NCI-DOE Collaboration Publications

The Joint Design of Advanced Computing Solutions for Cancer (JDACS4C) program is the focal point of the strategic, interagency collaboration between the National Cancer Institute (NCI) and the US Department of Energy (DOE) to simultaneously accelerate advances in precision oncology and scientific computing.

Based on a multidisciplinary, team science approach, JDACS4C’s three research pilots were co-designed by NCI and DOE; align with several existing NCI and DOE programs; and are jointly led by DOE and NCI supported scientists. These teams include scientists from NCI and Frederick National Laboratory for Cancer Research and experts from DOE national laboratories: principally Argonne, Lawrence Livermore, Los Alamos, and Oak Ridge.

Below is a list of the publications. 

 

Publications as of July 22, 2021:

 

ID Year Title, Publication Capability
72 2021 Converting Tabular Data into Images for Deep Learning with Convolutional Neural Networks, Scientific Reports Pilot 1: IGTD
71 2021 Enabling Rapid COVID-19 Small Molecule Drug Design Through Scalable Deep Learning of Generative Models, International Journal of High Performance Computing Applications  
70 2021 High-Throughput Virtual Screening of Small Molecule Inhibitors for SARS-CoV-2 Protein Targets with Deep Fusion Models, arXiv.org  
69 2021 Improved Protein–Ligand Binding Affinity Prediction with Structure-Based Deep Fusion Inference, J Chem Inf Model  
68 2021 Reimagining Dots and Dashes: Visualizing structure and function of organelles for high-content imaging analysis, Cell Chemical Biology  
67 2021 Deep Active Learning for Classifying Cancer Pathology Reports, BMC Bioinformatics Pilot 3: MT-CNN
66 2021 Limitations of Transformers on Clinical Text Classification, IEEE Journal of Biomedical and Health Informatics Pilot 3: MT-CNNHiSAN
65 2021 Using GANS with Adaptive Training Data to Search for New Molecules, Journal of Cheminformatics  
64 2021 Machine Learning Models to Predict Inhibition of the Bile Salt Export Pump, Journal of Chemical Information and Modeling ATOM: AMPL
63 2021 Uncertainty Bounds for Multivariate Machine Learning Predictions on High-Strain Brittle Fracture, arXiv.org  
62 2021 A Pre-Training and Self-Training Approach for Biomedical Named Entity Recognition, PLOS ONE  
61 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  
60 2020 Learning Curves for Drug Response Prediction in Cancer Cell Lines, arXiv.org Pilot 1: LC
59 2020 Predicting Volume of Distribution in Humans: Performance of in silico Methods for A Large Set of Structurally Diverse Clinical Compounds, Drug Metab Dispos  
58 2020 Accelerated Training of Boostrap Aggregation-based Deep Information Extraction Systems from Cancer Pathology Reports, Journal of Biomedical Informatics  
57 2020 Enhanced Co-Expression Extrapolation (COXEN) Gene Selection Method for Building Anti-Cancer Drug Response Prediction Models, Genes Pilot 1: Enhanced COXEN
56 2020 Wide Neural Networks with Bottlenecks are Deep Gaussian Processes, Journal of Machine Learning Research  
55 2020 DeepFreeze: Towards Scalable Asynchronous Checkpointing of Deep Learning Models, 20th IEEE/ACM International Symposium on Cluster, Cloud and Internet Computing  
54 2020 Accelerating Therapeutics for Opportunities in Medicine: A Paradigm Shift in Drug Discovery, Frontiers in Pharmacology ATOM: AMPL
53 2020 How Anionic Lipids Affect Spatiotemporal Properties of KRAS4B on Model Membranes, The Journal of Physical Chemistry B  
52 2020 Using Case-level Context to Classify Cancer Pathology Reports, PLOS One Pilot 3: MT-CNN
51 2020 Generation and Evaluation of Synthetic Patient Data, BMC Medical Research Methodology  
50 2020 Knowledge Graph-Enabled Cancer Data Analytics, IEEE Transactions on Emerging Topics in Computing  
49 2020 Distributed Bayesian Optimization of Deep Reinforcement Learning Algorithms, Journal of Parallel and Distributed Computing  
48 2020 AMPL: A Data-Driven Modeling Pipeline for Drug Discovery, Journal of Chemical Information and Modeling ATOM: AMPL
47 2020 Privacy-Preserving Deep Learning NLP Models for Cancer Registries, IEEE Transactions on Emerging Topics in Computing  
46 2020 Presence or Absence of Ras Dimerization Shows Distinct Kinetic Signature in Ras-Raf Interaction, Biophysical Journal  
45 2020 Information Extraction from Cancer Pathology Reports with Graph Convolution Networks for Natural Language Texts, 2019 IEEE International Conference on Big Data  
44 2020 Adversarial Training for Privacy-Preserving Deep Learning Model Distribution, 2019 IEEE International Conference on Big Data (Big Data)  
43 2020 The Plasma Membrane as a Competitive Inhibitor and Positive Allosteric Modulator of KRas4B Signaling, Biophysical Journal  
42 2020 Membrane interactions of the globular domain and the hypervariable region of KRAS4b define its unique diffusion behavior, eLife Pilot 2: KRas4B Campaign 1
41 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  
40 2019 Rethinking drug design in the artificial intelligence era, Nature Reviews Drug Discovery  
39 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
38 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
37 2019 Unsupervised Machine Learning for Analysis of Phase Separation in Ternary Lipid Mixture, Journal of Chemical Theory and Computation  
36 2019 Classifying Cancer Pathology Reports with Hierarchical Self-attention Networks, Artificial Intelligence in Medicine  
35 2019 AI Meets Exascale Computing: Advancing Cancer Research With Large-Scale High Performance Computing, Frontiers in Oncology  
34 2019 Computationally Efficient Learning of Quality Controlled Word Embeddings for Natural Language Processing, 2019 IEEE Computer Society Annual Symposium on VLSI  
33 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  
32 2019 A Knowledge Graph Approach for the Secondary Use of Cancer Registry Data, 2019 IEEE EMBS International Conference on Biomedical & Health Informatics  
31 2019 Inverse Regression for Extraction of Tumor Site from Cancer Pathology Reports, 2019 IEEE EMBS International Conference on Biomedical & Health Informatics  
30 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
29 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"  
28 2019 Computing Long Time Scale Biomolecular Dynamics Using Quasi-stationary Distribution Kinetic Monte Carlo (QSD-KMC), The Journal of Chemical Physics  
27 2019 On Mixup Training: Improved Calibration and Predictive Uncertainty for Deep Neural Networks, Advances in Neural Information Processing Systems 32  
26 2019 Combating Label Noise in Deep Learning Using Abstention, Proceedings of the 36th International Conference on Machine Learning  
25 2019 Artificial Intelligence and Pharmacometrics: Time to Embrace, Capitalize, and Advance?, CPT: Pharmacometrics and Systems Pharmacology  
24 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
23 2019 Autoencoder Node Saliency: Selecting Relevant Latent Representations, Pattern Recognition Pilot 1: ANS
22 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)  
21 2019 New Insights into RAS Biology Reinvigorate Interest in Mathematical Modeling of RAS Signaling, Seminars in Cancer Biology  
20 2019 Retrofitting Word Embeddings with the UMLS Metathesaurus for Clinical Information Extraction, 2018 IEEE International Conference on Big Data  
19 2019 Modeling Cell Line-specific Recruitment of Signaling Proteins to the Insulin-like Growth Factor 1 Receptor, PLOS Computational Biology Pilot 3: MT-CNN
18 2019 The Need for Uncertainty Quantification in Machine-assisted Medical Decision Making, Nature Machine Intelligence  
17 2018 Predicting Tumor Cell Line Response to Drug Pairs with Deep Learning, BMC Bioinformatics Pilot 1: Combo
16 2018 CANDLE/Supervisor: A Workflow Framework for Machine Learning Applied to Cancer Research, BMC Bioinformatics  
15 2018 Scalable Deep Text Comprehension for Cancer Surveillance on High-Performance Computing, BMC Bioinformatics  
14 2018 CAT: Computer Aided Triage Improving Upon the Bayes Risk Through Ε-Refusal Triage Rules, BMC Bioinformatics  
13 2018 Sparse Coding of Pathology Slides Compared to Transfer Learning with Deep Neural Networks, BMC Bioinformatics  
12 2018 Capturing Phase Behavior of Ternary Lipid Mixtures with a Refined Martini Coarse-Grained Force Field, Journal of Chemical Theory and Computation  
11 2018 Methionine 170 is an Environmentally Sensitive Membrane Anchor In The Disordered HVR of K-Ras4B, The Journal of Physical Chemistry B  
10 2018 Dissecting RAF Inhibitor Resistance by Structure-Based Modeling Reveals Ways to Overcome Oncogenic RAS Signaling, Cell Systems  
9 2018 Molecular Recognition of RAS/RAF Complex at the Membrane: Role of RAF Cysteine-Rich Domain, Scientific Reports  
8 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 Pilot 3: MT-CNN
7 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 Pilot 3: MT-CNN
6 2018 Hierarchical Attention Networks for Information Extraction from Cancer Pathology Reports, Journal of the American Medical Informatics Association  
5 2018 Energy Efficient Stochastic-Based Deep Spiking Neural Networks for Sparse Datasets, 2017 IEEE International Conference on Big Data  
4 2017 Computational Lipidomics of the Neuronal Plasma Membrane, Biophysical Journal  
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, IEEE International Conference on Biomedical Health  
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


 

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