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Multi-scale models of whole cells: progress and challenges

Frontiers in cell and developmental biology, 2023-11, Vol.11, p.1260507-1260507

2023

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Scalable Topological Data Analysis and Visualization for Evaluating Data-Driven Models in Scientific Applications

IEEE transactions on visualization and computer graphics, 2020-01, Vol.26 (1), p.291-300

2020

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Programming Multiprocessors with Explicitly Managed Memory Hierarchies

Computer (Long Beach, Calif.), 2009-12, Vol.42 (12), p.28-34

2009

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Enabling machine learning-ready HPC ensembles with Merlin

Future generation computer systems, 2022-06, Vol.131, p.255-268

2022

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TRAM: Optimizing Fine-Grained Communication with Topological Routing and Aggregation of Messages

2014 43rd International Conference on Parallel Processing, 2014, p.211-220

2014

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Parallelizing Training of Deep Generative Models on Massive Scientific Datasets

2019 IEEE International Conference on Cluster Computing (CLUSTER), 2019, p.1-10

2019

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Massively Parallel Simulations of Spread of Infectious Diseases over Realistic Social Networks

2017 17th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGRID), 2017, p.689-694

2017

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Security in All-Optical Networks: Self-Organization and Attack Avoidance

2007 IEEE International Conference on Communications, 2007, p.1329-1335

2007

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LibPowerMon: A Lightweight Profiling Framework to Profile Program Context and System-Level Metrics

2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), 2016, p.1132-1141

2016

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Exploratory Modeling and Simulation of the Evolutionary Dynamics of Single-Stranded RNA Virus Populations

2017 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), 2017, p.263-272

2017

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Predicting Cross-Architecture Performance of Parallel Programs

2024 IEEE International Parallel and Distributed Processing Symposium (IPDPS), 2024, p.570-581

2024

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Fluxion: A Scalable Graph-Based Resource Model for HPC Scheduling Challenges

Proceedings of the SC '23 Workshops of The International Conference on High Performance Computing, Network, Storage, and Analysis, 2023, p.2077-2088

2023

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Overcoming the Scalability Challenges of Epidemic Simulations on Blue Waters

2014 IEEE 28th International Parallel and Distributed Processing Symposium, 2014, p.755-764

2014

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Parallel Programming Models for Heterogeneous Multicore Architectures

IEEE MICRO, 2010-09, Vol.30 (5), p.42-53

2010

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Towards dynamic simulation of a whole cell model

Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, 2021, p.1-10

2021

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Charm++ and MPI: Combining the Best of Both Worlds

2015 IEEE International Parallel and Distributed Processing Symposium, 2015, p.655-664

2015

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Ubique: A New Model for Untangling Inter-task Data Dependence in Complex HPC Workflows

2022 IEEE 18th International Conference on e-Science (e-Science), 2022, p.421-422

2022

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Performance modeling under resource constraints using deep transfer learning

Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, 2017, p.1-12

2017

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One Step Closer to Converged Computing: Achieving Scalability with Cloud-Native HPC

2022 IEEE/ACM 4th International Workshop on Containers and New Orchestration Paradigms for Isolated Environments in HPC (CANOPIE-HPC), 2022, p.57-70

2022

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Strider: Runtime Support for Optimizing Strided Data Accesses on Multi-Cores with Explicitly Managed Memories

2010 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis, 2010, p.1-11

2010

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PADDLE: Performance Analysis Using a Data-Driven Learning Environment

2018 IEEE International Parallel and Distributed Processing Symposium (IPDPS), 2018, p.784-793

2018

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High-Performance Interaction-Based Simulation of Gut Immunopathologies with ENteric Immunity Simulator (ENISI)

2012 IEEE 26th International Parallel and Distributed Processing Symposium, 2012, p.48-59

2012

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Data-Driven Performance Modeling of Linear Solvers for Sparse Matrices

2016 7th International Workshop on Performance Modeling, Benchmarking and Simulation of High Performance Computer Systems (PMBS), 2016, p.32-42

2016

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Scalable Topological Data Analysis and Visualization for Evaluating Data-Driven Models in Scientific Applications

IEEE transactions on visualization and computer graphics, 2019-08, Vol.26 (1)

2019

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Programming multiprocessors with explicitly managed memory hierarchies

Computer (Long Beach, Calif.), 2011

2011

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Multi-scale models of whole cells: progress and challenges

Scalable Topological Data Analysis and Visualization for Evaluating Data-Driven Models in Scientific Applications

Programming Multiprocessors with Explicitly Managed Memory Hierarchies

Enabling machine learning-ready HPC ensembles with Merlin

TRAM: Optimizing Fine-Grained Communication with Topological Routing and Aggregation of Messages

Parallelizing Training of Deep Generative Models on Massive Scientific Datasets

Massively Parallel Simulations of Spread of Infectious Diseases over Realistic Social Networks

Security in All-Optical Networks: Self-Organization and Attack Avoidance

LibPowerMon: A Lightweight Profiling Framework to Profile Program Context and System-Level Metrics

Exploratory Modeling and Simulation of the Evolutionary Dynamics of Single-Stranded RNA Virus Populations

Predicting Cross-Architecture Performance of Parallel Programs

Fluxion: A Scalable Graph-Based Resource Model for HPC Scheduling Challenges

Overcoming the Scalability Challenges of Epidemic Simulations on Blue Waters

Parallel Programming Models for Heterogeneous Multicore Architectures

Towards dynamic simulation of a whole cell model

Charm++ and MPI: Combining the Best of Both Worlds

Ubique: A New Model for Untangling Inter-task Data Dependence in Complex HPC Workflows

Performance modeling under resource constraints using deep transfer learning

One Step Closer to Converged Computing: Achieving Scalability with Cloud-Native HPC

Strider: Runtime Support for Optimizing Strided Data Accesses on Multi-Cores with Explicitly Managed Memories

PADDLE: Performance Analysis Using a Data-Driven Learning Environment

High-Performance Interaction-Based Simulation of Gut Immunopathologies with ENteric Immunity Simulator (ENISI)

Data-Driven Performance Modeling of Linear Solvers for Sparse Matrices

Scalable Topological Data Analysis and Visualization for Evaluating Data-Driven Models in Scientific Applications

Programming multiprocessors with explicitly managed memory hierarchies

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