Staff information

PNNL Publications

2025

• Bilbrey J.A., J.S. Firoz, M. Lee, and S. Choudhury. 2025. "Uncertainty Quantification for Neural Network Potential Foundation Models." npj Computational Materials 11, no. 1:Art. No. 109. PNNL-SA-206884. doi:10.1038/s41524-025-01572-y
• Kaspar T.C., S.M. Akers, H.W. Sprueill, A.H. Ter-Petrosyan, J.A. Bilbrey, D.F. Hopkins, and A.V. Harilal, et al. 2025. "Machine-learning-enabled on-the-fly analysis of RHEED patterns during thin film deposition by molecular beam epitaxy." Journal of Vacuum Science & Technology A: International Journal Devoted to Vacuum, Surfaces, and Films 43, no. 3:Art. No. 032702. PNNL-SA-206700. doi:10.1116/6.0004493

2024

• Aksoy S.G., B. Fang, R. Gioiosa, W.W. Kay, H. Lee, J.A. Bilbrey, and M.R. Shapiro, et al. 2024. Unifying Combinatorial and Graphical Methods in Artificial Intelligence. PNNL-36839. Richland, WA: Pacific Northwest National Laboratory. Unifying Combinatorial and Graphical Methods in Artificial Intelligence
• Bylaska E.J., A.R. Panyala, N.P. Bauman, B. Peng, H. Pathak, D. Mejia-Rodriguez, and N. Govind, et al. 2024. "Electronic structure simulations in the cloud computing environment." The Journal of Chemical Physics 161, no. 15:Art. No. 150902. PNNL-SA-199904. doi:10.1063/5.0226437
• Eshun J., N.C. Lamar, S.G. Aksoy, S.M. Akers, B.J. Garcia, H.S. Cunningham, and G. Chin, et al. 2024. "Identifying Sample Provenance from SEM/EDS Automated Particle Analysis via Few-shot Learning coupled with Similarity Graph Clustering." Microscopy and Microanalysis 30, no. 4:Art. No. ozae068. PNNL-SA-191238. doi:10.1093/mam/ozae068
• Helal H., J.S. Firoz, J.A. Bilbrey, H.W. Sprueill, K.M. Herman, M.M. Krell, and T. Murray, et al. 2024. "Acceleration of Graph Neural Network-based Prediction Models in Chemistry via Co-design Optimization on Intelligence Processing Units." Journal of Chemical Information and Modeling 64, no. 5:1568-1580. PNNL-SA-193670. doi:10.1021/acs.jcim.3c01312

2023

• Holden M.J., C.M. Doty, A.H. Ter-Petrosyan, J.A. Bilbrey, S.M. Akers, and S.R. Spurgeon. 2023. Automated Energy-Dispersive X-ray Spectroscopy Analysis for Multi-Modal Few-Shot Learning. PNNL-35397. Richland, WA: Pacific Northwest National Laboratory. Automated Energy-Dispersive X-ray Spectroscopy Analysis for Multi-Modal Few-Shot Learning
• Muller S.E., M.P. Prange, Z. Lu, W.S. Rosenthal, and J.A. Bilbrey. 2023. "An open database of computed bulk ternary transition metal dichalcogenides." Scientific Data 10. PNNL-SA-177921. doi:10.1038/s41597-023-02103-4
• Sprueill H.W., J.A. Bilbrey, Q. Pang, and P.V. Sushko. 2023. "Active Sampling for Neural Network Potentials: Accelerated Simulations of Shear-induced Deformation in Cu-Ni Multilayers." Journal of Chemical Physics 158, no. 11:Art. No. 114103. PNNL-SA-179331. doi:10.1063/5.0133023

2022

• Bilbrey J.A., N. Chen, S. Hu, and P.V. Sushko. 2022. "Graph-Component Approach to Defect Identification in Large Atomistic Simulations." Computational Materials Science 214. PNNL-SA-173243. doi:10.1016/j.commatsci.2022.111700
• Knutson C.R., M.S. Bontha, J.A. Bilbrey, and N. Kumar. 2022. "Decoding the Protein-ligand Interactions Using Parallel Graph Neural Networks." Scientific Reports 12. PNNL-SA-166075. doi:10.1038/s41598-022-10418-2

2021

• Alexander F.J., J.A. Ang, J.A. Bilbrey, J. Balewski, T.A. Casey, R. Chard, and J. Choi, et al. 2021. "Co-design Center for Exascale Machine Learning Technologies (ExaLearn)." The International Journal of High Performance Computing Applications 35, no. 6:598-616. PNNL-SA-156070. doi:10.1177/10943420211029302

2020

• Bilbrey J.A., C.M. Ortiz Marrero, M. Sassi, A.M. Ritzmann, N.J. Henson, and M. Schram. 2020. "Tracking the chemical evolution of iodine species using recurrent neural networks." ACS Omega 5, no. 9:4588-4594. PNNL-SA-148824. doi:10.1021/acsomega.9b04104
• Bilbrey J.A., E.F. Ramirez, J.M. Brandi-Lozano, C. Sivaraman, J. Short, I.D. Lewis, and B.D. Barnes, et al. 2020. "Improving Radiograph Analysis Throughput through Transfer Learning and Object Detection." Journal of Medical Artificial Intelligence 3. PNNL-SA-149813. doi:10.21037/jmai-20-2
• Bilbrey J.A., J. Heindel, M. Schram, P. Bandyopadhyay, S.S. Xantheas, and S. Choudhury. 2020. "A Look Inside the Black Box: Using graph-theoretical descriptors to interpret a Continuous-Filter Convolutional Neural Network (CF-CNN) trained on the global and local minimum energy structures of neutral water clusters." Journal of Chemical Physics 153, no. 2:024302. PNNL-SA-152462. doi:10.1063/5.0009933