2024
No Free Lunch: Fundamental Limits of Learning Non-Hallucinating Generative Models.
CoRR, 2024
Deconvolving Complex Neuronal Networks into Interpretable Task-Specific Connectomes.
CoRR, 2024
Cascade Reward Sampling for Efficient Decoding-Time Alignment.
CoRR, 2024
Integrating ML/AI workflows in a Streaming Data Management and Processing Platform for Building Energy Research.
Proceedings of the Practice and Experience in Advanced Research Computing 2024: Human Powered Computing, 2024
Information-theoretic Limits of Online Classification with Noisy Labels.
Proceedings of the Advances in Neural Information Processing Systems 38: Annual Conference on Neural Information Processing Systems 2024, 2024
A Theory of Fault-Tolerant Learning.
Proceedings of the Forty-first International Conference on Machine Learning, 2024
Generalized Learning of Coefficients in Spectral Graph Convolutional Networks.
Proceedings of the IEEE International Conference on Knowledge Graph, 2024
2023
Regret Bounds for Log-Loss via Bayesian Algorithms.
IEEE Trans. Inf. Theory, September, 2023
Aligning Spatially Constrained Graphs.
IEEE Trans. Knowl. Data Eng., August, 2023
Expected Worst Case Regret via Stochastic Sequential Covering.
Trans. Mach. Learn. Res., 2023
Robust Online Classification: From Estimation to Denoising.
CoRR, 2023
Learning Functional Distributions with Private Labels.
Proceedings of the International Conference on Machine Learning, 2023
Online Learning in Dynamically Changing Environments.
Proceedings of the Thirty Sixth Annual Conference on Learning Theory, 2023
2022
CKH: Causal Knowledge Hierarchy for Estimating Structural Causal Models from Data and Priors.
CoRR, 2022
Precise Regret Bounds for Log-loss via a Truncated Bayesian Algorithm.
Proceedings of the Advances in Neural Information Processing Systems 35: Annual Conference on Neural Information Processing Systems 2022, 2022
Sequential vs. Fixed Design Regrets in Online Learning.
Proceedings of the IEEE International Symposium on Information Theory, 2022
Toward Physically Realizable Quantum Neural Networks.
Proceedings of the Thirty-Sixth AAAI Conference on Artificial Intelligence, 2022
2021
Adaptive Erasure Coded Fault Tolerant Linear System Solver.
ACM Trans. Parallel Comput., 2021
Scalable Algorithms for Multiple Network Alignment.
SIAM J. Sci. Comput., 2021
De-anonymization Attacks on Neuroimaging Datasets.
Proceedings of the SIGMOD '21: International Conference on Management of Data, 2021
Identifying Coherent Subgraphs In Dynamic Brain Networks.
Proceedings of the 2021 IEEE International Conference on Image Processing, 2021
2020
Randomized Linear Algebra Approaches to Estimate the von Neumann Entropy of Density Matrices.
IEEE Trans. Inf. Theory, 2020
Optimistic scheduling with service guarantees.
J. Parallel Distributed Comput., 2020
Integrated querying and version control of context-specific biological networks.
Database J. Biol. Databases Curation, 2020
Newton-ADMM: a distributed GPU-accelerated optimizer for multiclass classification problems.
Proceedings of the International Conference for High Performance Computing, 2020
Characterizing Similarity of Visual Stimulus from Associated Neuronal Response.
Proceedings of the Twenty-Ninth International Joint Conference on Artificial Intelligence, 2020
A Unified Cloud-Native Architecture For Heterogeneous Data Aggregation And Computation.
Proceedings of the BCB '20: 11th ACM International Conference on Bioinformatics, 2020
Collaborative Cloud Computing Framework for Health Data with Open Source Technologies.
Proceedings of the BCB '20: 11th ACM International Conference on Bioinformatics, 2020
2019
AIKYATAN: mapping distal regulatory elements using convolutional learning on GPU.
BMC Bioinform., 2019
MG-RAST version 4 - lessons learned from a decade of low-budget ultra-high-throughput metagenome analysis.
Briefings Bioinform., 2019
Federation in genomics pipelines: techniques and challenges.
Briefings Bioinform., 2019
GPU Accelerated Sub-Sampled Newton's Method for Convex Classification Problems.
Proceedings of the 2019 SIAM International Conference on Data Mining, 2019
Proceedings of the Complex Networks and Their Applications VIII, 2019
2018
A Distributed Classifier for MicroRNA Target Prediction with Validation Through TCGA Expression Data.
IEEE ACM Trans. Comput. Biol. Bioinform., 2018
Indexed Fast Network Proximity Querying.
Proc. VLDB Endow., 2018
VAYU: Accelerating stream processing applications through dynamic network-aware topology re-optimization.
J. Parallel Distributed Comput., 2018
Low rank methods for multiple network alignment.
CoRR, 2018
Distributed Second-order Convex Optimization.
CoRR, 2018
Constructing Compact Brain Connectomes for Individual Fingerprinting.
CoRR, 2018
GPU Accelerated Sub-Sampled Newton\textsf{'}s Method.
CoRR, 2018
Frontiers of Science of Information: Shannon Meets Turing.
Computer, 2018
Low Rank Spectral Network Alignment.
Proceedings of the 2018 World Wide Web Conference on World Wide Web, 2018
TIMES: Temporal Information Maximally Extracted from Structures.
Proceedings of the 2018 World Wide Web Conference on World Wide Web, 2018
MODE: automated neural network model debugging via state differential analysis and input selection.
Proceedings of the 2018 ACM Joint Meeting on European Software Engineering Conference and Symposium on the Foundations of Software Engineering, 2018
Randomized Linear Algebra Approaches to Estimate the Von Neumann Entropy of Density Matrices.
Proceedings of the 2018 IEEE International Symposium on Information Theory, 2018
UBIS: Utilization-Aware Cluster Scheduling.
Proceedings of the 2018 IEEE International Parallel and Distributed Processing Symposium, 2018
2017
Reactive Molecular Dynamics on Massively Parallel Heterogeneous Architectures.
IEEE Trans. Parallel Distributed Syst., 2017
Pluribus - Exploring the Limits of Error Correction Using a Suffix Tree.
IEEE ACM Trans. Comput. Biol. Bioinform., 2017
Triangular Alignment (TAME): A Tensor-Based Approach for Higher-Order Network Alignment.
IEEE ACM Trans. Comput. Biol. Bioinform., 2017
Erasure Coding for Fault-Oblivious Linear System Solvers.
SIAM J. Sci. Comput., 2017
A Critical Survey of Deconvolution Methods for Separating Cell Types in Complex Tissues.
Proc. IEEE, 2017
Principles and Applications of Science of Information.
Proc. IEEE, 2017
Rafiki: a middleware for parameter tuning of NoSQL datastores for dynamic metagenomics workloads.
Proceedings of the 18th ACM/IFIP/USENIX Middleware Conference, Las Vegas, NV, USA, December 11, 2017
Recovery of vertex orderings in dynamic graphs.
Proceedings of the 2017 IEEE International Symposium on Information Theory, 2017
Introduction to HiCOMB Workshop.
Proceedings of the 2017 IEEE International Parallel and Distributed Processing Symposium Workshops, 2017
Distributed Fault Tolerant Linear System Solvers Based on Erasure Coding.
Proceedings of the 37th IEEE International Conference on Distributed Computing Systems, 2017
Suitability of NoSQL systems - Cassandra and ScyllaDB - For IoT workloads.
Proceedings of the 9th International Conference on Communication Systems and Networks, 2017
2016
Fundamental Bounds for Sequence Reconstruction From Nanopore Sequencers.
IEEE Trans. Mol. Biol. Multi Scale Commun., 2016
Social ties and checkin sites: connections and latent structures in location-based social networks.
Soc. Netw. Anal. Min., 2016
The MG-RAST metagenomics database and portal in 2015.
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Nucleic Acids Res., 2016
Combining Density and Overlap (CoDO): A New Method for Assessing the Significance of Overlap Among Subgraphs.
CoRR, 2016
Fundamental Bounds and Approaches to Sequence Reconstruction from Nanopore Sequencers.
CoRR, 2016
Opening up the blackbox: an interpretable deep neural network-based classifier for cell-type specific enhancer predictions.
BMC Syst. Biol., 2016
A convex optimization approach for identification of human tissue-specific interactomes.
Bioinform., 2016
Efficient Processing of Network Proximity Queries via Chebyshev Acceleration.
Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 2016
Context-Specific Recommendation System for Predicting Similar PubMed Articles.
Proceedings of the IEEE International Conference on Data Mining Workshops, 2016
Fast training on large genomics data using distributed Support Vector Machines.
Proceedings of the 8th International Conference on Communication Systems and Networks, 2016
Closing the Data Loop: An Integrated Open Access Analysis Platform for the MIMIC Database.
Proceedings of the Computing in Cardiology, CinC 2016, Vancouver, 2016
De novo identification of cell type hierarchy with application to compound marker detection.
Proceedings of the 7th ACM International Conference on Bioinformatics, 2016
2015
Scope and limitations of yeast as a model organism for studying human tissue-specific pathways.
BMC Syst. Biol., 2015
Interpretable deep neural networks for enhancer prediction.
Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015
An ensemble SVM model for the accurate prediction of non-canonical MicroRNA targets.
Proceedings of the 6th ACM Conference on Bioinformatics, 2015
2014
Surfing the Network for Ranking by Multidamping.
IEEE Trans. Knowl. Data Eng., 2014
Multiple network alignment on quantum computers.
Quantum Inf. Process., 2014
A universal quantum circuit scheme for finding complex eigenvalues.
Quantum Inf. Process., 2014
Parallel matrix algorithms.
Parallel Comput., 2014
Fast parallel algorithms for graph similarity and matching.
J. Parallel Distributed Comput., 2014
Trends in big data analytics.
J. Parallel Distributed Comput., 2014
PuReMD-GPU: A reactive molecular dynamics simulation package for GPUs.
J. Comput. Phys., 2014
Quantum Random State Generation with Predefined Entanglement Constraint.
CoRR, 2014
2013
Concurrent programming constructs for parallel MPI applications - The MPI threads library.
J. Supercomput., 2013
A Universal Quantum Circuit Scheme For Finding Complex Eigenvalues of Non-unitary Matrices
CoRR, 2013
Inferring the effective TOR-dependent network: a computational study in yeast.
BMC Syst. Biol., 2013
Using hierarchical data mining to characterize performance of wireless system configurations.
Adv. Eng. Softw., 2013
Suffix-Tree Based Error Correction of NGS Reads Using Multiple Manifestations of an Error.
Proceedings of the ACM Conference on Bioinformatics, 2013
M-Lock: Accelerating Distributed Transactions on Key-Value Stores through Dynamic Lock Localization.
Proceedings of the 2013 IEEE Sixth International Conference on Cloud Computing, Santa Clara, CA, USA, June 28, 2013
2012
Network Similarity Decomposition (NSD): A Fast and Scalable Approach to Network Alignment.
IEEE Trans. Knowl. Data Eng., 2012
Reactive Molecular Dynamics: Numerical Methods and Algorithmic Techniques.
SIAM J. Sci. Comput., 2012
Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques.
Parallel Comput., 2012
Universal Programmable Quantum Circuit Schemes to Emulate an Operator
CoRR, 2012
Role of Synthetic Genetic Interactions in Understanding Functional Interactions Among Pathways.
Proceedings of the Biocomputing 2012: Proceedings of the Pacific Symposium, 2012
Parallel Numerical Computing from Illiac IV to Exascale - The Contributions of Ahmed H. Sameh.
Proceedings of the High-Performance Scientific Computing - Algorithms and Applications., 2012
2011
Asynchronous Iterative Algorithms.
Proceedings of the Encyclopedia of Parallel Computing, 2011
<i>N</i>-Body Computational Methods.
Proceedings of the Encyclopedia of Parallel Computing, 2011
Performance models for the Spike banded linear system solver.
Sci. Program., 2011
TransMR: Data-Centric Programming Beyond Data Parallelism.
Proceedings of the 3rd USENIX Workshop on Hot Topics in Cloud Computing, 2011
2010
Weighted Matrix Ordering and Parallel Banded Preconditioners for Iterative Linear System Solvers.
SIAM J. Sci. Comput., 2010
Special issue on Parallel Matrix Algorithms and Applications.
Parallel Comput., 2010
Functional characterization and topological modularity of molecular interaction networks.
BMC Bioinform., 2010
Asynchronous Algorithms in MapReduce.
Proceedings of the 2010 IEEE International Conference on Cluster Computing, 2010
2009
Load Balancing for Parallel Optimization Techniques.
Proceedings of the Encyclopedia of Optimization, Second Edition, 2009
Efficient tag detection in RFID systems.
J. Parallel Distributed Comput., 2009
2008
Semantic indexing in structured peer-to-peer networks.
J. Parallel Distributed Comput., 2008
Protocol Inference Using Static Path Profiles.
Proceedings of the Static Analysis, 15th International Symposium, 2008
PHALANX: a graph-theoretic framework for test case prioritization.
Proceedings of the 2008 ACM Symposium on Applied Computing (SAC), 2008
Annotating Pathways of Interaction Networks.
Proceedings of the Biocomputing 2008, 2008
Scalable Data Collection in Sensor Networks.
Proceedings of the High Performance Computing, 2008
Functional coherence in domain interaction networks.
Proceedings of the ECCB'08 Proceedings, 2008
2007
Scalability of Parallel Programs.
Proceedings of the Handbook of Parallel Computing - Models, Algorithms and Applications., 2007
Randomized Protocols for Duplicate Elimination in Peer-to-Peer Storage Systems.
IEEE Trans. Parallel Distributed Syst., 2007
Assessing Significance of Connectivity and Conservation in Protein Interaction Networks.
J. Comput. Biol., 2007
Identifying Statistical Dependence in Genomic Sequences via Mutual Information Estimates.
EURASIP J. Bioinform. Syst. Biol., 2007
Randomized leader election.
Distributed Comput., 2007
Static specification inference using predicate mining.
Proceedings of the ACM SIGPLAN 2007 Conference on Programming Language Design and Implementation, 2007
Functional annotation of regulatory pathways.
Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007
Statistical Dependence in Biological Sequences.
Proceedings of the IEEE International Symposium on Information Theory, 2007
Path-Sensitive Inference of Function Precedence Protocols.
Proceedings of the 29th International Conference on Software Engineering (ICSE 2007), 2007
Building Verifiable Sensing Applications Through Temporal Logic Specification.
Proceedings of the Computational Science, 2007
Macroprogramming heterogeneous sensor networks using cosmos.
Proceedings of the 2007 EuroSys Conference, Lisbon, Portugal, March 21-23, 2007, 2007
2006
Redundancy and coverage detection in sensor networks.
ACM Trans. Sens. Networks, 2006
Nonorthogonal decomposition of binary matrices for bounded-error data compression and analysis.
ACM Trans. Math. Softw., 2006
Unstructured peer-to-peer networks for sharing processor cycles.
Parallel Comput., 2006
Locality in structured peer-to-peer networks.
J. Parallel Distributed Comput., 2006
Pairwise Alignment of Protein Interaction Networks.
J. Comput. Biol., 2006
Detecting Conserved Interaction Patterns in Biological Networks.
J. Comput. Biol., 2006
Inferring functional information from domain co-evolution.
Bioinform., 2006
CONQUEST: A Coarse-Grained Algorithm for Constructing Summaries of Distributed Discrete Datasets.
Algorithmica, 2006
Sieve: A Tool for Automatically Detecting Variations Across Program Versions.
Proceedings of the 21st IEEE/ACM International Conference on Automated Software Engineering (ASE 2006), 2006
The Omni Macroprogramming Environment for Sensor Networks.
Proceedings of the Computational Science, 2006
Distributed Uniform Sampling in Unstructured Peer-to-Peer Networks.
Proceedings of the 39th Hawaii International International Conference on Systems Science (HICSS-39 2006), 2006
Trace-Based Memory Aliasing Across Program Versions.
Proceedings of the Fundamental Approaches to Software Engineering, 2006
2005
Compression, Clustering, and Pattern Discovery in Very High-Dimensional Discrete-Attribute Data Sets.
IEEE Trans. Knowl. Data Eng., 2005
Adaptive data structures for IP lookups.
ACM J. Exp. Algorithmics, 2005
Level compressed DAGs for lookup tables.
Comput. Networks, 2005
Redundant reader elimination in RFID systems.
Proceedings of the Second Annual IEEE Communications Society Conference on Sensor and Ad Hoc Communications and Networks, 2005
Pairwise Local Alignment of Protein Interaction Networks Guided by Models of Evolution.
Proceedings of the Research in Computational Molecular Biology, 2005
Search with Probabilistic Guarantees in Unstructured Peer-to-Peer Networks.
Proceedings of the Fifth IEEE International Conference on Peer-to-Peer Computing (P2P 2005), 31 August, 2005
High-Fidelity Simulation of Large-Scale Structures.
Proceedings of the Computational Science, 2005
2004
Coverage preserving redundancy elimination in sensor networks.
Proceedings of the First Annual IEEE Communications Society Conference on Sensor and Ad Hoc Communications and Networks, 2004
Conquest: A Distributed Tool for Constructing Summaries of High-Dimensional Discrete Attribute Data Sets.
Proceedings of the Fourth SIAM International Conference on Data Mining, 2004
An efficient algorithm for detecting frequent subgraphs in biological networks.
Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004
A public key algorithm for ad-hoc networks.
Proceedings of the 23rd IEEE International Performance Computing and Communications Conference, 2004
Impact of far-field interactions on performance of multipole-based preconditioners for sparse linear systems.
Proceedings of the 18th Annual International Conference on Supercomputing, 2004
Enhancing Locality in Structured Peer-to-Peer Networks.
Proceedings of the 10th International Conference on Parallel and Distributed Systems, 2004
Distributed and Dynamic Voronoi Overlays for Coverage Detection and Distributed Hash Tables in Ad-Hoc Networks.
Proceedings of the 10th International Conference on Parallel and Distributed Systems, 2004
A Secure Crediting Protocol for Hybrid Cellular and Ad-Hoc Networks.
Proceedings of the ICETE 2004, 2004
Extended Consistent Hashing: An Efficient Framework for Object Location.
Proceedings of the 24th International Conference on Distributed Computing Systems (ICDCS 2004), 2004
Model Reduction of Large-Scale Dynamical Systems.
Proceedings of the Computational Science, 2004
Parallel Performance of Hierarchical Multipole Algorithms for Inductance Extraction.
Proceedings of the High Performance Computing, 2004
Plethora: An EfficientWide-Area Storage System.
Proceedings of the High Performance Computing, 2004
Biclustering Gene-Feature Matrices for Statistically Significant Dense Patterns.
Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004
2003
Multipole-based preconditioners for large sparse linear systems.
Parallel Comput., 2003
PROXIMUS: a framework for analyzing very high dimensional discrete-attributed datasets.
Proceedings of the Ninth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, Washington, DC, USA, August 24, 2003
Spectral LPM: An Optimal Locality-Preserving Mapping using the Spectral (not Fractal) Order.
Proceedings of the 19th International Conference on Data Engineering, 2003
An Efficient Protocol for Yao?s Millionaires? Problem.
Proceedings of the 36th Hawaii International Conference on System Sciences (HICSS-36 2003), 2003
An IP address based caching scheme for peer-to-peer networks.
Proceedings of the Global Telecommunications Conference, 2003
Algorithms for Bounded-Error Correlation of High Dimensional Data in Microarray Experiments.
Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003
2002
2D-pattern matching image and video compression: theory, algorithms, and experiments.
IEEE Trans. Image Process., 2002
Algebraic Techniques for Analysis of Large Discrete-Valued Datasets.
Proceedings of the Principles of Data Mining and Knowledge Discovery, 2002
A Secure Protocol for Computing Dot-Products in Clustered and Distributed Environments.
Proceedings of the 31st International Conference on Parallel Processing (ICPP 2002), 2002
MOBY - A Mobile Peer-to-Peer Service and Data Network.
Proceedings of the 31st International Conference on Parallel Processing (ICPP 2002), 2002
Oceanus: A Distributed Web-Based Framework for Execution of Genetic Algorithms.
Proceedings of the Late Breaking papers at the Genetic and Evolutionary Computation Conference (GECCO-2002), 2002
Semi-discrete Matrix Transforms (SDD) for Image and Video Compression.
Proceedings of the 2002 Data Compression Conference (DCC 2002), 2002
2001
Compression of particle data from hierarchical approximate methods.
ACM Trans. Math. Softw., 2001
Privacy Risks in Recommender Systems.
IEEE Internet Comput., 2001
When being Weak is Brave: Privacy in Recommender Systems
CoRR, 2001
Architecture Independent Analysis of Parallel Programs.
Proceedings of the Computational Science - ICCS 2001, 2001
Real-Time Decompression of Streaming Video Using Mobile Code.
Proceedings of the Data Compression Conference, 2001
2000
Improving Error Bounds for Multipole-Based Treecodes.
SIAM J. Sci. Comput., 2000
Summary Structures for Frequency Queries on Large Transaction Sets.
Proceedings of the Data Compression Conference, 2000
1999
State of the Art in Parallel Search Techniques for Discrete Optimization Problems.
IEEE Trans. Knowl. Data Eng., 1999
Data Mining: From Serendipity to Science - Guest Editors' Introduction.
Computer, 1999
Bounded-Error Compression of Particle Data from Hierarchical Approximate Methods.
Proceedings of the ACM/IEEE Conference on Supercomputing, 1999
2D-Pattern Matching Image and Video Compression.
Proceedings of the Data Compression Conference, 1999
1998
Parallel Hierarchical Solvers and Preconditioners for Boundary Element Methods.
SIAM J. Sci. Comput., 1998
Scalable Parallel Formulations of the Barnes-Hut Method for <i>n</i>-Body Simulations.
Parallel Comput., 1998
Analyzing the Error Bounds of Multipole-Based Treecodes.
Proceedings of the ACM/IEEE Conference on Supercomputing, 1998
1997
Role of Message-Passing in Performance Oriented Parallel Programming.
Proceedings of the Eighth SIAM Conference on Parallel Processing for Scientific Computing, 1997
1995
Parallel Search Algorithms for Discrete Optimization Problems.
INFORMS J. Comput., 1995
Parallel Matrix-Vector Product Using Approximate Hierarchical Methods.
Proceedings of the Proceedings Supercomputing '95, San Diego, CA, USA, December 4-8, 1995, 1995
Fast volume rendering using an efficient, scalable parallel formulation of the shear-warp algorithm.
Proceedings of the IEEE Symposium on Parallel Rendering, 1995
N-Body Simulations Using Message Passsing Parallel Computers.
Proceedings of the Seventh SIAM Conference on Parallel Processing for Scientific Computing, 1995
1994
Scalable Load Balancing Techniques for Parallel Computers.
J. Parallel Distributed Comput., 1994
Introduction to Parallel Computing.
Benjamin/Cummings, ISBN: 0-8053-3170-0, 1994
1993
Isoefficiency: measuring the scalability of parallel algorithms and architectures.
IEEE Parallel Distributed Technol. Syst. Appl., 1993
1992
Scalability Analysis of Partitioning Strategies for Finite Element Graphs: A Summary of Results.
Proceedings of the Proceedings Supercomputing '92, 1992