Download Yang Xiang - The Ohio State University College of Medicine

Yang Xiang
Email: [email protected] or [email protected]
Homepage: http://bmi.osu.edu/~yxiang
Research Assistant Professor
Department of Biomedical Informatics
The Ohio State University
Columbus, OH 43210
Google Scholar Profile: http://scholar.google.com/citations?user=SK6wCRoAAAAJ
Lab: Network Laboratory of Biomedical Informatics (https://netlab.bmi.osumc.edu)
Research Interests
Bioinformatics, Computational Biology, Translational Informatics, Systems pharmacology, Data/Graph
Mining, Graph Databases, Algorithmic Graph Theory, Biomedical Text Processing, Visualization
Education / Training
PostDoc
Biomedical Informatics
The Ohio State Univ.
01/2010-08/2012
Ph.D.
Computer Science
Kent State Univ.
12/2009
M.E.
Computer Application
Nanjing Univ. of Aero. & Astro., China
03/2003
B.E.
Computer Software
Nanjing Univ. of Aero. & Astro., China
06/1999
Positions
Research Assistant Professor
Biomedical Informatics Dept., The Ohio State Univ.
09/2012-Present
Graduate Faculty Status
(M-level)
Computer Science & Engineering Dept.,
The Ohio State Univ.
07/2013-Present
CIFellow (NSF/CRA/CCC)
Biomedical Informatics Dept., The Ohio State Univ.
09/2010-08/2012
Postdoctoral
Researcher
Comprehensive Cancer Center,
Biomedical Informatics Dept., The Ohio State Univ.
01/2010-08/2010
Graduate Appointee/
Student Employee
Computer Science Dept. Kent State Univ.
08/2004-12/2009
Selected Awards / Honors
Outstanding Paper
American Medical Informatics Association
2010
Computing Innovation Fellow (CIFellow)
CRA & NSF & CCC
2010
KDD Student Travel Award
ACM SIGKDD
2008
Graduate Assistantship
Computer Science Dept., Kent State Univ.
2004-2009
GPA 4.0 /4.0
Kent State Univ.
2004-2009
Research Support
Completed Research Support
NSF CIFellows Project
09/01/10-08/31/12
Indexing and Mining Biomedical Data: Information Retrieval and Knowledge Discovery
The goal of this project is to advance graph indexing and graph mining techniques and applying them in
processing biomedical data. We have developed a number of techniques and have used them for
hypotheses generation and knowledge discovery in biomedical applications. Two representative works
are: (1) transactional database transformation, published in TCBB, which answers the challenge that
faces matrix completion techniques, and can unbiasedly evaluate a relationship in a bipartite biomedical
data; (2) k-neighborhood decentralization labeling scheme (kDLS), published in JBI, which is the first
graph indexing scheme that works on the whole UMLS for large scale knowledge discovery.
Role: Computing Innovation Fellow
Publications
In Journals
1
Y. Xiang, "Answering exact distance queries on real-world graphs with bounded
performance guarantees", The VLDB Journal, In press.
2
Y. Xiang, J. Zhang, K. Huang, "Mining the tissue-tissue gene co-expression network for
tumor microenvironment study and biomarker prediction, BMC Genomics, 14 (Suppl 5),
S4.
3
J. Zhang, S. Ni, Y. Xiang, J. Parvin, Y. Yang, Y. Zhou, K. Huang,"Gene Co-expression
Analysis Predicts Chromosomal Aberration Loci Associated with Colon Cancer
Metastasis", International Journal of Computational Biology and Drug Design, 2013, 6(1),
60-71.
4
F.F Dragan, Y. Xiang, "How to use spanning trees to navigate in graphs", Algorithmica.
2013, Vol 66, Issue 3, pp 479-511 (early version in in MFCS'09).
5
P. Zhang, R. Mourad, Y. Xiang, K. Huang, T. Huang, K. Nephew, Y. Liu, L. Li, "A dynamic
time order network for time-series gene expression data analysis", BMC System Biology.
2012, 6 (Suppl 3):S9.
6
J. Zhang, K. Lu, Y. Xiang, M. Islam, S. Kotian, Z. Kais, C. Lee, M. Arora, H. Liu, J. Parvin, K.
Huang "Weighted Frequent Gene Co-expression Network Mining to Identify Genes
Involved in Genome Stability", PLoS Computational Biology. 2012, 8(8): e1002656.
7
Y. Xiang, D. Fuhry, K. Kaya, R. Jin, U. Catalyurek, K. Huang, "Merging Network Patterns: A
General Framework to Summarize Biomedical Network Data", Network Modeling
Analysis in Health Informatics and Bioinformatics. 2012, Volume 1, Number 3, pp 103106.
8
F. F. Dragan, D. G. Corneil, E. Koehler, Y. Xiang, "Collective Additive Tree Spanners for
Circle Graphs and Polygonal Graphs", Discrete Applied Mathematics. 2012, vol 160, issue
12, pp 1717-1729.
9
C. Yan, Y. Xiang, F. F. Dragan, "Compact and Low Delay Routing Labeling Scheme for Unit
Disk Graphs", Computational Geometry. 2012, Vol 45, Issue 7, pp 305-325.
10
Y. Xiang, K. Lu, S. L. James, T. B. Borlawsky, K. Huang, P.R.O. Payne, "k-neighborhood
Decentralization: A Comprehensive Solution to Index the UMLS for Large Scale
Knowledge Discovery", Journal of Biomedical Informatics. 2012, Vol 45, Issue 2, pp 323336.
11
Y. Xiang, C.Q. Zhang, K. Huang, "Predicting glioblastoma prognosis networks using
weighted gene co-expression network analysis on TCGA data", BMC Bioinformatics.
2012, 13(Suppl 2):S12.
12
Y. Xiang, P.R.O. Payne, K. Huang, "Transactional Database Transformation and Its
Application in Prioritizing Human Disease Genes", IEEE-ACM Transactions on
Computational Biology and Bioinformatics. 2012, Vol 45, Issue 2, pp 323-336.
13
V. Chepoi, F. F. Dragan, B. Estellon, M. Habib, Y. Vaxès, and Y. Xiang, "Additive Spanners
and Distance and Routing Labeling Schemes for Hyperbolic Graphs", Algorithmica. 2012,
Vol 62, Numbers 3-4, 713-732.
14
R. Jin, N. Ruan, Y. Xiang, H. Wang, "Path-Tree: An Efficient Reachability Indexing Scheme
for Large Directed Graphs ", ACM Transactions on Database Systems. 2011, Vol 36, Issue
1, pp 7:1-7:44.
(early version in SIGMOD'08)
15
Y. Xiang, R. Jin, D. Fuhry, F. F. Dragan, "Summarizing transactional databases with
overlapped hyperrectangles", Data Mining and Knowledge Discovery. 2011, Vol 23, Issue
2, pp 215-251.
(early version in KDD'08)
16
J. Zhang, Y. Xiang, L. Ding, K. Keen-Circle, T. B Borlawsky, H. G. Ozer, R. Jin, P. Payne, K.
Huang "Using gene co-expression network analysis to predict biomarkers for chronic
lymphocytic leukemia", BMC Bioinformatics. 2010, 11(Suppl 9):S5.
(An outstanding paper of 2010 AMIA Summit on Translational Bioinformatics)
In Conferences/Workshops/Symposiums
17
R. Jin, N. Ruan, Y. Xiang, V. Lee, "A Highway-Centric Labeling Approach for Answering
Distance Queries on Large Sparse Graphs", Proc. of ACM SIGMOD Conference, 2012,
445-456.
18
Y. Xiang, D. Fuhry, R. Jin, Y. Zhao, K. Huang, "Visualizing Clusters in Parallel Coordinates
for Visual Knowledge Discovery", The 16th Pacific-Asia Conference on Knowledge
Discovery and Data Mining (PAKDD'12), 2012, pp 505-516.
19
R. Jin, Y. Xiang, H. Hong, K. Huang, “Block Interaction: A Generative Summarization
Scheme for Frequent Patterns”, Proc. of ACM SIGKDD Workshop on Useful Patterns
(UP'10), 2010, pp 55-64.
20
P. Uppalapati, Y. Xiang, K. Huang, "Predicting Prognostic Markers for Glioma Using Gene
Co-Expression Network Analysis", Workshop Gene Network and Pathway Generation
and Analysis, Proc. of the First ACM International Conference on Bioinformatics and
Computational Biology (BCB'10), 2010, pp 546-551.
21
R. Jin, H. Hong, H. Wang, N. Ruan, Y. Xiang, “Computing Label-Constraint Reachability in
Graph Databases”, Proc. of ACM SIGMOD Conference, 2010, pp 123-134.
22
F. F. Dragan, Y. Xiang, “How to use spanning trees to navigate in graphs”, in Proc. of 34st
International Symposium on Mathematical Foundations of Computer Science (MCFS'09),
2009, pp. 282-294.
23
C. Yan, Y. Xiang, F. F. Dragan, “Compact and Low Delay Routing Labeling Scheme for
Unit Disk Graphs”, Proc. of Algorithms and Data Structures Symposium (WADS'09), 2009,
pp 566-577.
24
J. Zhang, K. Huang, Y. Xiang, and R. Jin, “Using Frequent Co-expression Network to
Identify Gene Clusters for Breast Cancer Prognosis”, Proc. of International Joint
Conferences on Bioinformatics, System Biology and Intelligent Computing (IJCBS'09),
2009, pp. 428-434.
25
R. Jin, Y. Xiang, L. Liu, “Cartesian Contour: A Concise Representation for a Collection of
Frequent Sets”, Proc. of ACM SIGKDD Conference on Knowledge Discovery and Data
Mining (KDD'09), 2009, pp 417-426.
26
R. Jin, Y. Xiang, N. Ruan, D. Fuhry, “3-HOP: A High-Compression Indexing Scheme for
Reachability Query”, Proc. of ACM SIGMOD Conference 2009, pp 813-826.
27
R. Jin, S. Mccallen, C. Liu, Y. Xiang, E. Almaas, and X. J. Zhou, “Identifying Dynamic
Network Modules with Temporal and Spatial Constraints”, Pacific Symposium on
Biocomputing (PSB'09), 14, 2009, pp. 203-214.
28
R. Jin, Y. Xiang, D. Fuhry, F. F. Dragan, “Overlapping Matrix Pattern Visualization: a
Hypergraph Approach”, Proc. of Eighth IEEE International Conference on Data Mining
(ICDM'08), 2008, pp. 313-322.
29
Y. Xiang, R. Jin, D. Fuhry, F. F. Dragan, “Succinct Summarization of Transactional
Databases: An Overlapped Hyperrectangle Scheme”, Proc. of ACM SIGKDD Conference
on Knowledge Discovery and Data Mining (KDD'08), 2008, pp. 758-766.
30
R. Jin, M. Abu-Ata, Y. Xiang, N. Ruan, “Effective and Efficient Itemset Pattern
Summarization: Regression-based Approaches”, Proc. of ACM SIGKDD Conference on
Knowledge Discovery and Data Mining (KDD'08), 2008, pp. 399-407.
31
R. Jin, Y. Xiang, N. Ruan, H. Wang, “Efficiently Answering Reachability Queries on Very
Large Directed Graphs”, Proc. of ACM SIGMOD Conference, 2008, pp. 595-608.
32
F. F. Dragan, D. G. Corneil, E. Koehler and Y. Xiang, “Additive Spanners for Circle Graphs
and Polygonal Graphs”, Proc. of 34th International Workshop on Graph-Theoretic
Concepts in Computer Science (WG'08), 2008, pp. 110-121.
33
F. F. Dragan, C. Yan and Y. Xiang, “Collective Additive Tree Spanners of Homogeneously
Orderable Graphs”, Proc. of the 8th Latin American Theoretical Informatics (LATIN'08),
April 7-11, 2008, pp. 555-567.
34
A. Brandstädt, F.F. Dragan, Y. Xiang and C. Yan, “Generalized Powers of Graphs and
Their Algorithmic Use”, Proc. of the 10th Scandinavian Workshop on Algorithm Theory
(SWAT'06), 2006, pp. 423-434.
Posters/Abstracts
35
Y. Xiang, K. Lu, S. L. James, T. B. Borlawsky, K. Huang, P.R.O. Payne, "Indexing the UMLS
for Large Scale Knowledge Discovery in Biomedical Applications" (Poster Abstract), 2012
AMIA Summit on Translational Bioinformatics. 184.
36
P.Y. Yen, Y. Xiang, K. Huang, M. McDonagh, J. Merrill, "A proposal of an article network
analysis approach to reduce systematic review workload" (Poster Abstract), 11th
International Congress on Nursing Informatics, 2012. 685.
Invited Talks
• Indexing the Unified Medical Language System for Biomedical Knowledge Discovery, Indiana
University, April 2013
• Mining Genomic Data for Cancer Biomarker Prediction, Kent State University, March 2013
Services
PC Member for
• ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics (ACM BCB 2013)
• International Conference on Knowledge Discovery and Information Retrieval (KDIR 2013)
• IADIS European Conference on Data Mining (ECDM 2013)
• 24th IEEE International Conference on Tools with Artificial Intelligence (ICTAI 2012)
• International Conference on Knowledge Discovery and Information Retrieval (KDIR 2012)
• 7th International Conference on Advanced Data Mining (ADMA 2011)
• 23rd IEEE International Conference on Tools with Artificial Intelligence (ICTAI 2011)
• International Conference on Knowledge Discovery and Information Retrieval (KDIR 2011)
• The 2011 IEEE International Conference on Granular Computing (GrC 2011)
• IADIS European Conference on Data Mining (ECDM 2011)
Reviewer for the following journals:
• Bioinformatics
• CPT: Pharmacometrics & Systems Pharmacology
• PLOS ONE
• The VLDB Journal
• Data Mining and Knowledge Discovery
• Data & Knowledge Engineering
• Knowledge and Information Systems (KAIS)
• IEEE Transactions on Knowledge and Data Engineering (TKDE)
• IEICE Transactions on Information and Systems
• Journal of Systems and Software
• Information Sciences
• Neurocomputing
• Journal of Biomedical Informatics (JBI)
• Network Modeling Analysis in Health Informatics and Bioinformatics (NHIB)
• Algorithms for Molecular biology
• International Journal of Data Mining and Bioinformatics (IJDMB)
• International Journal of Ad Hoc and Ubiquitous Computing (IJAHUC)
• BMC Medical Genomics
• BMC Genomics
External reviewer for the following conferences/workshops/symposiums
• 2011 International Conference on Advances in Social Networks Analysis and Mining (ASONAM 2011)
• 2011 International Conference on Intelligent Computing (ICIC 2011)
• 13th Eurographics / IEEE Symposium on Visualization (EuroVis 2011)
• 6th International Conference on Intelligent Computing (ICIC 2010)
• 16th ACM SIGKDD Conference On Knowledge Discovery and Data Mining (KDD 2010)
• 14th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD 2010)
• 4th International Conference on Information Systems, Technology and Management (ICISTM 2010)
• 35th International Workshop on Graph-Theoretic Concepts in Computer Science (WG 2009)
• 15th ACM SIGKDD Conference On Knowledge Discovery and Data Mining (KDD 2009)
• 9th International Conference On Web-Age Information Management (WAIM2008)
• 20th International Symposium on Distributed Computing (DISC2006)
Memberships
• IEEE Member
• ACM Professional Member
• Sigma Xi Member
Lecturing at The Ohio State University
BMI5740 Introduction to Research Informatics -- Data Mining and Visualization
Spring 2013
IBGP/BMI705 Introduction to Biomedical Informatics -- Literature mining and Ontology Winter 2012
IBGP/BMI730 Biomedical Informatics I -- Literature mining and Ontology
Autumn 2011
IBGP/BMI705 Introduction to Biomedical Informatics -- Literature mining and Ontology Winter 2011
IBGP/BMI730 Biomedical Informatics I -- Literature mining and Ontology
Autumn 2010
Teaching at Kent State University
CS 10061 Intro to Computer Prog
Fall 2007
CS 10001 Computer Literacy
Spring 2007
CS 10001 Computer Literacy
Fall 2006
Grading at Kent State University
CS 6/76101 Advanced Topics in Algorithms
Fall 2009
CS 4/56101 Design and Analysis of Algorithms
Spring 2009
CS 4/56101 Algorithms
Spring 2006
CS 35101 Computer Architecture
Fall 2005
CS 6/76101 Advanced Algorithms
Fall 2005
CS 33211 Operating Systems
Spring 2005
CS 4/56101 Algorithms
Spring 2005
CS 4/55201 Comp Comm Networks
Fall 2004
CS 4/56101 Algorithms
Fall 2004