology and Bioinformatics. To appear, 2011. [pdf]

Tracking a generator by persistence
with O. Busaryev and T. K. Dey. Discrete Mathematics, Algorithms and Applications, 2 (4): 539--552, 2010. [DOI:10.1142/S1793830910000875]

Hausdorff distance under translation for points and balls
with P. K. Agarwal, S. Har-Peled, and M. Sharir. ACM Trans. Alg. 6 (4), 2010. [ pdf ]

Persistent Heat Signature for Pose-oblivious Matching of Incomplete Models
with T. K. Dey, K. Li, C. Luo, P. Ranjan, and I. Safa. Comput. Graph. Forum 2010 (SGP) . To appear. [pdf]

Generating and Exploring a Collection of Topological Landscapes for Visualization of Scalar-Valued Functions
with W. Harvey. Comput. Graph. Forum 2010 (EuroVis) . To appear. [pdf]

Approximating Gradients for Meshes and Point Clouds via Diffusion Metric
with C. Luo and I. Safa. Comput. Graph. Forum 2009, 28(5): 1497--1508. [pdf]

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 ]

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

An efficient computation of handle and tunnel loops via Reeb graphs
with T. K. Dey and F. Fan. ACM SIGGRAPH 2013, to appear. The paper is [here], and the supplementary file for proofs is [here].

Measuring similarity between curves on 2-manifolds via homotopy area
with E. W. Chambers. ACM Sympos. Comput. Geom. (SoCG) , 2013, to appear. The archive version is [here].

Graph induced complex on point data
with T. K. Dey and F. Fan. ACM Sympos. Comput. Geom. (SoCG) , 2013, to appear. [Full version is here.]

Weighted graph Laplace operator under Topological noise
with T. K. Dey and P. Ranjan. ACM-SIAM Sympos. Discrete Alg. (SODA) , 2013, to appear. [pdf]

Feature-preserving reconstruction of singular surfaces
with T. K. Dey, X. Ge, Q. Que, I. Safa, and L. Wang. Symposium on Geometric Processing (SGP). 2012. [pdf]

Towards understading complex spaces: graph Laplacians on manifolds with singularities and boundaries
with M. Belkin, Q. Que, and X. Zhou. COLT 2012 (To appear). , 2012. [pdf]

Eigen deformation of 3D models
with T. K. Dey and P. Ranjan. Computer Graphics International (CGI). 2012. [pdf] [video]

Annotating Simplices with a Homology Basis and Its Applications
with O. Busaryev, S. Cabello, C. Chen and T. Dey. SWAT 2012. To appear.[pdf]

Data Skeletonization via Reeb Graphs
with X. Ge, I. Safa and M. Belkin. NIPS 2011. To appear. [pdf (full version)]

Reeb Graphs: Approximation and Persistence
with T. K. Dey. ACM Symposium on Computational Geometry (SOCG) 2011. To appear. [pdf]

Enhanced Topology-sensitive Clustering by Reeb Graph Shattering
with W. Harvey, O. Rubel, V. Pascucci, and P. -T. Bremer. TopoInVis 2011. To appear. [pdf]

Persistent Heat Signature for Pose-oblivious Matching of Incomplete Models
with T. K. Dey, K. Li, C. Luo, P. Ranjan, and I. Safa. Eurographics Symposium on Geometric Processing (SGP) , 2010. [pdf]

Generating and Exploring a Collection of Topological Landscapes for Visualization of Scalar-Valued Functions
with W. Harvey. EuroVis 2010. Won 3rd Best Paper Award! [pdf]

A Randomized O(m log m) Time Algorithm for Computing Reeb Graph of Arbitrary Simplicial Complexes
with W. Harvey and R. Wenger. ACM Symposium on Computational Geometry (SOCG) 2010. To appear. [pdf] and [code by W. Harvey]

Approximating Loops in a Shortest Homology Basis from Point Data
with T. K. Dey and J. Sun. ACM Symposium on Computational Geometry (SOCG) 2010. To appear. [full-version][software by O. Busaryev]
Note: the title for the journal version is Approximating Cycles in a Shortest Basis of the First Homology Group from Point Data.

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. [original pdf][modified pdf]
(The modified pdf has a minor correction in the paper after Lemma 3.3.)

Tracking a generator by persistence
with O. Busaryev and T. K. Dey. 16th Annu. Internat. Computating and Combinatorics Conf. (COCOON), 2010, 278--287. [pdf]

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

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 ] [ Note (erratum): The eps-approximation algorithm in Section 4.2 is not correct (Theorem 4.5 thus does not hold). ]

Awards

• Lumley Research Award, College of Engineering, OSU, 2011.
• 3rd Best Paper Award, EuroVis 2010.
• NSF Career Award, 2008
• DOE Career Award, 2006
• Outstanding PhD Dissertation Award, CS Dept, Duke, 2004

Current Teaching

Spring 2012: CSE780: Algorithms

Links

CV: [PDF]

Personal: Little Sasha and Julia [pic].