Survey
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
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