
Yusu Wang
Professor
Computer
Science and Engineering
The Ohio State University
487 Dreese Lab
2015 Neil Ave.
Columbus, Ohio 43210
Phone: (614) 2921309
Fax : (614) 2922911
yusu at cse dot ohiostate dot edu


I obtained my M.S and Ph.D degree from
Duke Univ. (where I received the Best PhD Dissertation Awards at CS Dept),
and B.S. degree from
Tsinghua Univ (graduated with First Class Honors). Before joining OSU, I was a postdoctoral researcher at
Geometric Computing lab in
Stanford Univ. from 20042005. 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).
I belong to the
Theory and
TGDA (Topology, Geometry, and Data Analysis) groups at OSU.
For more details, see my
CV here.

I will be giving a minicourse on Computational topology in Spring School on Discrete and Computational Geometry at Simons Center for Geometry and Physics in Stony Brook. The weeklong spring school (organized by Christopher Bishop and Joe Mitchell) is from April 1721, 2017. Applications deadline is March 17, 2017.

Congratulations to Justin Eldridge (coadvised by Dr. Belkin and myself) who received OSU Presedential Fellowship 2017! Great Job Justin!

Together with Partha Mitra from CSHL, we recently received a NIH RO1 grant on retrieving and analysing neuron structures.

We have an opening of a postdoc position to work with Dr. Tamal Dey and myself at OSU. We are looking for someone with strong background in different geoemtric / topological data analysis related areas and who is interested in computational topology and geometry. The position is supported under NSF RTG grant (see description here ). Applicants must be US citizens or permanent residents. Interested candidates should send your CV to Dr. Tamal Dey and myself.
 Our paper "Graphons, mergeons, and so on" is selected for Oral Presentation at NIPS 2016. Congratulations Justin!

I am a coorganizer of the TGDA@OSU Conference 2016 (webpage): Note that there are some funding available to support PhD students and junior researchers. Send your applications in soon!
 I am chairing the CG Week 2016 Workshops Committee (webpage) and a committee member for the Joint STOC/SoCG Workshop Day 2016 (webpage). Send your proposals in!
 Our paper "Efficient map reconstruction and augmentation via topological methods" won Best Paper Award at ACM SIGSPATIAL 2015. Congratulations Suyi and Yanjie!
Prospective Students / Postdoc:


I am looking for motivated graduate students with strong interests in geometric/topological algorithms and data analysis to work with. Interested students are encouraged to drop by my office to chat or send me emails with your CV.

I am happy to work with motivated undergraduate students on data analysis projects. Students should be interested in algorithm design and data analysis. Interested students are encouraged to send me emails.

We have an opening of a postdoc position to work with Dr. Tamal Dey and myself at OSU. We are looking for someone with strong background in different geoemtric / topological data analysis related areas and who is interested in computational topology and geometry. The position is supported under NSF RTG grant (see description here ). Applicants must be US citizens or permanent residents. Interested candidates should send your CV to Dr. Tamal Dey and myself.

I primarily work in the fields of Computational geometry, and Computational and applied topology. My work lies at the intersection of computer science (especially algorithms) and applied mathematics (especially applied topology, discrete and combinatorial geometry).
I am particularly interested in developing effective and theoretically justified algorithms for data / shape analysis using geometric and topological ideas and methods. I aim to both provide theoretical understanding of various computational methods developed, and to apply them to practical domains, including computational biology, computational neuroanatomy, geometric modeling, computer graphics and visualization.
 I am a member of the Theory, TGDA (Topology, Geometry, and Data Analysis), as well as Graphics groups at OSU.

My research has been supported by NSF, NIH and DOE.
Fall 2016:
CSE2331/5331:
Foundations II: Data structures and algorithms
Spring 2016:
CSE5559:
Computational topology: Theory, algorithms, and applications to data analysis
Our group has developed several software packages. Some tools are listed / described below. Also see our [
CompuTopoOSU] website (maintained by Dr. Dey and myself) for recent computational topology software.

denali [webpage]: A software package (developed by [J. Eldridge]) for a terrain metaphor platform for general scalar trees, with a callback system for general data analysis applications. The algorithm behind the software is based on our earlier work [Harvey and Wang, CFG2010]. Our software Ayla below is a collaborative and integrative framework targeted at molecular simulation data sets, while Denali aims to serve as a generic framework for general data.

SimBa [download here]: A software package (developed by Dayu Shi) for approximating the persistence diagram induced by the Rips filtration of a set of points in both Euclidean space or more general metric space via batch collpase.

TopMapRecon[webpage]: The Morsebased map reconstruction software developed by [Suyi Wang]).

Simpers [download here]: A software package developed by Dayu Shi (with some earlier work by Fengtao Fan) for computing the persistent homology of a filtration connected by simplicial maps. It is based on the algorithm we proposed in [Dey, Fan, Wang, SoCG 2014].

Ayla [webpage]: A collaborative visual analytic platform (developed by W. Harvey) which produces a 2Dterrain metaphor for researchers to visualize and explore the highdimensinoal molecular simulation data. The paper describing Ayla is available [here]. See a youtube video describing the tool [here], and also an image of the interface on the right and [here].

Smolign [webserver]: A complete software suite to compare multiple protein structures. It uses a novel method to extract and align spatial motifs from protein structures.

EPO [webserver]: An Enhanced PartialOrder Graph algorithm for comparing multiple (possibly high dimensional) curves. It aims at capturing low level of similarity.

LFMPro [download]: A tool for detecting significant local structural sites in proteins.

Journal / Conference Publications
Visualizing attributed graphs via terrain metaphor.
Y. Zhang, Y. Wang and S. Parthasarathy.
23rd
SIGKDD Conference on Knowledge Discovery and Data Mining (KDD)
2017. To appear.
Composing Tree Graphical Models with Persistent Homology Features for Clustering MixedType Data.
X. Ni, N. Quadrianto, Y. Wang and C. Chen.
34th Intl. Conf. Machine Learning (ICML) 2017. To appear.
A quest to unravel the metric structure behind perturbed networks.
S. Parthasarathy, D. Sivakoff, M. Tian and Y. Wang.
Sympos. Comput. Geom. (SoCG) 2017. To appear.
Declutter and Resample: Towards parameter free denoising.
M. Buchet, T. Dey, J. Wang and Y. Wang.
Sympos. Comput. Geom. (SoCG) 2017. To appear.
Topological Analysis of Nerves, Reeb Spaces, Mappers, and Multiscale Mappers.
T. Dey, F. Memoli and Y. Wang.
Sympos. Comput. Geom. (SoCG) 2017. To appear.
Metric embeddings with outliers A. Sidiropoulos, D. Wang and Y. Wang.
ACMSIAM Sympos. Discrete Alg. (SoDA) , pages 670689, 2017.
Parameterfree topology inference and sparsification for data on manifolds T. K. Dey, Z. Dong and Yusu Wang.
ACMSIAM Sympos. Discrete Alg. (SoDA) , pages 27332747, 2017.
Graphons, mergeons, and so on! J. Eldridge, M. Belkin and Y. Wang.
NIPS 2016, pages 23072315. (
Selected for oral presentation!).
SimBa: An Efficient Tool for Approximating RipsFiltration Persistence via Simplicial BatchCollapse T. K. Dey, D. Shi and Y. Wang.
Euro. Symp. Algorithms (ESA) 2016, 35:135:16. The software package (developed by Dayu Shi) can be downloaded [
here]
Multiscale Mapper: Topological summarization via codomain covers T. K. Dey, F. Memoli and Y. Wang.
ACMSIAM Sympos. Discrete Alg. (SoDA) 2016. Also available on arXiv:1504.03763v1
Efficient map reconstruction and augmentation via topological methods S. Wang, Y. Wang, and Y. Li.
ACM SIGSPATIAL 2015. [
project page]
(
Won Best Paper Award!)
Beyond Hartigan consistency: Merge distortion metric for hierarchical clustering J. Eldridge, M. Belkin and Y. Wang.
Conf. Learning Theory (COLT) 2015. ( Won Best Student Paper Award! ).
Comparing graphs via persistence distortion T. Dey, D. Shi and Y. Wang.
Sympos. Comput. Geom. (SoCG) 2015 , To appear. Code by Dayu Shi can be downloaded here: [
sourcezip] and
[
exezip]
Strong equivalence of the interleaving and functional distortion metrics for Reeb graphs U. Bauer, E. Munch and Y. Wang.
Sympos. Comput. Geom. (SoCG) 2015 , To appear.
Maintaining contour trees of dynamic terrains P.K. Agarwal, T. Molhave, M. Revsbak, I. Safa, Y. Wang and J. Yang.
Sympos. Comput. Geom. (SoCG) 2015 , To appear.
Topological analysis of scalar fields with outliers M. Buchet, F. Chazal, T. Dey, F. Fan, S. Oudot and Y. Wang.
Sympos. Comput. Geom. (SoCG) 2015 , To appear.
Learning with Fredholm Kernels Q. Que, M. Belkin and Y. Wang.
NIPS 2014 , To appear.
A collaborative visual analytics suite for protein folding research W. Harvey, I. Park, O. Rubel, V. Pascucci, PT. Bremer, C. Li and Y. Wang.
Journal of Molecular Graphics and Modelling (JMG) , 53, 5971, 2014. The link is [
here].
Measuring Distance Between Reeb Graphs U. Bauer, X. Ge, and Y. Wang.
ACM Sympos. Comput. Geom. (SoCG) 2014.
JSGraph of Join and Split Trees S. Wang, Y. Wang and R. Wenger.
ACM Sympos. Comput. Geom. (SoCG) 2014.
Computing Topological Persistence for Simplicial Maps T. K. Dey, F. Fan, and Y. Wang.
ACM Sympos. Comput. Geom. (SoCG) 2014. The paper is [
here]. The full version is also on arXiv at [
here]. The software package (developed by Dayu Shi) is [
here].
An efficient computation of handle and tunnel loops via Reeb graphs T. K. Dey, F. Fan, and Y. Wang.
ACM Trans. Graphics (Special issue from SIGGRAPH), 2013. The paper is [
here], and the supplementary file for proofs is [
here]. The software can be downloaded [
here].
Bilateral Blue Noise Sampling
J. Chen, X. Ge, LY. Wei, B. Wang, Y. Wang, H. Wang, Y. Fei, K. Qian, J. Yong, W. Wang.
ACM Trans. Graphics (Special issue from SIGGRAPH Asia), 2013. [
Project page]
Measuring similarity between curves on 2manifolds via homotopy area with E. W. Chambers.
ACM Sympos. Comput. Geom. (SoCG) , 2013. The archive version is [
here].
Graph induced complex on point data with T. K. Dey and F. Fan.
ACM Sympos. Comput. Geom. (SoCG) , 2013. Full version is [
here.] The accompanying software is [
here.]
Weighted graph Laplace operator under Topological noise with T. K. Dey and P. Ranjan.
ACMSIAM Sympos. Discrete Alg. (SODA) , 2013. [
pdf]
Reeb Graphs: Approximation and Persistence
with T. K. Dey.
Discrete and Computational Geometry 2012. [
pdf]
Featurepreserving 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), 17871796. 2012. [
pdf]
Eigendeformation of 3D models. with T. K. Dey and P. Ranjan.
The Visual Computer 28 (68): 585595, 2012. [
video] (Conference version appeared in
Computer Graphics International (CGI) 2012. )
Featureaware streamline generation of planar vector fields via topological methods. with C. Luo and I. Safa.
Computers and Graphics 36(6): 754766, 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. [
fullversion][
software by O. Busaryev]
Towards understading complex spaces: graph Laplacians on manifolds with singularities and boundaries with M. Belkin, Q. Que, and X. Zhou.
COLT 2012. , 2012. [
pdf]
Annotating simplices with a homology basis and its applications
with O. Busaryev, S. Cabello, C. Chen and T. Dey.
SWAT , 189200, 2012.
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. 2011. [
pdf]
Data Skeletonization via Reeb Graphs
with X. Ge, I. Safa and M. Belkin.
NIPS 2011.
[
pdf (full version)][
software (in matlab)]
Reeb Graphs: Approximation and Persistence
with T. K. Dey.
ACM Symposium on Computational Geometry (SOCG) 2011. [
pdf]
Enhanced Topologysensitive Clustering by Reeb Graph Shattering
with W. Harvey, O. Rubel, V. Pascucci, and P. T. Bremer.
TopoInVis 2011. [
pdf]
Tracking a generator by persistence
with O. Busaryev and T. K. Dey.
Discrete Mathematics, Algorithms and Applications, 2 (4): 539552, 2010. [
DOI:10.1142/S1793830910000875]
Hausdorff distance under translation for points and balls with P. K. Agarwal, S. HarPeled, and M. Sharir.
ACM Trans. Alg. 6 (4), 2010. [
pdf ]
Persistent Heat Signature for Poseoblivious Matching of Incomplete Models
with T. K. Dey, K. Li, C. Luo, P. Ranjan, and I. Safa.
Comput. Graph. Forum 2010 (SGP) . [
pdf]
Generating and Exploring a Collection of Topological
Landscapes for Visualization of ScalarValued Functions
with W. Harvey.
Comput. Graph. Forum 2010 (EuroVis) . (
Won 3rd Best Paper Award at EuroVis 2010! ) [
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. [
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. [
fullversion][
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.
ACMSIAM Symposium on Discrete Algorithms (SODA), 2010. [
original pdf][
modified pdf]
(The modified pdf has a minor correction in the paper after Lemma 3.3.)
Integral Estimation from Point Cloud in dDimensional 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.
ACMSIAM Symposium on Discrete Algorithms (SODA), 2009, 10311040. [
pdf]
[
code (by J. Sun) ]
Exact Partial Curve Matching under the Frechet Distance
ACMSIAM Symposium on Discrete Algorithms (SODA), 2009, 645654. [
Originalversion]
with K. Buchin and M. Buchin, [
!! Improvedversion !!]
Approximating Gradients for Meshes and Point Clouds via Diffusion Metric
with C. Luo and I. Safa.
Comput. Graph. Forum 2009, 28(5): 14971508. [
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.
[
webserver]
[
pdf ]
Distributed Roadmap Aided Routing in Sensor Networks
with Z. Zheng, K. Fan, and P. Sinha.
IEEE MASS 2008, 347352. [
pdf]
Discrete Laplace Operator for Meshed Surfaces
with M. Belkin and J. Sun.
ACM SOCG 2008. [
pdf ] [
code (by J. Sun) ]
Approximating Nearest Neighbor Among Triangles in Convex Position Information Processing Letters. 2008. [
pdf ]
Towards Unsupervised Segmentation of Semirigid Lowresolution Molecular Surfaces
with L. J. Guibas.
Algorithmica. 48 (4): 433448 (Aug. 2007). [
pdf ]
PlacementProximityBased Voltage Island Grouping under Performance Requirement
with H. Wu, M. Wong, and I. Liu.
IEEE Trans. ComputerAided Design. 26 (7): 12561269 (July 2007). [
pdf ]
LFMPro: A Tool for Detecting Significant Local Structural Sites in Proteins
with A. Sacan, O. Ozturk and H. Ferhatosmanoglu.
BioInformatics. 23 (6): 709716 (Mar. 2007). [
pdf ]
Efficient Algorithms for Contactmap Overlap Problem
with P. K. Agarwal and N. Mustafa.
J. Comput. Biology (JCB) . 14 (2): 131143 (Mar. 2007). [
pdf ]
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, 299310.
Relations Between Two Common Types of Rectangular Tiling
Proc. Intl. Symp. Algorithms and Computation, LNCS 4288, SpringerVerlag, 2006, 193202.
Frechet Distances for Curves, Revisited
with B. Aronov, S. HarPeled, C. Kauner and C. Wenk,
ESA 2006, 5263.
Distancesensitive routing and information brokerage in
sensor networks
with S. Funke, L. J. Guibas and A. Nguyen.
DOCSS 2006, 234251.
A TwoDimensional Kinetic Triangulation with NearQuadratic Topological Changes
with P. K. Agarwal and H. Yu.
Discrete and Computational Geometry (DCG) 36 (4): 573592 (Dec. 2006). [
pdf ]
Extreme Elevation on a 2Manifold
with P. K. Agarwal, H. Edelsbrunner, and J. Harer.
Discrete and Computational Geometry (DCG). 36 (4): 553572 (Dec. 2006).
Segmenting molecular surfaces
with V. Natarajan, P. Bremer, V. Pascucci and B. Hamann.
Computer Aided Geometric Design (CAGD). 23: 495509 (June 2006). [
pdf ]
Nearlinear time approximation algorithms for curve simplification
in two and threedimensions
with P. K. Agarwal, S. HarPeled, and N. Mustafa.
Algorithmica. 42(3/4):
203221 (2005). [
pdf ]
Postplacement voltage island generation under performance requirement
with H. Wu, I. Liu, and M. D. F. Wong,
ICCAD 2005, 309316
Low bounds for sparse geometric spanners
with P. K. Agarwal and P. Yin,
SODA 2005, 670671
Coarse and reliable geometric alignment for protein docking
with P. K. Agarwal, P. Brown, H. Edelsbrunner and J. Rudolph,
PSB 2005,
6677
Shape fitting with outliers
with S. HarPeled.
SIAM J. Comput. 33(2): 269285 (2004). [
pdf ]
Computing the writhing number of a polygonal knot
with P. K. Agarwal and
H. Edelsbrunner.
Discrete and Computational Geometry (DCG) 32(1):
3753 (2004). [
pdf ]
A 2D kinetic triangulation with nearquadratic topological changes
with P. K. Agarwal and H. Yu,
SOCG 2004, 180189
Extreme elevation on a 2manifold
with P. K. Agarwal, H. Edelsbrunner and J. Harer,
SOCG 2004, 357365
Hausdorff distance under translation for points and balls
with P. K. Agarwal, S. HarPeled and M. Sharir,
SOCG 2003, 282291
Shape fitting with outliers
with S. HarPeled, SOCG 2003, 2938
Nearlinear time approximation algorithms for curve simplification
with P. K. Agarwal, S. HarPeled, and N. Mustafa,
ESA 2002, 2941
Computing the writhing number of a polygonal knot
with P. K. Agarwal and H. Edelsbrunner,
SODA 2002, 791799
Occlusion culling for fast walkthrough in urban areas
with P. K. Agarwal and S. HarPeled,
EuroGraphics (short paper) 2001.
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, 237256, 2008. [
pdf ]

TechReports and Submitted
Measuring Similarity between Curves on 2Manifolds via Minimum Deformation Area
Manuscript, 2008. [
pdf]
Exact Algorithm for Partial Curve Matching via the Frechet Distance
Tech Report OSUCISRC9/08TR48, 2008. [
pdf]
Note: The result is then improved in the SODA'09 paper above.
Approximating Nearest Neighbor Among Triangles in Convex Position
Tech Report OSUCISRC5/07TR41, 2007
Partial Curve Matching under the Frechet Distance
with S. HarPeled.
Manuscript [
pdf ] [
Note (erratum): The epsapproximation algorithm in Section 4.2 is not correct (Theorem 4.5 thus does not hold). ]

Best Paper Award, ACM SIGSPATIAL 2015.

Best Student Paper Award, COLT 2015.

Lumley Research Award, College of Engineering, OSU, 2011.

3rd Best Paper Award, EuroVis 2010.

NSF Career Award, 2008

Top Reviewer for journal Computational Geometry: Theory and Applciations , 2008

DOE Career Award, 2006

Best PhD Dissertation Award, CS Dept, Duke, 2004
CV: [PDF]
Personal: Little Sasha and Julia
[pic].