Chris Ding Publications

Publications of Chris H.Q. Ding

Publications tracked by DBLP: "Chris HQ Ding"

Subject area: Bioinformatics / Computational Biology ,
High Performance Computing , Data Assimilation using Kalman Filter ,
Spectral Clustering , Nonnegative Matrix Factorization ,
PCA and Extensions, Correspondence Analysis
Level Sets Clustering and Hierarchical Clustering
Markov Chain Monte Carlo

- 2011 -

Consensus Spectral Clustering. Dijun Luo, Chris Ding, Heng Huang. ICDE 2011, accepted to appear.

- 2010 -

On the eigenvectors of p-Laplacian. Dijun Luo, Heng Huang, Chris Ding, Feiping Nie. Machine Learning 81(1): 37-51 (2010)

Efficient and Robust Feature Selection via Joint L2,1-Norms Minimization, Feiping Nie, Heng Huang, Cai Xiao, Chris Ding. NIPS 2010

Towards Structural Sparsity: An Explicit L2/L0 Approach. Dijun Luo, Chris Ding, Heng Huang. ICDM 2010.

Multi-Label Linear Discriminant Analysis, Hua Wang, Chris Ding, Heng Huang. The 11th European Conference on Computer Vision (ECCV 2010).

Image Categorization Using Directed Graphs. Hua Wang, Heng Huang, Chris Ding. ECCV (3) 2010: 762-775

Multi-label Feature Transform for Image Classifications. Hua Wang, Heng Huang, Chris Ding. ECCV (4) 2010: 793-806

Discriminant Laplacian Embedding. Hua Wang, Heng Huang, Chris Ding. AAAI 2010

Multi-Label Classification: Inconsistency and Class Balanced K-Nearest Neighbor. Hua Wang, Chris Ding, Heng Huang. AAAI 2010

Exploiting user interests for collaborative filtering: interests expansion via personalized ranking. Qi Liu, Enhong Chen, Hui Xiong, Chris Ding. CIKM 2010: pp1697-1700.

Hierarchical Ensemble Clustering. Li Zheng, Tao Li, and Chris Ding. In Proceedings of 2010 IEEE International Conference on Data Mining (ICDM 2010).

Weighted Feature Subset Non-Negative Matrix Factorization and its Applications to Document Understanding. Dingding Wang, Chris Ding, and Tao Li. In Proceedings of 2010 IEEE International Conference on Data Mining (ICDM 2010).

Feature subset non-negative matrix factorization and its applications to document understanding. Dingding Wang, Chris Ding, Tao Li. SIGIR 2010, pp:805-806

Closed form solution of similarity algorithms. Yuanzhe Cai, Miao Zhang, Chris Ding, Sharma Chakravarthy. SIGIR 2010: 709-710

Directed Graph Learning via High-Order Co-linkage Analysis. Hua Wang, Chris Ding, Heng Huang. ECML/PKDD (3) 2010: 451-466.

Community Discovery Using Nonnegative Matrix Factorization. Fei Wang, Tao Li, Xin Wang, Shenghuo Zhu, and Chris Ding. Data Mining and Knowledge Discovery, to appear, 2010.

Bridging Domains with Words: Opinion Analysis with Matrix Tri-factorizations. Tao Li, Vikas Sindhwani, Chris Ding, Yi Zhang. SDM 2010: 293-302

Binary matrix factorization for analyzing gene expression data. Zhongyuan Zhang, Tao Li, Chris Ding, Xian-Wen Ren, Xiangsun Zhang. Data Min. Knowl. Discov. 20(1): 28-52 (2010)

Collaborative Filtering: Weighted Nonnegative Matrix Factorization Incorporating User and Item Graphs. Quanquan Gu, Jie Zhou, Chris Ding. SDM 2010: 199-210

- 2009 -

Convex and Semi-Nonnegative Matrix Factorizations [PDF]
[New variants of NMF with enhanced interpretability]
Chris Ding, Tao Li, Michael I. Jordan.
IEEE Transactions on Pattern Analysis and Machine Intelligence, 2009.

Consensus Group Based Stable Feature Selection [PDF]
Steven Loscalzo, Lei Yu, and Chris Ding.
Proceedings of the 15th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD-09), Paris, France, June, 2009. (Full paper, acceptance rate: 10%)

Symmetric Two Dimensional Linear Discriminant Analysis (2DLDA) [PDF]
Dijun Luo, Chris Ding, Heng Huang.
Proceedings of IEEE Conference on Computer Vision and Pattern Recognition (CVPR 2009).

Cross-Domain Sentiment Classification.
Tao Li, Vikas Sindhwani, Chris Ding.
Proceedings of 32st Annual International ACM SIGIR Conference (SIGIR 2009), 2009 ( poster paper).

Integrated KL (K-means - Laplacian) Clustering: A New Clustering Approach by Combining Attribute Data and Pairwise Relations. [PDF]
Fei Wang, Chris Ding, Tao Li.
Proceedings of SIAM International Conference on Data Mining (SDM 2009).

Non-negative Laplacian Embedding,
Dijun Luo, Chris Ding, Heng Huang.
IEEE International Conference on Data Mining (ICDM 2009).

Image Annotation Using Multi-label Correlated Green's Function,
Hua Wang, Heng Huang, Chris Ding.
IEEE Conference on Computer Vision (ICCV 2009), pp. 1-8.

Binary Matrix Factorization for Analyzing Gene Expression Data.
Zhong-Yuan Zhang, Tao Li, Chris Ding, Xian-Wen Ren, and Xiang-Sun Zhang.
Data Mining and Knowledge Discovery, to appear, 2009.

K-Subspace Clustering.
Dingding Wang, Chris Ding, and Tao Li.
Proceedings of the European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML/PKDD 2009)

- 2008 -

Nonnegative Matrix Factorization for Combinatorial Optimization: Spectral Clustering, Graph Matching, and Clique Finding (PDF)
Chris Ding, Tao Li, Michael I. Jordan
Proc. of IEEE International Conference on Data Mining (ICDM 2008) pp.183-192, 2008

Simultaneous Tensor Subspace Selection and Clustering: The Equivalence of High Order SVD and K-Means Clustering. (PDF)
Heng Huang, Chris Ding, Dijun Luo, Tao Li.
Proc. ACM Int'l Conf. on Knowledge Discovery and Data Mining (KDD) 2008. (Full paper, acceptance rate: 10%)

Tensor Reduction Error Analysis -- Applications to Video Compression and Classification. (PDF)
Chris Ding, Heng Huang, Dijun Luo.
IEEE Conference on Computer Vision and Pattern Recognition (CVPR 2008), accepted to appear.

Stable Feature Selection via Dense Feature Groups. (PDF)
Lei Yu, Chris Ding, Steven Loscalzo.
Proc. ACM Int'l Conf. on Knowledge Discovery and Data Mining (KDD) 2008. (Full paper, acceptance rate: 10%)

On the Equivalence Between Nonnegative Matrix Factorization and Probabilistic Latent Semantic Indexing. (PDF)
Chris Ding, Tao Li and Wei Peng.
Computational Statistics and Data Analysis, vol.52, 2008.
(Journal version of our AAAI 2006 conference paper with same title)

Robust Tensor Factorization Using R1 Norm (PDF)
Heng Huang and Chris Ding.
IEEE Conference on Computer Vision and Pattern Recognition (CVPR 2008), accepted to appear.

Knowledge Transformation from Word Space to Document Space. (PDF)
Tao Li, Chris Ding, Yi Zhang, and Bo Shao.
Proc. Annual International ACM SIGIR Conference (SIGIR 2008), pp: 187-194, 2008.

Multi-Document Summarization via Sentence-Level Semantic Analysis and Symmetric Matrix Factorization.
Dingding Wang, Tao Li, Shenghuo Zhu,and Chris Ding.
Proceedings of 31st Annual International ACM SIGIR Conference (SIGIR 2008), to appear.

Posterior Probabilistic Clustering using NMF. (PDF)
Chris Ding, Tao Li, Dijun Luo and Wei Peng.
Proceedings of 31st Annual International ACM SIGIR Conference (SIGIR 2008), pp.831-832, 2008 ( poster paper).

Weighted Consensus Clustering.
Tao Li and Chris Ding.
Proceedings of 2008 SIAM International Conference on Data Mining (SDM 2008), to appear.

Efficient Parallel I/O in Community Atmosphere Model (CAM)
Yu-Heng Tseng and Chris Ding
Int'l Journal of High Performance Computing Applications, Vol. 22, No. 2, 206-218 (2008) )
Gene Selection Algorithm by Combining ReliefF and mRMR.
Yi Zhang, Chris Ding and Tao Li
BMC Bioinformatics. 2008, vol.9:S27. ( paper online )
Estimating Support for Protein-Protein Interaction Data with Applications to Function Prediction (PDF)
Erliang Zeng, Chris Ding, Giri Narasimhan, Stephen R. Holbrook
Int'l Conf. Computational Systems Bioinformatics (CSB 2008), pp.73-84, August 2008. Stanford, CA.

- 2007 -

Consistent Dissection of the Protein Interaction Network by Combining Global and Local Metrics (PDF)
Chunlin Wang, Chris Ding, Qiaofeng Yang and Stephen R Holbrook,
Genome Biology, Vol.8, R271, 2007
A Learning Framework Using Green's Function and Kernel Regularization with Application for Recommender System
Chris Ding, Rong Jin, Tao Li, and Horst D. Simon.
Proc. ACM Int'l Conf. on Knowledge Discovery and Data Mining (KDD) 2007. (Full paper, acceptance rate: 40/500=8%)
Adaptive Dimension Reduction Using Discriminant Analysis and K-means Clustering (PDF file)
(Follow-up work of our ICDM'02 paper. Using LDA to determine the optimal subspace while using K-means to generate class labels.)
Chris Ding and Tao Li.
Proc. Int'l Conf. on Machine Learning (ICML) 2007.
Solving Consensus and Semi-supervised Clustering Problems Using Nonnegative Matrix Factorization (PDF file)
Tao Li, Chris Ding, and Michael Jordan.
To appear in Proc. IEEE Int'l Conf. on Data Mining (ICDM) 2007.
Binary Matrix Factorization with Applications (PDF file)
Zhongyuan Zhang, Tao Li, Chris Ding, and Xiang-Sun Zhang.
Proc. IEEE Int'l Conf. on Data Mining (ICDM) 2007.
A Two-Stage Gene Selection Algorithm by Combining ReliefF and mRMR (PDF file)
Yi Zhang, Chris Ding, and Tao Li.
Proc. IEEE Bioinformatics and Bio-engineering (BIBE) 2007 Conference.
Finding Hotspots in Document Collection
Wei Peng, Chris Ding, Tao Li, Tong Sun
Proc. IEEE International Conference on Tools with Artificial Intelligence (ICTAI) 2007.

- 2006 -

The Relationships Among Various Nonnegative Matrix Factorization Methods for Clustering (PDF file)
(summary of NMF formulations and their usages; clarify normalization, convergence rate, optimality issues)
Tao Li and Chris Ding.
Proc. IEEE Int'l Conf. on Data Mining (ICDM'06) 2006. pp.362-371.
On the Equivalence of (Convex-) Nonegative Matrix Factorization and K-meaning Clustering ( Slides.PDF, Paper.PDF )
[Propose semi NMF, convex NMF, kernel NMF]
In Stanford Workshop on Algorithms for Modern Massive Data Sets (MMDS 2006), June 2006.
Transitive Closure and Metric Inequality of Weighted Graphs --- Detecting Protein Interaction Modules Using Cliques (PDF).
Chris Ding, Xiaofeng He, Hui Xiong, Hanchuan Peng, Stephen R. Holbrook
Int'l J. Data Mining and Bioinformatics, Vol. 1, No. 2, pp. 162 - 177, 2006.
Supernova Recognition using Support Vector Machines (PDF).
Raquel Romano, Cecilia Aragon, Chris Ding
Proc. Int'l Conf. Machine Learning and Applications (ICMLA'06) 2006.
Best Application Paper Award.
PSoL: A Positive Sample Only Learning Algorithm for Finding Non-coding RNA Genes (PDF file)
[Since the publication, the 1st, 3rd and 4th predicted RNAs in E. Coli (locations and structures shown in the Supplement) are confirmed to be "very likely" by experimentalists (near 6S RNA, IstR RNA, and Ig containing IRU17)]
Chunlin Wang, Chris Ding, Richard Meraz, Stephen Holbrook.
Bioinformatics, vol.22, pp:2590-2596, 2006.
Dynamic Cluster Formation Using Level Set Methods (PDF).
[Advancing contours to find density peaks using level sets. Ample pictures show the adaptivity of contours]
Andy M. Yip, Chris Ding, Tony F. Chan.
IEEE Trans. Pattern Analysis Machine Intelligence, v.28, pp:877-889, 2006.
Nonnegative Matrix Factorization and Probabilistic Latent Semantic Indexing: Equivalence, Chi-square Statistic, and a Hybrid Method ( PDF file)
Chris Ding, Tao Li, Wei Peng
Proc. of AAAI National Conf. on Artificial Intelligence (AAAI-06), July 2006.
(A poster version of this paper also appears in SIGIR 2006)
R1-PCA: Rotational Invariant L1-norm Principal Component Analysis for Robust Subspace Factorization ( PDF file)
Chris Ding, Ding Zhou, Xiaofeng He, Hongyuan Zha
Proc. of Int'l Conf. Machine Learning (ICML 2006), June 2006.
Orthogonal Nonnegative Matrix Tri-factorizations for Clustering ( PDF file)
Chris Ding, Tao Li, Wei Peng, Haesun Park
Proc Int'l Conf. on Knowledge Discovery and Data Mining (KDD 2006), August 2006.

- 2005 -

Two-dimensional Singular Value Decomposition (2DSVD) for 2D Maps and Images (PDF file),
[PCA/SVD computes low-rank representation of a matrix (a set of 1D vectors); 2DSVD (2DPCA or 2D factorization of 3D Tensor) computes low-rank representation for a set of matrices, such as 2D images or weather maps. See wikipedia) ).
Chris Ding and Jieping Ye.
Proc. SIAM Int'l Conf. Data Mining (SDM'05), pp:32-43, April 2005.
A Probabilistic Approach for Optimizing Spectral Clustering
Rong Jin, Chris Ding and Fang Kang
Proc 9th Annual Conf. on Neural Information Processing Systems (NIPS 2005)
Minimum Redundancy - Maximum Relevance Feature Selection. (PDF)
Hanchuan Peng, Chris Ding, Fuhui Long.
IEEE Intelligent Systems Magazine, V.20, No.6, pp:70-71, Dec 2005.
A Multi-Level Approach to SCOP Fold Recognition. ((PDF)
Keith Marsolo, Srinivasan Parthasarathy, Chris Ding
IEEE Int'l Symposium of Bioinformatics and Bioengineering (BIBE 2005), pp:57-64
Cluster Aggregate Inequality and Multi-Level Hierarchical Clustering ( PS file)
[If the linkage function satisfies an inequality, a fast algorithm computes the agglomerative hierarchical clustering in O(n^2)]
Chris Ding and Xiaofeng He,
Proc. European Conf. Principles of Data Mining and Knowledge Discovery (PKDD 2005), Porto, Oct 2005.
On the Equivalence of Nonnegative Matrix Factorization and Spectral Clustering. (PDF file, PS file)
Chris Ding, Xiaofeng He, and Horst D. Simon.
Proc. SIAM Int'l Conf. Data Mining (SDM'05), pp:606-610, April 2005.
Feature selection based on mutual information: criteria of max-dependency, max-relevance, and min-redundancy (PDF)
Hanchuan Peng, Fuhui Long, Chris Ding
IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol. 27, No. 8, pp.1226-1238, 2005.
Coupling Multi-Component Models with MPH on Distributed Memory Computer Architectures. (PDF file)
Yun He and Chris Ding
Int'l Journal of High Performance Computing Applications, Vol. 19, No. 3, August 2005.
(Journel version of IPDPS'04 paper with same title)
CPL6: The New Extensible, High-Performance Parallel Coupler for the Community Climate System Model,
A.P. Craig, R.L. Jacob, B. Kauffman, T. Bettge, J. Larson, E. Ong, C. Ding, and Y. He.
Int'l Journal of High Performance Computing Applications, Vol. 19, No. 3, August 2005.
Comparative mapping of sequence-based and structure-based protein domains
Ya Zhang, John-Marc Chandonia, Chris Ding and Stephen Holbrook.
BMC Bioinformatics. 2005, 6:77. ( paper online )
A Probabilistic Model for Latent Semantic Indexing.
[Show LSI index vectors are optimal maximum-likelihood solutions to a probabilistic generative model of documents]
Chris Ding.
J. American Society for Information Science & Technology, v.56, 2005, pp:597-608. ( pdf file)
(Journal version of the SIGIR'99 paper with same title)
Term Norm Distribution and its Effects on Latent Semantic Indexing
Parry Husbands, Horst Simon, and Chris Ding.
Information Processing and Management, v.41, pp:777-787, 2005. ( pdf file)
(Journal version of the SIAM Computational IR Workshop paper with same title)
Identification of Functional Modules in Protein Complexes via Hyperclique Pattern Discovery,
Hui Xiong, Xiaofeng He, Chris Ding, Ya Zhang, Vipin Kumar, Stephen R. Holbrook,
Proc. of the Pacific Symposium on Biocomputing (PSB 2005), January 2005. ( pdf file)
Minimum redundancy feature selection from microarray gene expression data.
Chris Ding and Hanchuan Peng.
Journal of Bioinformatics and Computational Biology, Vol. 3, No. 2, pp.185-205, 2005. ( pdf file )
(Journal version of our CSB'03 paper with same title)

- 2004 -

Link Analysis: Hubs and Authorities on the World Wide Web
(Assume the Web is a fixed-degree-sequence random graph with link matrix L, we obtain expectation values of the authority matrix < L'L> and hub matrix < LL'>, their eigenvectors in closed form, and show surprising properties of webpage ranking)
Chris Ding, Hongyuan Zha, Xiaofeng He, Parry Husbands and Horst D. Simon
SIAM Review v.46, pp.256-268, June 2004. (submitted May 2001) ( pdf file)
K-means Clustering via Principal Component Analysis.
(Show that the solution of K-means are given by PCA. Follow-up work on NIPS'01 paper on Spectral Relaxation of K-means by Zha et al)
Chris Ding and Xiaofeng He.
Proc. of Int'l Conf. Machine Learning (ICML 2004), pp 225-232. July 2004. ( PDF file)
Linearized Cluster Assignment via Spectral Ordering
(Reduce multi-way spectral clustering to 1-D clustering)
Chris Ding and Xiaofeng He.
Proc. of Int'l Conf. Machine Learning (ICML 2004), pp.233-240. July 2004. ( PDF file, PS file)
K-nearest-neighbor consistency in data clustering: incorporating local information into global optimization.
Chris Ding and Xiaofeng He.
Proc. of ACM Symposium on Applied Computing (SAC 2004), pp.584-589. March 2004. ( PS file)
Positive Sample Only Learning (PSOL) for Predicting RNA Genes in E. coli
(Predict functional RNAs by identify most likely negative examples from unlabeled set and discriminate against positive examples using SVM)
Richard Meraz, Xiaofeng He, Chris Ding, Stephen R Holbrook
Proc. IEEE Computer Society Bioinformatics Conference, pp.535-538, August 2004. Stanford, CA.
(pdf file)
Contraction Graphs for Representation and Analysis of RNA Secondary Structure.
Chris Ding, Richard Meraz, Xiaofeng He, Stephen R Holbrook
Proc. IEEE Computer Society Bioinformatics Conference, pp.716-717, August 2004. Stanford, CA.
A Unified Representation for Multi-Protein Complex Data for Modeling Protein Interaction Networks. (pdf file)
(A bipartite graph is used to represent protein - protein complex relationship, out of which protein-protein and complex-complex interactions arise naturally. MinMaxCut clustering produces meaningful protein modules and supercomplexes.)
Chris Ding, Xiaofeng He, Richard Meraz, Stephen R Holbrook
Proteins: Structure, Function, and Bioinformatics, v.57, pp:99-108, June 2004.
Integrating Program Component Executables on Distributed Memory Architectures via MPH.
Chris Ding and Yun He.
Proc. Int'l Parallel and Distributed Processing Symposium (IPDPS 2004), April 2004, Santa Fe, New Mexico, USA.

- 2003 -

Document Retrieval and Clustering: from Principal Component Analysis to Self-aggregation Networks.
(Refined objective functions for simultaneous clustering of rows and columns of a rectangle data matrix using connectivity networks)
Chris Ding.
Proc. Int'l Parallel and Distributed Processing Symposium Proceedings of 9th Int'l Workshop on Artificial Intelligence and Statistics, January 2003, Key West, Florida, Eds. C.M. Bishop and B.J. Frey (editors)
( ps file)
Tutorial: Bioinformatics and Machine Learning Methods
at IEEE Int'l Conference on Data Mining (ICDM'03), November 19, 2003
Minimum Redundancy Feature Selection for Gene Expression Data
(Select Features that are minimally redundant among themselves while maximally relevant to class prediction)
Chris Ding and Hanchuan Peng.
Proc. IEEE Computer Society Bioinformatics Conference (CSB 2003), pp.523-529, August 2003. Stanford, CA.
(pdf file)
Unsupervised feature selection via two-way ordering in gene expression analysis
Chris Ding.
Bioinformatics. v.19, pp.1259-1266, 2003.
(Paper and supplimentary data)
Data Clustering: Principal Components, Hopfield and Self-Aggregation Networks.
(Clustering objectives and solutions: evolution from the simple to the sophisticated)
Chris Ding.
Proc. Int'l Joint Conf on Artificial Intelligence (IJCAI 2003), pp.479-484. August 2003 ( Postscript file)
Structure Search and Stability Enhancement of Bayesian Networks
Hanchuan Peng and Chris Ding
(LBNL Tech Report 51006, October 2002.) Proc. IEEE Int'l Conf. Data Mining. pp.621-624, Melbourne, Florida, Nov 2003.
(pdf file)

- 2002 -

Adaptive Dimension Reduction for Clustering High Dimensional Data. (see further development)
(Recursive projection to cluster centroid subspace instead of PCA subspace)
Chris Ding, Xiaofeng He, Hongyuan Zha, Horst Simon.
Proc. 2nd IEEE Int'l Conf. Data Mining, pp.147-154, Dec. 2002. Maebashi, Japan.
( Postscript file)
Analysis of gene expression profiles: class discovery and leaf ordering.
Chris Ding.
Proc. Conf. Research in Comp.Mol.Bio (RECOMB 2002), pp.127-136. April 2002, Washington, DC.
(PDF file)
Unsupervised Learning: Self-aggregation in Scaled Principal Component Space.
(Self-aggregation in Laplacian eigenspace and connectivity networks for cluster structure identification)
C. Ding, X. He, Hongyuan Zha, and H. Simon.
6th European Conference on Principles of Data Mining and Knowledge Discovery (PKDD 2002), T. Elomaa, H. Mannila, H. Toivonen (Eds.), Lecture Notes in Artificial Intelligence, Vol. 2431, pp. 112-124.
( PDF file, Postscript file)
Cluster merge and split in hierarchical clustering
(Recursive 2-way spectral clustering with refined cluster selections)
Chris Ding and Xiaofeng He
Proc. 2nd IEEE Int'l Conf. Data Mining. 2002. Maebashi, Japan. pp.139-146.
( Postscript file)
PageRank, HITS and a Unified Framework for Link Analysis.
(Combine mutual re-enforcement and link weight normalization into a single framework)
Chris Ding, Xiaofeng He, Parry Husbands, Hongyuan Zha and Horst D. Simon
Proc. of 25th ACM SIGIR Conf. pp.353-354, 2002, Tampere, Finland.
( Postscript file)
Web Document Clustering Using Hyperlink Structures,
Xiaofeng He, Hongyuan Zha, Chris Ding and Horst Simon.
Computational Statistics and Data Analysis. v.41, pp.19-45, 2002
(Journel version of the ICDM'01 paper "Automatic Topic Identification Using Webpage Clustering")
An efficient parallel computing method for modeling non-isothermal multi-phase Fluid multi-component transport in porpus and fractured media.
K. Zhang, Y.S. Wu, C. Ding, K. Pruess, E. Elmroth, G,S. Bodvarsson
Advances in Water Resources, vol. 25, pp.243-261, 2002
MPI and OpenMP Paradiagms on Cluster of SMP Architecture: the Vacancy Tracking Algorithm for Multi-Dimensional Array Transpose.
Yun He and Chris Ding.
Proc. of Supercomputing 2002, Nov 2002. (in pdf)

- 2001 -

An Optimal Index Reshuffle Algorithm for Multidimensional Arrays and Its Applications for Parallel Architectures.
(3D array remapping as used in climate models, FFTs, ADIs)
Chris Ding.
IEEE Transactions on Parallel and Distributed Systems Vol.12, pp.306-315, 2001, ( ps file)
Using Accurate Arithmetics to Improve Numerical Reproducibility and Stability in Parallel Applications. ( PDF file)
Yun He and Chris Ding.
Journal of Supercomputing , vol.18, pp.259-277, 2001. (Journal version of the ICS 2000 paper with same title)
A Ghost Cell Expansion Method for Reducing Communications in Solving PDE Problems.
Chris Ding and Yun He.
Proc. of Supercomputing 2001, Nov 2001. (paper in PDF)
Multi-class Protein Fold Recognition Using Support Vector Machines and Neural Networks.
(Applying SVM on protein 3D structure prediction)
Chris Ding and Inna Dubchak.
Bioinformatics, April 2001, Vol 17, No 4, pp.349-358.
(Paper and data)
Spectral Relaxation for K-means Clustering (PDF)
(Cluster indicators for K-means relax to principal components)
Hongyuan Zha, Chris Ding, Ming Gu, Xiaofeng He and Horst Simon.
Neural Information Processing Systems vol.14 (NIPS 2001). pp. 1057-1064, Vancouver, Canada. Dec. 2001.
Spectral Relaxation Models and Structure Analysis for K-way Graph Clustering and Bi-clustering.
(Spectral relaxation of Multi-way Normalized Cut and MinMaxCut)
Ming Gu, Hongyuan Zha, Chris Ding, Xiaofeng He and Horst Simon.
Technical Report, 2001. ( Postscript file)
A Min-Max Cut for Graph Partitioning and Data Clustering,
(Spectral clustering that minimizes between-cluster similarities and maximizes within-cluster similarities)
Chris Ding, Xiaofeng He, Hongyuan Zha, Ming Gu and Horst Simon.
Proc. of 1st IEEE Int'l Conf. Data Mining. San Jose, CA, 2001. pp.107-114.
( PS file, Journal version PS file)
A Spectral Method to Separate Disconnected and Nearly-disconnected Web Graph Components.
(Perturbation analysis of the Laplacian matrix and spectral clustering objective functions)
Chris Ding, Xiaofeng He and Hongyuan Zha.
Proc 7th Int'l Conf. on Knowledge Discovery and Data Mining (KDD 2001) pp.275-280, August 2001.
( Postscript file)
Bipartite Graph Partitioning and Data Clustering,
(Simultaneous clustering of rows and columns of a rectangle data matrix with a coherent objective function)
Hongyuan Zha, Xiaofeng He, Chris Ding, Ming Gu and Horst Simon.
Proc. of ACM 10th Int'l Conf. Information and Knowledge Management (CIKM 2001), pp.25-31, 2001, Atlanta, USA.
( Postscript file)
Automatic Topic Identification Using Webpage Clustering
(Web graph clustering using 1st and 2nd order link matrices with noise elimination using word similarities)
Xiaofeng He, Chris Ding, Hongyuan Zha, Horst D. Simon
Proc. IEEE Int'l Conf. Data Mining. San Jose, CA, 2001. (ICDM'01) pp.195-202.
( Postscript file)
High Performance Computations for Large Scale Simulations of Subsurface Multiphase Fluid and Heat Flow.
E. Elmroth, C.H.Q. Ding and Y.-S. Wu.
Journal of Supercomputing, vol.18, pp.235-258, 2001. (Journal version of the Supercomputing'99 paper with same title) ( ps file )
Parallel Computing Techniques for Large Scale Reservoir Simulations of Multi-Component Multiphase Fluid Flow.
K. Zhang, Y.S. Wu, C.H.Q. Ding, K. Pruess and E. Elmroth.
Proceedings of SPE Reservoir Simulation Symposium, Feb 2001, Houston, TX.

- 2000 -

Using Accurate Arithmetics to Improve Numerical Reproducibility and Stability in Parallel Applications.
Yun He and Chris Ding.
Proc. Int'l Conference on Supercomputing, May 2000.
Term Norm Distribution and its Effects on Latent Semantic Indexing
Parry Husbands, Horst Simon, Chris Ding.
Proc. of 1st SIAM Comput. Information Retrieval Workshop October 2000. Raleigh, NC.
A Probabilistic Model for Dimensionality Reduction in Information Retrieval and Filtering.
Chris Ding.
Proc. of 1st SIAM Comput. Information Retrieval Workshop October 2000. Raleigh, NC.

- 1999 -

A Similarity-based Probability Model for Latent Semantic Indexing.
(Show LSI index vectors are optimal solutions to maximum-likelihood of a probabilistic generative model)
Chris Ding.
Proc. ACM SIGIR Conference, pp:59-65. August 1999. ( ps file)
Data Organization and I/O in a Parallel Ocean Circulation Model (pdf),
Chris Ding and Yun He.
Proc. of Supercomputing 1999 , Nov. 1999.
See also Parallel I/O on distributied memory computers (link),
High Performance Computations for Large Scale Simulations of Subsurface Multiphase Fluid and Heat Flow.
E. Elmroth, C.H.Q. Ding and Y.-S. Wu.
Proc. of Supercomputing'99, Nov. 1999.
High Performance Fortran for Practical Scientific Algorithms: a up-to-date Evaluation (PS)
Chris H.Q. Ding,
Journal of Future Generation Computer Systems. v.15, pp:343-352, April 1999. Journal version of the HPF paper in HPCN'98.

- 1998 -

Evaluations of HPF (High Performance Fortran) for Practical Scientific Algorithms (html)
Chris Ding
Proc. Int'l Conf High-Performance Computing and Networking, (HPCN 1998), pp:223-232, 1998.
An 18 GFLOPS Parallel Climate Data Assimilation PSAS Package,
H.Q.Ding and R.D.Ferraro.
Int'l J. Mathematics & Computation, v.35, pp: 55-63, 1998,
Journal version of ISUG'96 paper.

- Before 1997 (by subject area) -

A Tutorial of High Performance Fortran (PS), at Princeton Plasma Physics Laboratory June 1997.
A Tutorial on MPI/PVM Optimizations (PS), at Lawrence Berkeley National Laboratory, March 1997
A Tutorial on Parallel Programming with MPI at Lawrence Berkeley National Laboratory, January 1997
Atmospheric Data Assimilation
A Parallel Climate Data Assimilation Package
H.Q.Ding and R.D.Ferraro,
Front page article on Nov 1996 issue of SIAM News.
Climate Data Assimilation on Massively Parallel Supercomputers (html),
H.Q.Ding and R.D.Ferraro,
Proc. of Supercomputing '96.
An 18 GFLOPS Parallel Climate Data Assimilation PSAS Package (PS),
H.Q.Ding and R.D.Ferraro.
Annual Conf. Intel Supercomputer User Group(ISUG'96), Knoxville,TN, June 1996,
Best Performance Paper Award
Parallel Sparse Matrix Solvers
A General Purpose Sparse Matrix Parallel Solvers Package (PS)
H.Q.Ding and F.D.Ferraro,
Proceedings of the 9th International Parallel Processing Symposium, pp.70-76, 1995.
Graph Partitioning
An Element-Based Concurrent Partitioner for Unstructured Finite Element Meshes. H.Q.Ding and F.D.Ferraro,
Proceedings of the 10th Inti'l Parallel Processing Symposium, pp.601-605. IEEE Computer Society Press,1996.
Parallel FFT
A Portable Parallel FFT's for Distributed Architectures (PS)
H.Q.Ding, D.B.Gennery, F.D.Ferraro,
Proc. 7th SIAM conference on Parallel Processing for Scientific Computing, pp.70-71. 1995.
Hybrid Metropolis- Gibbs Sampling
An Improved Heat Bath Method for Vectorized Processing,
H.Q. Ding,
J. of Computational Physics, v.67, p:28-38 (1986).

Performance Analysis of Parallel Applications
Simulating Lattice QCD on a Caltech/JPL Hypercube,
H.Q. Ding,
Int'l J. of Supercomputer Applications, v.5, pp:73-80 (1991).
Monte Carlo Simulations of Quantum Systems on Massively Parallel Supercomputers (PS),
H.Q. Ding,
Computers in Physics, v.7,pp:687-695 (1993).
Molecular Dynammics Computational Methods
"Atomic Level Simulations of on a Million Particles: The Cell Multipole Method for Coulomb and London Interactions", H.Q. Ding, N. Karasawa and W.A. Goddard, J. of Chemical Physics, v.97, pp:4309-4315 (1992).
"The Reduced Cell Multipole Method for Coulomb Interactions in Periodic Systems with Million-Atom Unit Cells", H.Q. Ding, N.Karasawa, W.A.Goddard, Chemical Physics Letters, v.196, p.6 (1992).
"Polymer Simulation on the Hypercube", H.Q. Ding, Proceedings of the Third Conference on Hypercube Concurrent Computers and Applications, Ed. G. Fox, 1988, p.1044.
"Optimal Spline Cutoffs for Coulomb and van der Waals Interactions", H.Q. Ding, N. Karasawa, W.A. Goddard, Chemical Physics letters, v.193, pp:197-201 (1992).
Quantum Monte Carlo methods for Materials Sciences
"Could In-Plane Exchange Anisotropy Induce the Observed Antiferromagnetic Transitions in the Undoped High-Tc Materials?" H.Q. Ding, Physical Review Letters v.68, pp.1927-1930 (1992).
"Spin Correlations of 2D Quantum Antiferro-magnets at Low Temperature and A Direct Comparison with Neutron Scattering Experiments", H.Q. Ding and M.S. Makivic, Physical Review Letters v.64, pp.1449-1452 (1990).
"Band Structure, Magnetic Fluctuations and the Quasiparticle of A Hole in the 2D three-band Hubbard Model", H.Q. Ding, G.H. Lang, W.A. Goddard, Physical Review B v.46, p.14317 (1992).
"Antiferromagnetic Transitions in High-Tc Materials", H.Q. Ding, J. Physics: Condensed Matter, v.2, p.7979 (1990).
"Momentum Distribution and Fermi Surface in the t-J Model", H.Q. Ding, Physica, v.C203, p.91 (1992).
"Elementary Excitations for the Two-Dimensional Quantum Heisenberg Antiferromagnet", G. Chen, H.Q. Ding, and W.A. Goddard, Physical Review B, v.46, pp:2933-2941 (1992).
"Spin and Charge Dynamics in a One-Dimensional Two-Band Hubbard Model", H.Q. Ding and W.A. Goddard, Physical Review B v.47, p.1149 (1993).
"Spin Correlations of 2D Quantum Antiferro-magnets at Low Temperature and A Direct Comparison with Neutron Scattering Experiments -- a reply", H.Q. Ding and M.S. Makivic, Physical Review Letters, v.65, p.1520 (1990).
"Spin Correlations in the Antiferromagnetic Crystals La2CuO4 and KNiF4", H.Q. Ding and M.S. Makivic, Modern Physics Letters B v.4, p.697, (1990).
"Two Dimensional Spin-1/2 Heisenberg Antiferromagnet: A Quantum Monter Carlo Study", M.S. Makivic and H.Q. Ding, Physical Review B, v.43, pp:3562-3574 (1991).
"Two-Dimensional Antiferromagnet at Low Temperatures" H.Q. Ding Physics Letters v.A159 , p.355 (1991).
"Comment on `Crossover to Effectively Two-Dimensional Vortices for High-Tc Superconductors' ", H.Q. Ding Physical Review Letters v.68, p.3819 (1992).
"Phase Transition and Thermodynamics of Quantum XY Model in Two Dimensions", H.Q. Ding, Physical Review B v.45, pp:230-242 (1992).
"A Kosterlitz-Thouless Transition in the Two-Dimensional Quantum XY Model", H.Q. Ding and M.S. Makivic, Physical Review B v.42, p.6827 (1990).
"A Kosterlitz-Thouless Transition in the Two-Dimensional Quantum XY Model -- a Reply", H.Q. Ding, M.S. Makivic, Physical Review v.B45, p491 (1992).
"Momentum Distributions and Fermi-surface in t-J Model", H.Q.Ding, PHYSICA C, v.203, pp:91-97 (1992).
Monte Carlo Simulations of Lattice QCD
"Latent Heat and Critical Temperature of the Color Deconfining Phase Transition", N.H. Christ and H.Q. Ding, Physical Review Letters, v.60, pp.1367-1370 (1988).
"Computing quark potential on a parallel supercomputer", H.Q. Ding, Computer Physics Communication, v.65, pp:92-99 (1991).
"Lattice Gauge Theory at Finite Temperature: A Monte Carlo Study", H.Q. Ding, invited talk in Symposium/Workshop on Lattice Gauge Theory Using Parallel Processors, Beijing, 1987. Published in Lattice Gauge Theory Using Parallel Processors, Eds. Li, Qiu and Ren, (Gordon and Breach, New York, 1987, p.155.
"A Determination of the Q-bar Q Potential with Very High Statistics", H.Q. Ding, Physics Letters B v.200, p.133 (1988).
"A Comparison of Langevin and Microcanonical Simulations for Fermions", H.Q. Ding and O. Martin, Nuclear Physics, v.B280, p.497 (1987).
"Calculation of the Heavy Quark Potential at Large Distances on a hypercube parallel computer", H.Q. Ding, C.F. Baillie and G.C. Fox, Physical Review D , v.41, p:2912-2920 (1990).
"Asymptotic Scaling of the Heavy Quark Potential in Lattice QCD", H.Q. Ding, Physical Review D , v.42, p:2350-2358 (1990).
"Improved Determination of the Heavy Quark Potential in Lattice QCD", H.Q. Ding, Physical Review D , v.44, pp.2200-2206 (1991).
"Heavy Quark Potential in Lattice QCD: A Review of Recent Progress at Caltech", H.Q. Ding, Int'l J. of Modern Physics C , v.42, p.2350 (1991).