Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication-transcription machinery in action.

[BibT_eX]

[DOI]

Int. J. High Perform. Comput. Appl., 2022

Deep Surrogate Docking: Accelerating Automated Drug Discovery with Graph Neural Networks.

[BibT_eX]

[DOI]

CoRR, 2022

Coupling streaming AI and HPC ensembles to achieve 100-1000× faster biomolecular simulations.

[BibT_eX]

[DOI]

Proceedings of the 2022 IEEE International Parallel and Distributed Processing Symposium, 2022

Shaping Noise for Robust Attributions in Neural Stochastic Differential Equations.

[BibT_eX]

[DOI]

Proceedings of the Thirty-Sixth AAAI Conference on Artificial Intelligence, 2022

2021

Uncertainty-Informed Deep Transfer Learning of Perfluoroalkyl and Polyfluoroalkyl Substance Toxicity.

[BibT_eX]

[DOI]

Álvaro Vázquez-Mayagoitia

J. Chem. Inf. Model., 2021

Dynamic Profiling of β-Coronavirus 3CL Mpro Protease Ligand-Binding Sites.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2021

AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics.

[BibT_eX]

[DOI]

Int. J. High Perform. Comput. Appl., 2021

Protein Folding Neural Networks Are Not Robust.

[BibT_eX]

[DOI]

CoRR, 2021

CrossedWires: A Dataset of Syntactically Equivalent but Semantically Disparate Deep Learning Models.

[BibT_eX]

[DOI]

CoRR, 2021

Protein-Ligand Docking Surrogate Models: A SARS-CoV-2 Benchmark for Deep Learning Accelerated Virtual Screening.

[BibT_eX]

[DOI]

CoRR, 2021

Achieving 100X faster simulations of complex biological phenomena by coupling ML to HPC ensembles.

[BibT_eX]

[DOI]

CoRR, 2021

Scaffold Embeddings: Learning the Structure Spanned by Chemical Fragments, Scaffolds and Compounds.

[BibT_eX]

[DOI]

Austin Clyde

Arvind Ramanathan

Rick Stevens

CoRR, 2021

Pandemic Drugs at Pandemic Speed: Accelerating COVID-19 Drug Discovery with Hybrid Machine Learning- and Physics-based Simulations on High Performance Computers.

[BibT_eX]

[DOI]

CoRR, 2021

Adversarial Attacks against AI-driven Experimental Peptide Design Workflows.

[BibT_eX]

[DOI]

Arvind Ramanathan

Sumit Kumar Jha

Proceedings of the 3rd Annual Workshop on Extreme-scale Experiment-in-the-Loop Computing, 2021

Scalable HPC & AI infrastructure for COVID-19 therapeutics.

[BibT_eX]

[DOI]

Proceedings of the PASC '21: Platform for Advanced Scientific Computing Conference, 2021

Stream-AI-MD: streaming AI-driven adaptive molecular simulations for heterogeneous computing platforms.

[BibT_eX]

[DOI]

Proceedings of the PASC '21: Platform for Advanced Scientific Computing Conference, 2021

Prototypical Models for Classifying High-Risk Atypical Breast Lesions.

[BibT_eX]

[DOI]

S. Chakra Chennubhotla

Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2021 - 24th International Conference, Strasbourg, France, September 27, 2021

The 4th International Workshop on Epidemiology meets Data Mining and Knowledge Discovery (epiDAMIK 4.0 @ KDD2021).

[BibT_eX]

[DOI]

Proceedings of the KDD '21: The 27th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, 2021

IMPECCABLE: Integrated Modeling PipelinE for COVID Cure by Assessing Better LEads.

[BibT_eX]

[DOI]

Proceedings of the ICPP 2021: 50th International Conference on Parallel Processing, Lemont, IL, USA, August 9, 2021

2020

Attacking NIST biometric image software using nonlinear optimization.

[BibT_eX]

[DOI]

Sunny Raj

Jodh S. Pannu

Steven Lawrence Fernandes

Arvind Ramanathan

Laura L. Pullum

Sumit Kumar Jha

Pattern Recognit. Lett., 2020

Distributed Bayesian optimization of deep reinforcement learning algorithms.

[BibT_eX]

[DOI]

J. Parallel Distributed Comput., 2020

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19.

[BibT_eX]

[DOI]

Mathialakan Thavappiragasam

J. Chem. Inf. Model., 2020

Artificial intelligence techniques for integrative structural biology of intrinsically disordered proteins.

[BibT_eX]

[DOI]

Arvind Ramanathan

Heng Ma

Akash Parvatikar

S. Chakra Chennubhotla

CoRR, 2020

Scalable HPC and AI Infrastructure for COVID-19 Therapeutics.

[BibT_eX]

[DOI]

CoRR, 2020

Targeting SARS-CoV-2 with AI- and HPC-enabled Lead Generation: A First Data Release.

[BibT_eX]

[DOI]

CoRR, 2020

Modeling Histological Patterns for Differential Diagnosis of Atypical Breast Lesions.

[BibT_eX]

[DOI]

S. Chakra Chennubhotla

Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2020, 2020

2019

Data-driven efficient network and surveillance-based immunization.

[BibT_eX]

[DOI]

Knowl. Inf. Syst., 2019

Classifying cancer pathology reports with hierarchical self-attention networks.

[BibT_eX]

[DOI]

Noah Schaefferkoetter

Hong-Jun Yoon

James Blair Christian

Artif. Intell. Medicine, 2019

DeepDriveMD: Deep-Learning Driven Adaptive Molecular Simulations for Protein Folding.

[BibT_eX]

[DOI]

Proceedings of the Third IEEE/ACM Workshop on Deep Learning on Supercomputers, 2019

Deep Generative Model Driven Protein Folding Simulations.

[BibT_eX]

[DOI]

Proceedings of the Parallel Computing: Technology Trends, 2019

Towards Native Execution of Deep Learning on a Leadership-Class HPC System.

[BibT_eX]

[DOI]

Proceedings of the IEEE International Parallel and Distributed Processing Symposium Workshops, 2019

Visual Analytics for Deep Embeddings of Large Scale Molecular Dynamics Simulations.

[BibT_eX]

[DOI]

Proceedings of the 2019 IEEE International Conference on Big Data (IEEE BigData), 2019

Model-based Hyperparameter Optimization of Convolutional Neural Networks for Information Extraction from Cancer Pathology Reports on HPC.

[BibT_eX]

[DOI]

Proceedings of the 2019 IEEE EMBS International Conference on Biomedical & Health Informatics, 2019

2018

Hierarchical attention networks for information extraction from cancer pathology reports.

[BibT_eX]

[DOI]

James Blair Christian

Paul A. Fearn

Georgia D. Tourassi

Arvind Ramanathan

J. Am. Medical Informatics Assoc., 2018

Scalable deep text comprehension for Cancer surveillance on high-performance computing.

[BibT_eX]

[DOI]

James Blair Christian

BMC Bioinform., 2018

Deep clustering of protein folding simulations.

[BibT_eX]

[DOI]

BMC Bioinform., 2018

HyperSpace: Distributed Bayesian Hyperparameter Optimization.

[BibT_eX]

[DOI]

Proceedings of the 30th International Symposium on Computer Architecture and High Performance Computing, 2018

Hierarchical Convolutional Attention Networks for Text Classification.

[BibT_eX]

[DOI]

Shang Gao

Arvind Ramanathan

Georgia D. Tourassi

Proceedings of The Third Workshop on Representation Learning for NLP, 2018

Deep radiogenomics for predicting clinical phenotypes in invasive breast cancer.

[BibT_eX]

[DOI]

Proceedings of the 14th International Workshop on Breast Imaging, 2018

2017

Data-Driven Immunization.

[BibT_eX]

[DOI]

Proceedings of the 2017 IEEE International Conference on Data Mining, 2017

Adversarial attacks on computer vision algorithms using natural perturbations.

[BibT_eX]

[DOI]

Proceedings of the Tenth International Conference on Contemporary Computing, 2017

<i>SATYA</i> : Defending Against Adversarial Attacks Using Statistical Hypothesis Testing.

[BibT_eX]

[DOI]

Proceedings of the Foundations and Practice of Security - 10th International Symposium, 2017

Testing autonomous cyber-physical systems using fuzzing features from convolutional neural networks: work-in-progress.

[BibT_eX]

[DOI]

Proceedings of the Thirteenth ACM International Conference on Embedded Software 2017 Companion, 2017

2016

Analyzing the impact of modeling choices and assumptions in compartmental epidemiological models.

[BibT_eX]

[DOI]

Simul., 2016

Multi-task Deep Neural Networks for Automated Extraction of Primary Site and Laterality Information from Cancer Pathology Reports.

[BibT_eX]

[DOI]

Hong-Jun Yoon

Arvind Ramanathan

Georgia D. Tourassi

Proceedings of the Advances in Big Data, 2016

Integrating symbolic and statistical methods for testing intelligent systems: Applications to machine learning and computer vision.

[BibT_eX]

[DOI]

Arvind Ramanathan

Laura L. Pullum

Faraz Hussain

Dwaipayan Chakrabarty

Sumit Kumar Jha

Proceedings of the 2016 Design, Automation & Test in Europe Conference & Exhibition, 2016

Constellation: A science graph network for scalable data and knowledge discovery in extreme-scale scientific collaborations.

[BibT_eX]

[DOI]

Sudharshan S. Vazhkudai

Proceedings of the 2016 IEEE International Conference on Big Data (IEEE BigData 2016), 2016

2015

ORBiT: Oak Ridge biosurveillance toolkit for public health dynamics.

[BibT_eX]

[DOI]

Chakra S. Chennubhotla

Silvia Valkova

BMC Bioinform., December, 2015

NoC Architectures as Enablers of Biological Discovery for Personalized and Precision Medicine.

[BibT_eX]

[DOI]

Proceedings of the 9th International Symposium on Networks-on-Chip, 2015

Sequential pattern mining of electronic healthcare reimbursement claims: Experiences and challenges in uncovering how patients are treated by physicians.

[BibT_eX]

[DOI]

Proceedings of the 2015 IEEE International Conference on Big Data (IEEE BigData 2015), Santa Clara, CA, USA, October 29, 2015

2014

Oak Ridge Biosurveillance Toolkit: Scalable machine learning for public health surveillance.

[BibT_eX]

[DOI]