Nagiza F. Samatova

Sriram Lakshminarasimhan, Neil Shah, Stéphane Ethier, Seung-Hoe Ku, Choong-Seock Chang, Scott Klasky, Robert Latham, Robert B. Ross, Nagiza F. Samatova: ISABELA for effective in situ compression of scientific data. Concurrency and Computation: Practice and Experience 25(4): 524-540 (2013)

Zhengzhang Chen, William Hendrix, Nagiza F. Samatova: Community-based anomaly detection in evolutionary networks. J. Intell. Inf. Syst. 39(1): 59-85 (2012)

Matthew C. Schmidt, Andrea M. Rocha, Kanchana Padmanabhan, Yekaterina Shpanskaya, Jillian F. Banfield, Kathleen Scott, James R. Mihelcic, Nagiza F. Samatova: NIBBS-Search for Fast and Accurate Prediction of Phenotype-Biased Metabolic Systems. PLoS Computational Biology 8(5) (2012)

Neil Shah, Eric R. Schendel, Sriram Lakshminarasimhan, Saurabh V. Pendse, Terry Rogers, Nagiza F. Samatova: Improving I/O Throughput with PRIMACY: Preconditioning ID-Mapper for Compressing Incompressibility. CLUSTER 2012: 209-219

John Jenkins, James Dinan, Pavan Balaji, Nagiza F. Samatova, Rajeev Thakur: Enabling Fast, Noncontiguous GPU Data Movement in Hybrid MPI+GPU Environments. CLUSTER 2012: 468-476

John Jenkins, Isha Arkatkar, Sriram Lakshminarasimhan, Neil Shah, Eric R. Schendel, Stéphane Ethier, Choong-Seock Chang, Jacqueline H. Chen, Hemanth Kolla, Scott Klasky, Robert B. Ross, Nagiza F. Samatova: Analytics-Driven Lossless Data Compression for Rapid In-situ Indexing, Storing, and Querying. DEXA (2) 2012: 16-30

Sriram Lakshminarasimhan, Prabhat Kumar, Wei-keng Liao, Alok N. Choudhary, Vipin Kumar, Nagiza F. Samatova: On the path to sustainable, scalable, and energy-efficient data analytics: Challenges, promises, and future directions. IGCC 2012: 1-6

Eric R. Schendel, Saurabh V. Pendse, John Jenkins, David A. Boyuka II, Zhenhuan Gong, Sriram Lakshminarasimhan, Qing Liu, Hemanth Kolla, Jackie Chen, Scott Klasky, Robert B. Ross, Nagiza F. Samatova: ISOBAR hybrid compression-I/O interleaving for large-scale parallel I/O optimization. HPDC 2012: 61-72

Eric R. Schendel, Ye Jin, Neil Shah, Jackie Chen, Choong-Seock Chang, Seung-Hoe Ku, Stéphane Ethier, Scott Klasky, Robert Latham, Robert B. Ross, Nagiza F. Samatova: ISOBAR Preconditioner for Effective and High-throughput Lossless Data Compression. ICDE 2012: 138-149

Doel L. Gonzalez, Zhengzhang Chen, Isaac K. Tetteh, Tatdow Pansombut, Fredrick H. M. Semazzi, Vipin Kumar, Anatoli V. Melechko, Nagiza F. Samatova: Hierarchical Classifier-Regression Ensemble for Multi-phase Non-linear Dynamic System Response Prediction: Application to Climate Analysis. ICDM Workshops 2012: 781-788

Zhenhuan Gong, Terry Rogers, John Jenkins, Hemanth Kolla, Stéphane Ethier, Jackie Chen, Robert B. Ross, Scott Klasky, Nagiza F. Samatova: MLOC: Multi-level Layout Optimization Framework for Compressed Scientific Data Exploration with Heterogeneous Access Patterns. ICPP 2012: 239-248

Zhenhuan Gong, Sriram Lakshminarasimhan, John Jenkins, Hemanth Kolla, Stéphane Ethier, Jackie Chen, Robert B. Ross, Scott Klasky, Nagiza F. Samatova: Multi-level Layout Optimization for Efficient Spatio-temporal Queries on ISABELA-compressed Data. IPDPS 2012: 873-884

John Jenkins, Eric R. Schendel, Sriram Lakshminarasimhan, David A. Boyuka II, Terry Rogers, Stéphane Ethier, Robert B. Ross, Scott Klasky, Nagiza F. Samatova: Byte-precision level of detail processing for variable precision analytics. SC 2012: 48

Saurabh V. Pendse, Isaac K. Tetteh, Fredrick H. M. Semazzi, Vipin Kumar, Nagiza F. Samatova: Toward Data-driven, Semi-automatic Inference of Phenomenological Physical Models: Application to Eastern Sahel Rainfall. SDM 2012: 35-46

Matthew C. Schmidt, Andrea M. Rocha, Kanchana Padmanabhan, Zhengzhang Chen, Kathleen Scott, James R. Mihelcic, Nagiza F. Samatova: Efficient alpha, beta-motif Finder for Identification of Phenotype-related Functional Modules. BMC Bioinformatics 12: 440 (2011)

Wenbin Chen, Matthew C. Schmidt, Nagiza F. Samatova: On the parameterized complexity of the Multi-MCT and Multi-MCST problems. J. Comb. Optim. 21(2): 151-158 (2011)

Jiangtian Li, Xiaosong Ma, Srikanth B. Yoginath, Guruprasad Kora, Nagiza F. Samatova: Transparent runtime parallelization of the R scripting language. J. Parallel Distrib. Comput. 71(2): 157-168 (2011)

Heshan Lin, Xiaosong Ma, Wu-chun Feng, Nagiza F. Samatova: Coordinating Computation and I/O in Massively Parallel Sequence Search. IEEE Trans. Parallel Distrib. Syst. 22(4): 529-543 (2011)

Kevin A. Wilson, Andrea M. Rocha, Kanchana Padmanabhan, Kuangyu Wang, Zhengzhang Chen, Ye Jin, James R. Mihelcic, Nagiza F. Samatova: Detecting Pathway Cross-Talks by Analyzing Conserved Functional Modules across Multiple Phenotype-Expressing Organisms. BIBM 2011: 443-449

Jaya Kawale, Stefan Liess, Arjun Kumar, Michael Steinbach, Auroop R. Ganguly, Nagiza F. Samatova, Fredrick H. M. Semazzi, Peter K. Snyder, Vipin Kumar: Data Guided Discovery of Dynamic Climate Dipoles. CIDU 2011: 30-44

Sriram Lakshminarasimhan, Neil Shah, Stéphane Ethier, Scott Klasky, Robert Latham, Robert B. Ross, Nagiza F. Samatova: Compressing the Incompressible with ISABELA: In-situ Reduction of Spatio-temporal Data. Euro-Par (1) 2011: 366-379

John Jenkins, Isha Arkatkar, John D. Owens, Alok N. Choudhary, Nagiza F. Samatova: Lessons Learned from Exploring the Backtracking Paradigm on the GPU. Euro-Par (2) 2011: 425-437

Ye Jin, Sriram Lakshminarasimhan, Neil Shah, Zhenhuan Gong, Choong-Seock Chang, Jackie Chen, Stéphane Ethier, Hemanth Kolla, Seung-Hoe Ku, Scott Klasky, Robert Latham, Robert B. Ross, Karen Schuchardt, Nagiza F. Samatova: S-preconditioner for Multi-fold Data Reduction with Guaranteed User-Controlled Accuracy. ICDM 2011: 290-299

Tatdow Pansombut, William Hendrix, Zekai Jacob Gao, Brent E. Harrison, Nagiza F. Samatova: Biclustering-Driven Ensemble of Bayesian Belief Network Classifiers for Underdetermined Problems. IJCAI 2011: 1439-1445

Huseyin Sencan, Zhengzhang Chen, William Hendrix, Tatdow Pansombut, Fredrick H. M. Semazzi, Alok N. Choudhary, Vipin Kumar, Anatoli V. Melechko, Nagiza F. Samatova: Classification of Emerging Extreme Event Tracks in Multivariate Spatio-Temporal Physical Systems Using Dynamic Network Structures: Application to Hurricane Track Prediction. IJCAI 2011: 1478-1484

William Hendrix, Tatiana V. Karpinets, Byung-Hoon Park, Eric R. Schendel, Alok N. Choudhary, Nagiza F. Samatova: Sensitive and Specific Identification of Protein Complexes in "Perturbed" Protein Interaction Networks from Noisy Pull-Down Data. IPDPS Workshops 2011: 512-522

Sriram Lakshminarasimhan, John Jenkins, Isha Arkatkar, Zhenhuan Gong, Hemanth Kolla, Seung-Hoe Ku, Stéphane Ethier, Jackie Chen, Choong-Seock Chang, Scott Klasky, Robert Latham, Robert B. Ross, Nagiza F. Samatova: ISABELA-QA: query-driven analytics with ISABELA-compressed extreme-scale scientific data. SC 2011: 31

Chongle Pan, Byung-Hoon Park, William H. McDonald, Patricia A. Carey, Jillian F. Banfield, Nathan Verberkmoes, Robert L. Hettich, Nagiza F. Samatova: A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry. BMC Bioinformatics 11: 118 (2010)

William Hendrix, Matthew C. Schmidt, Paul Breimyer, Nagiza F. Samatova: Theoretical underpinnings for maximal clique enumeration on perturbed graphs. Theor. Comput. Sci. 411(26-28): 2520-2536 (2010)

William Hendrix, Andrea M. Rocha, Mark T. Elmore, Joe Trien, Nagiza F. Samatova: Discovery of Enriched Biological Motifs Using Knowledge Priors with Application to Biohydrogen Production. BIOCOMP 2010: 17-23

Wenhong Tian, Matthew C. Schmidt, Wenbin Chen, Nagiza F. Samatova: Multiple Alignment of Large Interaction Networks by Fast Identifying Maximal Conserved Patterns. BIOCOMP 2010: 178-184

Zhengzhang Chen, Kevin A. Wilson, Ye Jin, William Hendrix, Nagiza F. Samatova: Detecting and Tracking Community Dynamics in Evolutionary Networks. ICDM Workshops 2010: 318-327

Wenbin Chen, Andrea M. Rocha, William Hendrix, Matthew C. Schmidt, Nagiza F. Samatova: The Multiple Alignment Algorithm for Metabolic Pathways without Abstraction. ICDM Workshops 2010: 669-678

Tatdow Pansombut, Brent E. Harrison, Dennis Bahler, Nagiza F. Samatova: Improving the Performance of Bayesian Belief Network Classifiers via Decision Tree Based Feature Selection. IKE 2010: 49-56

Matthew C. Schmidt, Nagiza F. Samatova, Kevin Thomas, Byung-Hoon Park: A scalable, parallel algorithm for maximal clique enumeration. J. Parallel Distrib. Comput. 69(4): 417-428 (2009)

Wenbin Chen, Matthew C. Schmidt, Nagiza F. Samatova: On parameterized complexity of the Multi-MCS problem. Theor. Comput. Sci. 410(21-23): 2024-2032 (2009)

Matthew C. Schmidt, Nagiza F. Samatova: An Algorithm for the Discovery of Phenotype Related Metabolic Pathways. BIBM 2009: 60-65

Wenbin Chen, Matthew C. Schmidt, Wenhong Tian, Nagiza F. Samatova: A Fast, Accurate Algorithm for Identifying Functional Modules Through Pairwise Local Alignment of Protein Interaction Networks. BIOCOMP 2009: 816-821

Patricia Brent, Nathan David Green, Paul Breimyer, Ramya Krishnamurthy, Nagiza F. Samatova: Systematic Evaluation of Convergence Criteria in Iterative Training for NLP. FLAIRS Conference 2009

Paul Breimyer, Guruprasad Kora, William Hendrix, Neil Shah, Nagiza F. Samatova: PR: Automatic parallelization of data-parallel statistical computing codes for R in hybrid multi-node and multi-core environments. IADIS AC (2) 2009: 28-32

Paul Breimyer, Guruprasad Kora, Nagiza F. Samatova: Web-Enabled R for Large-Scale Collaborative Data Mining: A Survey. IKE 2009: 615-621

Paul Breimyer, William Hendrix, Guruprasad Kora, Nagiza F. Samatova: pR: Lightweight, Easy-to-Use Middleware to Plugin Parallel Analytical Computing with R. IKE 2009: 667-673

Amit C. Awekar, Nagiza F. Samatova, Paul Breimyer: Incremental All Pairs Similarity Search for Varying Similarity Thresholds with Reduced I/O Overhead. IKE 2009: 687-693

Amit C. Awekar, Nagiza F. Samatova, Paul Breimyer: Incremental all pairs similarity search for varying similarity thresholds. SNAKDD 2009: 1

William Hendrix, Matthew C. Schmidt, Paul Breimyer, Nagiza F. Samatova: On perturbation theory and an algorithm for maximal clique enumeration in uncertain and noisy graphs. KDD Workshop on Knowledge Discovery from Uncertain Data 2009: 48-56

Wenhong Tian, Nagiza F. Samatova: Pairwise Alignment of Interaction Networks by Fast Identification of Maximal Conserved Patterns. Pacific Symposium on Biocomputing 2009: 99-110

Amit C. Awekar, Nagiza F. Samatova: Fast Matching for All Pairs Similarity Search. Web Intelligence 2009: 295-300

Bing Zhang, Byung-Hoon Park, Tatiana V. Karpinets, Nagiza F. Samatova: From pull-down data to protein interaction networks and complexes with biological relevance. Bioinformatics 24(7): 979-986 (2008)

Byung-Hoon Park, Nagiza F. Samatova, Rajesh Munavalli, Ramya Krishnamurthy, Houssain Kettani, Al Geist: Rapid and robust ranking of text documents in a dynamically changing corpus. AICCSA 2008: 149-155

Byung-Hoon Park, Matthew C. Schmidt, Kevin Thomas, Tatiana V. Karpinets, Nagiza F. Samatova: Parallel, scalable, memory-efficient backtracking for combinatoria modeling of large-scale biological systems. IPDPS 2008: 1-8

Heshan Lin, Xiaosong Ma, Jiangtian Li, Ting Yu, Nagiza F. Samatova: Adaptive Request Scheduling for Parallel Scientific Web Services. SSDBM 2008: 276-294

Byung-Hoon Park, George Ostrouchov, Nagiza F. Samatova: Sampling streaming data with replacement. Computational Statistics & Data Analysis 52(2): 750-762 (2007)

Robert Sisneros, Chad Jones, Jian Huang, Jinzhu Gao, Byung-Hoon Park, Nagiza F. Samatova: A Multi-Level Cache Model for Run-Time Optimization of Remote Visualization. IEEE Trans. Vis. Comput. Graph. 13(5): 991-1003 (2007)

Faisal N. Abu-Khzam, Nagiza F. Samatova, Mohamad A. Rizk, Michael A. Langston: The Maximum Common Subgraph Problem: Faster Solutions via Vertex Cover. AICCSA 2007: 367-373

Byung-Hoon Park, Bing Zhang, Tatiana V. Karpinets, Nagiza F. Samatova: Multi-stage Framework to Infer Protein Functional Modules from Mass Spectrometry Pull-Down Data with Assessment of Biological Relevance. BIBM 2007: 223-229

Xiaosong Ma, Jiangtian Li, Nagiza F. Samatova: Automatic Parallelization of Scripting Languages: Toward Transparent Desktop Parallel Computing. IPDPS 2007: 1-6

Faisal N. Abu-Khzam, Mohamad A. Rizk, Deema A. Abdallah, Nagiza F. Samatova: The Buffered Work-Pool Approach for Search-Tree Based Optimization Algorithms. PPAM 2007: 170-179

James M. McCollum, Gregory D. Peterson, Chris D. Cox, Michael L. Simpson, Nagiza F. Samatova: The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior. Computational Biology and Chemistry 30(1): 39-49 (2006)

Christopher T. Symons, Nagiza F. Samatova, Ramya Krishnamurthy, Byung-Hoon Park, Tarik Umar, David Buttler, Terence Critchlow, David Hysom: Multi-Criterion Active Learning in Conditional Random Fields. ICTAI 2006: 323-331

George Ostrouchov, Nagiza F. Samatova: On FastMap and the Convex Hull of Multivariate Data: Toward Fast and Robust Dimension Reduction. IEEE Trans. Pattern Anal. Mach. Intell. 27(8): 1340-1343 (2005)

Srikanth B. Yoginath, Nagiza F. Samatova, David Bauer, Guruprasad Kora, George Fann, Al Geist: RScaLAPACK: High-Performance Parallel Statistical Computing with R and ScaLAPACK. ISCA PDCS 2005: 61-67

W. Henry Suters, Faisal N. Abu-Khzam, Yun Zhang, Christopher T. Symons, Nagiza F. Samatova, Michael A. Langston: A New Approach and Faster Exact Methods for the Maximum Common Subgraph Problem. COCOON 2005: 717-727

Brandon Thurmon, James M. McCollum, Gregory D. Peterson, Chris D. Cox, Nagiza F. Samatova, Gary Sayler, Michael L. Simpson: Accelerating Exact Stochastic Simulation Using Reconfigurable Computing. ERSA 2005: 105-111

Heshan Lin, Xiaosong Ma, Praveen Chandramohan, Al Geist, Nagiza F. Samatova: Efficient Data Access for Parallel BLAST. IPDPS 2005

Yun Zhang, Faisal N. Abu-Khzam, Nicole E. Baldwin, Elissa J. Chesler, Michael A. Langston, Nagiza F. Samatova: Genome-Scale Computational Approaches to Memory-Intensive Applications in Systems Biology. SC 2005: 12

Gong-Xin Yu, Byung-Hoon Park, Praveen Chandramohan, Al Geist, Nagiza F. Samatova: In-Silico Prediction of Surface Residue Clusters for Enzyme-Substrate Specificity. CSB 2004: 696-697

Byung-Hoon Park, George Ostrouchov, Nagiza F. Samatova, Al Geist: Reservoir-Based Random Sampling with Replacement from Data Stream. SDM 2004

Gong-Xin Yu, George Ostrouchov, Al Geist, Nagiza F. Samatova: An SVM-based Algorithm for Identification of Photosynthesis-specific Genome Features. CSB 2003: 235-243

Byung-Hoon Park, George Ostrouchov, Gong-Xin Yu, Al Geist, Andrey Gorin, Nagiza F. Samatova: Inference of Protein-Protein Interactions by Unlikely Profile Pair. ICDM 2003: 735-738

E. Wes Bethel, Greg Abram, John Shalf, Randy Frank, James P. Ahrens, Steve Parker, Nagiza F. Samatova, Mark Miller: Interoperability of Visualization Software and Data Models is NOT an Achievable Goal. IEEE Visualization 2003: 607-610

Nagiza F. Samatova, George Ostrouchov, Al Geist, Anatoli V. Melechko: RACHET: An Efficient Cover-Based Merging of Clustering Hierarchies from Distributed Datasets. Distributed and Parallel Databases 11(2): 157-180 (2002)

Thomas E. Potok, Mark T. Elmore, Joel W. Reed, Nagiza F. Samatova: An Ontology-Based HTML to XML Conversion Using Intelligent Agents. HICSS 2002: 120

Nagiza F. Samatova, Al Geist, George Ostrouchov, Anatoli V. Melechko: Parallel Out-of-Core Algorithm for Genome-Scale Enumeration of Metabolic Systemic Pathways. IPDPS 2002

Faisal N. Abu-Khzam, Nagiza F. Samatova, George Ostrouchov, Michael A. Langston, Al Geist: Distributed Dimension Reduction Algorithms for Widely Dispersed Data. IASTED PDCS 2002: 167-174

Thomas E. Potok, Nenad Ivezic, Nagiza F. Samatova: Agent-based Architecture for Flexible Lean Cell Design, Analysis and Evaluation. DIISM 2000: 181-188