NCI-DOE Collaboration Publications

NCI and DOE co-designed its collaboration’s scientific research and development teams based on a multidisciplinary, team science approach. These teams align with several existing NCI and DOE programs, and they are jointly led by DOE- and NCI-supported scientists. These teams include scientists from NCI and its Frederick National Laboratory for Cancer Research, as well as experts from DOE national laboratories: Argonne, Lawrence Livermore, Los Alamos, and Oak Ridge. To explore ways you can collaborate, email the NCI-DOE Resources Team.

Below is a list of the publications. 

 

 

Publications as of June 13, 2023:

 

ID Year Title, Publication Resource
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


 

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