|
134 |
2023 |
The confluence of machine learning and multiscale simulations, Current Opinion in Structural Biology |
ADMIRRAL |
133 |
2023 |
Data augmentation and multimodal learning for predicting drug response in patient-derived xenografts from gene expressions and histology images, Frontiers in Medicine |
IMPROVE |
132 |
2023 |
Deep learning methods for drug response prediction in cancer: Predominant and emerging trends, Frontiers in Medicine |
IMPROVE |
131 |
2023 |
Dynamic density functional theory of multicomponent cellular membranes, Physical Review Research |
ADMIRRAL, Pilot 2 |
130 |
2022 |
TULIP: An RNA-seq-based Primary Tumor Type Prediction Tool Using Convolutional Neural Networks, Cancer Informatics |
|
129 |
2022 |
A phase transition for finding needles in nonlinear haystacks with LASSO artificial neural networks, Statistics and Computing |
|
128 |
2022 |
Exploring approaches for predictive cancer patient digital twins: Opportunities for collaboration and innovation, Frontiers in Digital Health |
|
127 |
2022 |
Exploring CRD mobility during RAS/RAF engagement at the membrane, Biophysical Journal |
Pilot 2 |
126 |
2022 |
Using ensembles and distillation to optimize the deployment of deep learning models for the classification of electronic cancer pathology reports, JAMIA Open |
|
125 |
2022 |
Adaptive Language Model Training for Molecular Design, ChemRxiv |
CANDLE |
124 |
2022 |
A biology-informed similarity metric for simulated patches of human cell membrane, Machine Learning: Science and Technology |
|
123 |
2022 |
Computational Workflow for Accelerated Molecular Design Using Quantum Chemical Simulations and Deep Learning Models, ChemRxiv |
CANDLE |
122 |
2022 |
Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework, Journal of Chemical Theory and Computation |
Pilot 2 |
121 |
2022 |
Automatic information extraction from childhood cancer pathology reports, JAMIA Open |
|
120 |
2022 |
Multifactorial drug response modeling based on cancer organoid data, Journal of Clinical Oncology |
Pilot 1 |
119 |
2022 |
Drug response prediction in patient-derived xenografts with data augmentation and multimodal deep learning, Journal of Clinical Oncology |
Pilot 1 |
118 |
2022 |
A PDE Model of Breast Tumor Progression in MMTV-PyMT Mice, Journal of Personalized Medicine |
|
117 |
2022 |
Recapitulation of cell-like KRAS4b membrane dynamics on complex biomimetic membranes, iScience |
Pilot 2 |
116 |
2022 |
Optimal vocabulary selection approaches for privacy-preserving deep NLP model training for information extraction and career epidemiology, Cancer Biomarkers |
Pilot 3 |
115 |
2022 |
Automating Genetic Algorithm Mutations for Molecules Using a Masked Language Model, IEEE Transactions on Evolutionary Computation |
Pilot 3 |
114 |
2022 |
A Keyword-Enhanced Approach to Handle Class Imbalance in Clinical Text Classification, IEEE Journal of Biomedical and Health Informatics |
Pilot 3 |
113 |
2022 |
Class imbalance in out-of-distribution datasets: Improving the robustness of the TextCNN for the classification of rare cancer types, Journal of Biomedical Informatics |
Pilot 3 |
112 |
2022 |
A tipping point in cancer epidemiology: embracing a life course exposomic framework, Trends in Cancer |
|
111 |
2022 |
Predictive Radiation Oncology – A New NCI-DOE Scientific Space and Community, Radiation Research |
|
110 |
2022 |
Machine learning-driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins, Proceedings of the National Academy of Sciences |
Pilot 2: MuMMI |
109 |
2022 |
Generalizable coordination of large multiscale workflows: challenges and learnings at scale, Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis |
Pilot 2 |
108 |
2022 |
Pandemic Drugs at Pandemic Speed: Infrastructure for Accelerating COVID-19 Drug Discovery with Hybrid Machine Learning- and Physics-based Simulations on High Performance Computers, Interface Focus |
Pilot 1 |
107 |
2022 |
Digital twins for predictive oncology will be a paradigm shift for precision cancer care, Nature |
|
106 |
2022 |
Uncertainty Bounds for Multivariate Machine Learning Predictions on High-Strain Brittle Fracture, arXiv |
UQ |
105 |
2021 |
Artificial intelligence for drug response prediction in disease models, Briefings in Bioinformatics |
Pilot 1 |
104 |
2021 |
A cross-study analysis of drug response prediction in cancer cell lines, Briefings in Bioinformatics |
Pilot 1 |
103 |
2021 |
Evolution of Thyroglobulin Loop Kinetics in EpCAM, Life |
Pilot 2 |
102 |
2021 |
Discovery of Small-Molecule Inhibitors of SARS-CoV-2 Proteins Using a Computational and Experimental Pipeline, Frontiers in Molecular Biosciences |
Pilot 2 |
101 |
2021 |
Leveraging Topological Events in Tracking Graphs for Understanding Particle Diffusion, Computer Graphics Forum |
Pilot 2 |
100 |
2021 |
Converting tabular data into images for deep learning with convolutional neural networks, Scientific Reports |
Pilot 1: IGTD |
99 |
2021 |
Enabling rapid COVID-19 small molecule drug design through scalable deep learning of generative models, The International Journal of High Performance Computing Applications |
ATOM |
98 |
2021 |
Machine-learning-based dynamic-importance sampling for adaptive multiscale simulations, Nature Machine Intelligence |
Pilot 2 |
97 |
2021 |
High-Throughput Virtual Screening of Small Molecule Inhibitors for SARS-CoV-2 Protein Targets with Deep Fusion Models, arXiv |
ATOM |
96 |
2021 |
Unveiling the Dynamics of KRAS4b on Lipid Model Membranes, The Journal of Membrane Biology |
Pilot 2 |
95 |
2021 |
Improved Protein–Ligand Binding Affinity Prediction with Structure-Based Deep Fusion Inference, Journal of Chemical Information and Modeling |
ATOM |
94 |
2021 |
Reimagining dots and dashes: Visualizing structure and function of organelles for high-content imaging analysis, Cell Chemical Biology |
ATOM |
93 |
2021 |
Deep active learning for classifying cancer pathology reports, BMC Bioinformatics |
Pilot 3: MT-CNN, Active Learning for NLP Systems |
92 |
2021 |
Limitations of Transformers on Clinical Text Classification, IEEE Journal of Biomedical and Health Informatics |
Pilot 3: MT-CNN, HiSAN Pathology Reports |
91 |
2021 |
Using GANs with adaptive training data to search for new molecules, Journal of Cheminformatics |
Pilot 3 |
90 |
2021 |
Machine Learning Models to Predict Inhibition of the Bile Salt Export Pump, Journal of Chemical Information and Modeling |
ATOM: AMPL |
89 |
2021 |
A pre-training and self-training approach for biomedical named entity recognition, PLOS ONE |
Pilot 3 |
88 |
2020 |
Uncertainty Bounds for Multivariate Machine Learning Predictions on High-Strain Brittle Fracture, arXiv |
Pilot 3 |
87 |
2020 |
Multiparametric High-Content Assays to Measure Cell Health and Oxidative Damage as a Model for Drug-Induced Liver Injury, Current Protocols in Chemical Biology |
ATOM |
86 |
2020 |
Learning Curves for Drug Response Prediction in Cancer Cell Lines, arXiv |
Pilot 1: LC: Learning Curves |
85 |
2020 |
Predicting Volume of Distribution in Humans: Performance of in silico Methods for A Large Set of Structurally Diverse Clinical Compounds, Drug Metabolism and Disposition |
ATOM |
84 |
2020 |
High-bypass Learning: Automated Detection of Tumor Cells That Significantly Impact Drug Response, 2020 IEEE/ACM Workshop on Machine Learning in High Performance Computing Environments (MLHPC) and Workshop on Artificial Intelligence and Machine Learning for Scientific Applications (AI4S) |
CANDLE |
83 |
2020 |
Ensemble transfer learning for the prediction of anti-cancer drug response, Scientific Reports |
Pilot 1 |
82 |
2020 |
Accelerated training of bootstrap aggregation-based deep information extraction systems from cancer pathology reports, Journal of Biomedical Informatics |
Pilot 3 |
81 |
2020 |
Uncovering a membrane-distal conformation of KRAS available to recruit RAF to the plasma membrane, Proceedings of the National Academy of Sciences |
Pilot 2 |
80 |
2020 |
Enhanced Co-Expression Extrapolation (COXEN) Gene Selection Method for Building Anti-Cancer Drug Response Prediction Models, Genes |
Pilot 1: Enhanced Coxen |
79 |
2020 |
Capturing Biologically Complex Tissue-Specific Membranes at Different Levels of Compositional Complexity, The Journal of Physical Chemistry B |
Pilot 2 |
78 |
2020 |
Wide Neural Networks with Bottlenecks are Deep Gaussian Processes, Journal of Machine Learning Research |
Pilot 3 |
77 |
2020 |
Flux: Overcoming scheduling challenges for exascale workflows, Future Generation Computer Systems |
Pilot 2 |
76 |
2020 |
Anionic Lipids Impact RAS-Binding Site Accessibility and Membrane Binding Affinity of CRAF RBD-CRD, Biophysical Journal |
Pilot 2 |
75 |
2020 |
ddcMD: A fully GPU-accelerated molecular dynamics program for the Martini force field, The Journal of Chemical Physics |
Pilot 2 |
74 |
2020 |
DeepFreeze: Towards Scalable Asynchronous Checkpointing of Deep Learning Models, 20th IEEE/ACM International Symposium on Cluster, Cloud and Internet Computing |
CANDLE |
73 |
2020 |
Accelerating Therapeutics for Opportunities in Medicine: A Paradigm Shift in Drug Discovery, Frontiers in Pharmacology |
ATOM: AMPL |
72 |
2020 |
How Anionic Lipids Affect Spatiotemporal Properties of KRAS4B on Model Membranes, The Journal of Physical Chemistry B |
Pilot 2 |
71 |
2020 |
What needles do sparse neural networks find in nonlinear haystacks, arXiv |
Pilot 1 |
70 |
2020 |
Using case-level context to classify cancer pathology reports, PLOS ONE |
Pilot 3: MT-CNN |
69 |
2020 |
Generation and evaluation of synthetic patient data, BMC Medical Research Methodology |
Pilot 3: SYNDATA |
68 |
2020 |
Knowledge Graph-Enabled Cancer Data Analytics, IEEE Journal of Biomedical and Health Informatics |
Pilot 3 |
67 |
2020 |
Distributed Bayesian optimization of deep reinforcement learning algorithms, Journal of Parallel and Distributed Computing |
CANDLE |
66 |
2020 |
AMPL: A Data-Driven Modeling Pipeline for Drug Discovery, Journal of Chemical Information and Modeling |
ATOM: AMPL |
65 |
2020 |
Privacy-Preserving Deep Learning NLP Models for Cancer Registries, IEEE Transactions on Emerging Topics in Computing |
Pilot 3 |
64 |
2020 |
Presence or Absence of Ras Dimerization Shows Distinct Kinetic Signature in Ras-Raf Interaction, Biophysical Journal |
Pilot 2 |
63 |
2020 |
Information Extraction from Cancer Pathology Reports with Graph Convolution Networks for Natural Language Texts, 2019 IEEE International Conference on Big Data (Big Data) |
Pilot 3 |
62 |
2020 |
Adversarial Training for Privacy-Preserving Deep Learning Model Distribution, 2019 IEEE International Conference on Big Data (Big Data) |
Pilot 3 |
61 |
2020 |
The Plasma Membrane as a Competitive Inhibitor and Positive Allosteric Modulator of KRas4B Signaling, Biophysical Journal |
Pilot 2 |
60 |
2020 |
Membrane interactions of the globular domain and the hypervariable region of KRAS4b define its unique diffusion behavior, eLife |
Pilot 2: Data Set: KRas4b - Campaign 1 trajectory data |
59 |
2020 |
Automatic extraction of cancer registry reportable information from free-text pathology reports using multitask convolutional neural networks, Journal of the American Medical Informatics Association |
Pilot 3 |
58 |
2019 |
Rethinking drug design in the artificial intelligence era, Nature Reviews Drug Discovery |
ATOM |
57 |
2019 |
Scalable reinforcement-learning-based neural architecture search for cancer deep learning research, Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis |
Pilot 1: NT3 |
56 |
2019 |
A massively parallel infrastructure for adaptive multiscale simulations: modeling RAS initiation pathway for cancer, Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis |
Pilot 2: MuMMI |
55 |
2019 |
Unsupervised Machine Learning for Analysis of Phase Separation in Ternary Lipid Mixture, Journal of Chemical Theory and Computation |
Pilot 2 |
54 |
2019 |
Classifying cancer pathology reports with hierarchical self-attention networks, Artificial Intelligence in Medicine |
Pilot 3 |
53 |
2019 |
DeepDriveMD: Deep-Learning Driven Adaptive Molecular Simulations for Protein Folding, 2019 IEEE/ACM Third Workshop on Deep Learning on Supercomputers (DLS) |
Pilot 2 |
52 |
2019 |
Use of Natural Language Processing to Extract Clinical Cancer Phenotypes from Electronic Medical Records, Cancer Research |
Pilot 3 |
51 |
2019 |
AI Meets Exascale Computing: Advancing Cancer Research With Large-Scale High Performance Computing, Frontiers in Oncology |
|
50 |
2019 |
MemSurfer: A Tool for Robust Computation and Characterization of Curved Membranes, Journal of Chemical Theory and Computation |
Pilot 2: MemSurfer |
49 |
2019 |
PyBioNetFit and the Biological Property Specification Language, iScience |
UQ |
48 |
2019 |
Computationally Efficient Learning of Quality Controlled Word Embeddings for Natural Language Processing, 2019 IEEE Computer Society Annual Symposium on VLSI (ISVLSI) |
Pilot 3 |
47 |
2019 |
A Knowledge Graph Approach for the Secondary Use of Cancer Registry Data, 2019 IEEE EMBS International Conference on Biomedical & Health Informatics (BHI) |
Pilot 3 |
46 |
2019 |
Model-based Hyperparameter Optimization of Convolutional Neural Networks for Information Extraction from Cancer Pathology Reports on HPC, 2019 IEEE EMBS International Conference on Biomedical & Health Informatics |
Pilot 3 |
45 |
2019 |
Inverse Regression for Extraction of Tumor Site from Cancer Pathology Reports, 2019 IEEE EMBS International Conference on Biomedical & Health Informatics |
Pilot 3 |
44 |
2019 |
Deep Transfer Learning Across Cancer Registries for Information Extraction from Pathology Reports, 2019 IEEE EMBS International Conference on Biomedical & Health Informatics |
Pilot 3: MT-CNN |
43 |
2019 |
Extraction of Tumor Site from Cancer Pathology Reports using Deep Filters, "Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics - BCB '19" |
Pilot 3 |
42 |
2019 |
Computing Long Time Scale Biomolecular Dynamics Using Quasi-stationary Distribution Kinetic Monte Carlo (QSD-KMC), The Journal of Chemical Physics |
Pilot 2 |
41 |
2019 |
Performance, Energy, and Scalability Analysis and Improvement of Parallel Cancer Deep Learning CANDLE Benchmarks, Proceedings of the 48th International Conference on Parallel Processing |
CANDLE |
40 |
2019 |
Generalizing Gillespie’s Direct Method to Enable Network-Free Simulations, Bulletin of Mathematical Biology |
Pilot 1 |
39 |
2019 |
Deep Generative Model Driven Protein Folding Simulation, arXiv |
Pilot 3 |
38 |
2019 |
On Mixup Training: Improved Calibration and Predictive Uncertainty for Deep Neural Networks, Advances in Neural Information Processing Systems 32 |
UQ |
37 |
2019 |
Combating Label Noise in Deep Learning Using Abstention, Proceedings of the 36th International Conference on Machine Learning |
UQ |
36 |
2019 |
Semi-Supervised Information Extraction for Cancer Pathology Reports, 2019 IEEE EMBS International Conference on Biomedical Health Informatics (BHI) |
Pilot 3 |
35 |
2019 |
Artificial Intelligence and Pharmacometrics: Time to Embrace, Capitalize, and Advance?, CPT: Pharmacometrics and Systems Pharmacology |
ATOM |
34 |
2019 |
Selective Information Extraction Strategies for Cancer Pathology Reports with Convolutional Neural Networks, Recent Advances in Big Data and Deep Learning |
Pilot 3: MT-CNN |
33 |
2019 |
Autoencoder node saliency: Selecting relevant latent representations, Pattern Recognition |
Pilot 1: ANS |
32 |
2019 |
Portable and Reusable Deep Learning Infrastructure with Containers to Accelerate Cancer Studies, 2018 IEEE/ACM 4th International Workshop on Extreme Scale Programming Models and Middleware (ESPM2) |
CANDLE |
31 |
2019 |
New insights into RAS biology reinvigorate interest in mathematical modeling of RAS signaling, Seminars in Cancer Biology |
Pilot 1 |
30 |
2019 |
Quantitative biophysical analysis defines key components modulating recruitment of the GTPase KRAS to the plasma membrane, Journal of Biological Chemistry |
Pilot 2 |
29 |
2019 |
Memsurfer: A Tool for Robust Computation and Characterization of Bilayer Membranes, Biophysical Journal |
Pilot 2: MemSurfer |
28 |
2019 |
Retrofitting Word Embeddings with the UMLS Metathesaurus for Clinical Information Extraction, 2018 IEEE International Conference on Big Data (Big Data) |
Pilot 3 |
27 |
2019 |
Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor, PLoS Computational Biology |
|
26 |
2019 |
The need for uncertainty quantification in machine-assisted medical decision making, Nature Machine Intelligence |
UQ |
25 |
2018 |
Sparse coding of pathology slides compared to transfer learning with deep neural networks, BMC Bioinformatics |
Pilot 3 |
24 |
2018 |
Scalable deep text comprehension for Cancer surveillance on high-performance computing, BMC Bioinformatics |
Pilot 3 |
23 |
2018 |
Predicting tumor cell line response to drug pairs with deep learning, BMC Bioinformatics |
Pilot 1: Combo |
22 |
2018 |
CANDLE/Supervisor: a workflow framework for machine learning applied to cancer research, BMC Bioinformatics |
CANDLE |
21 |
2018 |
CAT: computer aided triage improving upon the Bayes risk through ε-refusal triage rules, BMC Bioinformatics |
Pilot 3 |
20 |
2018 |
Computational approaches for Cancer 2017 workshop overview, BMC Bioinformatics |
|
19 |
2018 |
Deep clustering of protein folding simulations, BMC Bioinformatics |
Pilot 2 |
18 |
2018 |
Capturing Phase Behavior of Ternary Lipid Mixtures with a Refined Martini Coarse-Grained Force Field, Journal of Chemical Theory and Computation |
Pilot 2 |
17 |
2018 |
Methionine 170 is an Environmentally Sensitive Membrane Anchor In The Disordered HVR of K-Ras4B, The Journal of Physical Chemistry B |
Pilot 2 |
16 |
2018 |
A Step-by-Step Guide to Using BioNetFit, arXiv |
Pilot 1 |
15 |
2018 |
HyperSpace: Distributed Bayesian Hyperparameter Optimization, 2018 30th International Symposium on Computer Architecture and High Performance Computing (SBAC-PAD) |
Pilot 2 |
14 |
2018 |
Microsimulation Model Calibration using Incremental Mixture Approximate Bayesian Computation, arXiv |
CANDLE |
13 |
2018 |
Dissecting RAF Inhibitor Resistance by Structure-based Modeling Reveals Ways to Overcome Oncogenic RAS Signaling, Cell Systems |
Pilot 1 |
12 |
2018 |
Hierarchical Convolutional Attention Networks for Text Classification, Proceedings of The Third Workshop on Representation Learning for NLP |
Pilot 2 |
11 |
2018 |
Molecular recognition of RAS/RAF complex at the membrane: Role of RAF cysteine-rich domain, Scientific Reports |
Pilot 2 |
10 |
2018 |
Precision Medicine as an Accelerator for Next Generation Cognitive Supercomputing, arXiv |
Pilot 3 |
9 |
2018 |
Filter pruning of Convolutional Neural Networks for text classification: A case study of cancer pathology report comprehension, 2018 IEEE EMBS International Conference on Biomedical & Health Informatics (BHI) |
Pilot 3: MT-CNN |
8 |
2018 |
Coarse-to-fine multi-task training of convolutional neural networks for automated information extraction from cancer pathology reports, 2018 IEEE EMBS International Conference on Biomedical & Health Informatics (BHI) |
Pilot 3: MT-CNN |
7 |
2018 |
Hierarchical attention networks for information extraction from cancer pathology reports, Journal of the American Medical Informatics Association |
Pilot 3 |
6 |
2018 |
Energy efficient stochastic-based deep spiking neural networks for sparse datasets, 2017 IEEE International Conference on Big Data (Big Data) |
Pilot 3 |
5 |
2017 |
Deep learning enabled national cancer surveillance, 2017 IEEE International Conference on Big Data (Big Data)
|
Pilot 3 |
4 |
2017 |
Computational Lipidomics of the Neuronal Plasma Membrane, Biophysical Journal |
Pilot 2 |
3 |
2017 |
Deep Learning for Automated Extraction of Primary Sites From Cancer Pathology Reports, IEEE Journal of Biomedical and Health Informatics |
Pilot 3: MT-CNN |
2 |
2017 |
Automated histologic grading from free-text pathology reports using graph-of-words features and machine learning, 2017 IEEE EMBS International Conference on Biomedical Health Informatics (BHI) |
Pilot 3 |
1 |
2016 |
Multi-task Deep Neural Networks for Automated Extraction of Primary Site and Laterality Information from Cancer Pathology Reports, Advances in Big Data |
Pilot 3: MT-CNN, DNN |