# Publications

#### Published

- Wenskovitch J.E., A.A. Anderson, S. Kincic, C. Fallon, D.K. Ciesielski, J.A. Baweja, and M.C. Mersinger, et al. 2022. "Operator Insights and Usability Evaluation of Machine Learning Assistance for Power Grid Contingency Analysis." In AHFE Conference Proceedings. PNNL-SA-170435
- Praggastis B.L., D.R. Brown, M.R. Shapiro, E. Purvine, and B. Wang. 2021. “
*DeepDataProfiler: An Overview*.” PNNL-31784. Richland, WA: Pacific Northwest National Laboratory. - Zucker J.D. J.R. Teuton K.L. Oxford C. Bakker O. Vitek K. Paneri and S. Mohammad-Taheri et al. 2020. “Leveraging Structured Biological Knowledge for Counterfactual Inference: A Case Study of Viral Pathogenesis." Transactions on Big Data. PNNL-SA-154544
- Bhattacharya A., T. Ramachandran, C.P. Dowling, S. Bopardikar, and S. Banik. 2020. "Automated Adversary Emulation for Cyber-Physical Systems via Reinforcement Learning." In IEEE International Conference on Intelligence and Security Informatics. PNNL-SA-156040
- Skomski E. S.S. Vasisht C.L. Wight A.R. Tuor J. Drgona and D.L. Vrabie. 2020. “Constrained Block Nonlinear Neural Dynamical Models." In Constrained Block Nonlinear Neural Dynamical Models. PNNL-SA-156893
- Ortiz Marrero C.M., N.O. Wiebe, and M. Kieferova. 2020. "Entanglement Induced Barren Plateaus."
*Physical Review Letters*. PNNL-SA-157287 - Oxford K.L. J.D. Zucker J.R. Teuton and M. Ostaszewski. 2020. “COVID-19 Disease Map a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms." bioRxiv preprint. PNNL-SA-157722
- Drgona J. A.R. Tuor S.E. Skomski S.S. Vasisht and D.L. Vrabie. 2021. “Deep Learning Explicit Differentiable Predictive Control Laws for Buildings." In 7th IFAC Conference on Nonlinear Model Predictive Control 2021 (July 11-14). PNNL-SA-159943
- Hirsh S.M., D.A. Barajas-Solano, and N. Kutz. 2021. "Sparsifying Priors for Bayesian Uncertainty Quantification in Model Discovery." Proceedings of the Royal Society A. PNNL-SA-160103
- Moses I., R. Joshi, B. Ozdemir, N. Kumar, J. Eickholt, and V. Barone. 2021. "Machine Learning Screening of Metal-ion Battery Electrode Materials."
*ACS Applied Materials & Interfaces*. PNNL-SA-160595. - Drgona J., E. Skomski, S.S. Vasisht, D.L. Vrabie, and A.R. Tuor. 2021. "Stability Analysis of Deep Neural Dynamical Systems." In Workshop on Machine Learning in Control. PNNL-SA-160834
- Tuor A.R. M. Klauco K. Kis J. Drgona and D.L. Vrabie. 2021. “Differentiable Predictive Control: Deep Learning Alternative to Explicit Model Predictive Control for Unknown Nonlinear Systems." Engineering Applications of Artificial Intelligence. PNNL-SA-162137
- Kvinge H.J., C.L. Wight, S.M. Akers, S.A. Howland, W. Choi, X. Ma, and K.S. Kappagantula, et al. 2021. "Dataset to Dataspace: A Topological-Framework to Improve Analysis of Machine Learning Model Performance." In ICML 2021 Workshop on Uncertainty & Robustness in Deep Learning. PNNL-SA-162755
- Emerson T.H., L. Kassab, S.A. Howland, H.J. Kvinge, and K.S. Kappagantula. 2022. "TopTemp: Parsing Precipitate Structure from Temper Topology." In 2022 ICLR Workshop on Geometric and Topological Representation Learning. PNNL-SA-170620
- Coda E.D., N.C. Courts, C.L. Wight, L.T. Truong, W. Choi, C.W. Godfrey, and T.H. Emerson, et al. 2022. "Fiber Bundle Morphisms as a Framework for Modeling Many-to-Many Maps." In ICLR 2022 Workshop on Geometrical and Topological Representation Learning. PNNL-SA-170544
- Wenskovitch J.E., B.A. Jefferson, A.A. Anderson, J.A. Baweja, D.K. Ciesielski, and C. Fallon. 2022. "A Methodology for Evaluating Operator Usage of Machine Learning Recommendations for Power Grid Contingency Analysis." Frontiers in Big Data: Recommender Systems. PNNL-SA-171158
- Knutson C.R., M.S. Bontha, J.A. Bilbrey, and N. Kumar. 2021. "Decoding the Protein-ligand Interactions Using Parallel Graph Neural Networks."
*Nature Machine Intelligence*. PNNL-SA-166075 - Drgona J., A.R. Tuor, V. Chandan, and D.L. Vrabie. 2021. "Physics-constrained Deep Learning of Multi-zone Building Thermal Dynamics."
*Energy and Buildings*243. PNNL-SA-166470 - Wilson B.A., K.R. Duskin, M. Subramanian, R. Goychayev, and A.F. Michel Zuniga. 2021. "Artificial Judgement Assistance from teXt (AJAX)." ESARDA Bulletin – The International Journal of Nuclear Safeguards and Non-proliferation: Special Issue on Data Analytics for Safeguards and Non-Proliferation. PNNL-SA-166914
- Courts N.C., and H.J. Kvinge. 2021. "Bundle Networks: Fiber Bundles, Local Trivializations, and a Generative Approach to Exploring Many-to-one Maps." In
*The Tenth International Conference on Learning Representations*. PNNL-SA-167143· Bontha M.S., A.D. McNaughton, C.R. Knutson, J.A. Bilbrey, and N. Kumar. 2021. "De novo design of target specific scaffold-based inhibitors via reinforcement learning." In*International Conference on Learnin**g Representations (ICLR)*. PNNL-SA-167262 - Visweswara Sathanur A., and M.H. Khan. 2021. "Scalable Approaches to Selecting Key Entities in Large Networked Infrastructure Systems." In
*IEEE International Conference on Big Data*. PNNL-SA-168122 - Truong L.T., W. Choi, C.L. Wight, E.D. Coda, T.H. Emerson, K.S. Kappagantula, and H.J. Kvinge. 2021. "Differential Property Prediction: A Machine Learning Approach to Experimental Design in Advanced Manufacturing." In
*AI for Design and Manufacturing*. PNNL-SA-168212

#### Presented

- Chiang T.Y. 03/31/2022. "Spectral Machine Learning Theory." Seattle, Washington. PNNL-SA-171449
- Vasisht S.S., J. Drgona, A.R. Tuor, and D.L. Vrabie. 03/15/2022. "Domain Aware Deep Learning Transforms Predictive Control." Presented by S.S. Vasisht at Workshop on Responsible and Trustworthy AI in Clean Energy, Online Conference, Washington. PNNL-SA-171134
- Vasisht S.S., D.L. Vrabie, W.E. Shaw Cortez, J. Drgona, and J.F. Strube. 03/23/2022. "Fieldable AI for Robotics?" Abstract submitted to Robotics use in Accelerators, Targets and Detectors, Online Conference, United States. PNNL-SA-170753
- Chiang T.Y., Z. Wang, I. Dumitriu, A.D. Sarwate, and A.W. Engel. 09/26/2022. "Spectral Machine Learning Theory." Abstract submitted to SIAM Mathematics of Data Science 2022, San Diego, California. PNNL-SA-171401
- Drgona J. D.L. Vrabie and A.R. Tuor. 02/24/2020. “Constrained Neural Differential Equations for System Identification and Control.” Presented by A.R. Tuor at IPAM: Intersections Between Optimization Learning and Control, Los Angeles California. PNNL-SA-151405
- Drgona J. A.R. Tuor and D.L. Vrabie. 06/04/2020. “Constrained Physics-Informed Deep Learning for Continuous Control.” Abstract submitted to PNNL TechFest Richland Washington. PNNL-SA-152180
- Drgona J. A.R. Tuor and D.L. Vrabie. 04/10/2020. “Combining Deep Learning and Domain Knowledge for Modeling and Control." Richland Washington. PNNL-SA-152658
- Drgona J. A.R. Tuor and D.L. Vrabie. 04/27/2020. “Stripping off the implementation complexity of physics-based model predictive control for buildings via deep learning: a follow-up." Presented by J. Drgona at ICLR 2020, Online United States. PNNL-SA-153118
- Wilson B.A., R. Goychayev, and K.R. Duskin. 07/14/2020. "July-2020 DOE-DHS Tech Summit AJAX Presentation." Presented by B.A. Wilson, R. Goychayev, K.R. Duskin at July-2020 DOE-DHS Tech Summit, Virtual, Washington. PNNL-SA-154045
- Wight C.L. J. Drgona A.R. Tuor D.H. Bacon and D.L. Vrabie. 07/27/2020. “Physics Informed Learning in Phase-field and Multiphase Flow Simulations." Presented by C.L. Wight at GAMM Juniors' Summer School on Applied Mathematics and Mechanics: Learning Models from Data Online Workshop Germany. PNNL-SA-154715
- Ortiz Marrero C.M. 10/23/2020. "Entanglement Induced Barren Plateaus in Quantum Neural Networks." Presented by C.M. Ortiz Marrero at QHub Seminar, North Carolina State University, North Carolina. PNNL-SA-157004
- Tuor A.R. E. Skomski J. Drgona D.L. Vrabie S.S. Vasisht and C.L. Wight. 10/15/2020. “Constrained Block Nonlinear Neural Dynamical Models." Presented by A.R. Tuor at Western Washington University Technical Talk Series, Online Conference Washington. PNNL-SA-157017
- Vrabie D.L. J. Drgona A.R. Tuor S.S. Vasisht C.L. Wight and S.E. Skomski. 10/14/2020. “Deep Learning for Model Predictive Control." Online Conference Washington. PNNL-SA-157274
- Skomski S.E., S.S. Vasisht, C.L. Wight, J. Drgona, A.R. Tuor, and D.L. Vrabie. 10/23/2020. "Domain Aware Machine Learning for Control Applications." Richland, Washington. PNNL-SA-157723
- Drgona J., A.R. Tuor, and D.L. Vrabie. 12/08/2020. "Combining Deep Learning and Physics for Cutting the Costs of Advanced Building Control." Presented by J. Drgona at Energy Data Analytics Symposium: Transforming Energy Systems with Data Science Techniques, Online Conference, Washington. PNNL-SA-158310
- Ortiz Marrero C.M., N. Wiebe, and M. Kieferova. 12/08/2020. "Entanglement Induced Barren Plateaus." Presented by C.M. Ortiz Marrero at 20th Asian Quantum Information Science Conference, Online Conference, Australia. PNNL-SA-158488
- Knutson C.R. M.S. Bontha J.A. Bilbrey and N. Kumar. 12/17/2019. “Graph-based approach for representing protein-small molecule interactions." Presented by C.R. Knutson at SULI Symposium, Richland Washington. PNNL-SA-158579.
- Knutson C.R. M.S. Bontha J.A. Vrabie D.L. 12/11/2020. "Deep Learning for Model Predictive Control." Online, Michigan. PNNL-SA-158648
- Drgona J. 01/05/2021. "Deep Learning of Dynamics, Dynamics of Deep Learning." Online Conference, United States. PNNL-SA-158921
- Vrabie D.L., A.R. Tuor, and J. Drgona. 01/21/2021. "Deep Learning Digital Twins for Model Predictive Control." Presented by J. Drgona at Artificial Intelligence for Robust Engineering & Science, Online Conference: Oak Ridge National Lab, Washington
- Praggastis B.L., E. Purvine, D.R. Brown, and M.R. Shapiro. 02/12/2021. "MARS DeepDataProfiler Updates." Online, United States. PNNL-SA-159650
- Praggastis B.L., E. Purvine, and E.A. Bishoff. 02/09/2021. "Deep Data Profiler (DDP)." Presented by B.L. Praggastis, E. Purvine, E.A. Bishoff at LLAMA workshop, Online, United States. PNNL-SA-159651
- Drgona J., D.L. Vrabie, S.E. Skomski, S.S. Vasisht, and A.R. Tuor. 02/16/2021. "Differentiable Predictive Control: An MPC Alternative for Unknown Nonlinear Systems using Constrained Deep Learning." Presented by A.R. Tuor at Internal Physics Informed Machine Learning Workshop, Online Conference, Washington
- Drgona J. A.R. Tuor E. Skomski S.S. Vasisht V. Chandan and D.L. Vrabie. 02/01/2021. “Physics-constrained Deep Learning for Modeling and Control of Buildings." Presented by J. Drgona at Invited talk: TU Graz 29th of February 2021 Online Conference Washington. PNNL-SA-160327
- Visweswara Sathanur A., and M.H. Khan. 2021. "Scalable Approaches to Selecting Key Entities in Networked Infrastructure Systems." In SIAM Conference on Applied and Computational Discrete Algorithms. PNNL-SA-160460
- Drgona J., A.R. Tuor, S.S. Vasisht, S.E. Skomski, D.L. Vrabie, and V. Chandan. 03/25/2021. "Constrained Deep Learning for Modeling and Control of Buildings." Presented by J. Drgona at Invited talk: KU Leuven, Belgium, Online, Washington. PNNL-SA-160886
- Drgona J., A.R. Tuor, S.E. Skomski, D.L. Vrabie, and S.S. Vasisht. 08/17/2021. "Constrained Deep Learning for System Identification and Differentiable Predictive Control of Nonlinear Systems." Presented by J. Drgona at ASME 2021 International Design Engineering Technical Conferences and Computers and Information in Engineering, Online, Washington.
- Skomski S.E. S.S. Vasisht C.L. Wight A.R. Tuor J. Drgona and D.L. Vrabie. 05/28/2021. “Constrained Block Nonlinear Neural Dynamical Models." Presented by S.E. Skomski at American Control Conference 2021 Online Conference Louisiana. PNNL-SA-161415
- Vrabie D.L. J. Drgona and A.R. Tuor. 04/20/2021. “Autonomous Control Systems and Learning." Online California. PNNL-SA-161598
- Brown D.R., and B.L. Praggastis. 03/15/2022. "DeepDataProfiler - Viewing Nuclear Forensics Data through the Lens of a DNN." Presented by D.R. Brown, B.L. Praggastis at Artificial Intelligence and Machine Learning for IAEA Safeguards, Online Workshop, Washington. PNNL-SA-170869
- Praggastis B.L., D.R. Brown, E. Purvine, M.R. Shapiro, and B. Wang. 04/23/2021. "DeepDataPorfiler: A Platform and Methodology for the Analysis and Interpretation of Neural Networks." Online, Washington. PNNL-SA-161631
- Ortiz Marrero C.M. 04/23/2021. "Explorations in Quantum Computing." Presented by C.M. Ortiz Marrero at Skidmore College, The Mathematics and Statistics, New York. PNNL-SA-161632
- Drgona J. A.R. Tuor D.L. Vrabie and V. Chandan. 04/26/2021. “Physics-constrained Deep Learning for Energy Efficient Control of Buildings." Presented by J. Drgona at AMLD EPFL 2021 Online Conference Washington. PNNL-SA-161704
- Chatterjee S., D.L. Vrabie, M. Schram, V.A. Adetola, N. Kumar, S. Choudhury, and C.P. Dowling, et al. 04/30/2021. "Reinforcement Learning (RL) Research Needs Workshop." Presented by S. Chatterjee, D.L. Vrabie, M. Schram, V.A. Adetola, N. Kumar, S. Choudhury, C.P. Dowling, A. Bhattacharya, Q. Huang, T. Vu, Z. Hou, J.C. Hardin at Reinforcement Learning (RL) Research Needs Workshop, Zoom, United States. PNNL-SA-161901
- Drgona J. 05/04/2021. “PMML Reading Group Presents Stability Analysis of Neural Dynamics by Jan Drgona." Presented by J. Drgona at PMML Reading Working Group Online/Zoom United States. PNNL-SA-161969."
- Drgona J. S.S. Vasisht E. Skomski V. Chandan D.L. Vrabie and A.R. Tuor. 05/05/2021. “Constrained Deep Learning for Modeling and Control of Unknown Nonlinear Dynamical Systems." Presented by J. Drgona at Mitsubishi Electric, Online Washington. PNNL-SA-162032
- Drgona J., V. Chandan, D.L. Vrabie, S.E. Skomski, A.R. Tuor, and S.S. Vasisht. 05/20/2021. "Constrained Physics-Informed Deep Learning for Stable System Identification and Continuous Control." Presented by J. Drgona at Western Washington Data-driven Discovery Seminar Series, Online, Washington. PNNL-SA-162308
- Skomski S.E., A.R. Tuor, and J. Drgona. 06/07/2021. "Automating Discovery of Physics-Informed Neural State Space Models via Learning and Evolution." Presented by S.E. Skomski at Learning for Dynamics and Control (L4DC) 2021, Online Conference, Switzerland. PNNL-SA-162392
- Drgona J., E. Skomski, S.S. Vasisht, D.L. Vrabie, and A.R. Tuor. 05/25/2021. "Stability Analysis of Deep Neural Dynamical Systems." Presented by J. Drgona at LEAC 2021, Online, Washington. PNNL-SA-162568
- Vrabie D.L., J. Drgona, A.R. Tuor, S.S. Vasisht, V. Chandan, and S.E. Skomski. 05/18/2021. "Differentiable Predictive Control: An MPC Alternative for Unknown Nonlinear Systems using Constrained Deep Learning." Online Conference, Denmark. PNNL-SA-162896
- Du Y., S. Chatterjee, and A. Bhattacharya. 06/24/2021. "Reinforcement Learning for Risk-Based Robust Cyber-Physical System Control." Presented by S. Chatterjee at 89th Military Operations Research Society Symposium, Virtual, United States. PNNL-SA-162898
- Praggastis B.L., E. Purvine, D.R. Brown, M.R. Shapiro, and B. Wang. 06/09/2021. "Deep Data Profiler (DDP)." Presented by B.L. Praggastis, E. Purvine at MARS All Hands Business Meeting, Seattle, Washington. PNNL-SA-163169
- Skomski S.E., S.S. Vasisht, D.L. Vrabie, J. Drgona, A.R. Tuor, and V. Chandan. 06/17/2021. "Physics Constrained Deep Learning for Modeling and Control of Buildings." Presented by J. Drgona at Invited Talk: Sidewalk Labs, Online Conference, Washington. PNNL-SA-163195
- Ortiz Marrero C.M. 07/05/2021. "Entanglement Induced Barren Plateaus." Presented by C.M. Ortiz Marrero at 16th Conference on the Theory of Quantum Computation, Communication and Cryptography, Online Conference, North Carolina. PNNL-SA-163233
- Drgona J., A.R. Tuor, E. Skomski, D.L. Vrabie, and S.S. Vasisht. 08/17/2021. "Constrained Deep Learning for System Identification and Differentiable Predictive Control of Nonlinear Systems." Presented by J. Drgona at International Design Engineering Technical Conferences & Computers and Information in Engineering Conference 2021, Online Conference, Washington. PNNL-SA-163249
- Drgona J., A.R. Tuor, S.S. Vasisht, S.E. Skomski, and D.L. Vrabie. 06/17/2021. "Constrained Deep Learning for System Identification and Differentiable Predictive Control of Nonlinear Systems." Presented by J. Drgona at Invited talk: IMT Lucca, Online Conference, Washington. PNNL-SA-163250
- Drgona J., A.R. Tuor, S.E. Skomski, S.S. Vasisht, and D.L. Vrabie. 07/14/2021. "Deep Learning Explicit Differentiable Predictive Control Laws for Buildings." Presented by J. Drgona at IFAC NMPC July 11-14, 2021, Online Conference, Slovakia (Slovak Republic). PNNL-SA-163686
- Ortiz Marrero C.M. 07/07/2021. "Explorations in Quantum Computing." Presented by C.M. Ortiz Marrero at LAS WRM seminar, North Carolina State University, North Carolina. PNNL-SA-163807
- Kvinge H.J., C.L. Wight, S.M. Akers, S.A. Howland, W. Choi, X. Ma, and L.J. Gosink, et al. 07/23/2021. "Dataset to Dataspace: A Topological-Framework to Improve Analysis of Machine Learning Model Performance." Virtual, Austria. PNNL-SA-163934
- Vrabie D.L., J. Drgona, A.R. Tuor, and S.E. Skomski. 07/23/2021. "Differentiable Predictive Control." Online Conference, United States. PNNL-SA-164535
- Vrabie D.L., J. Drgona, A.R. Tuor, S.E. Skomski, and S.S. Vasisht. 07/23/2021. "Differentiable Predictive Control." Online Conference, United States. PNNL-SA-164554
- Anderson A.A., and B.A. Jefferson. 08/25/2021. "Human-Machine Teaming in Power System Operations." Online, Washington. PNNL-SA-165882
- Emerson T.H., K.M. Loew, S.A. Howland, H.J. Kvinge, K.S. Kappagantula, L.J. Gosink, and N.R. Overman, et al. 04/04/2022. "Generating Realistic Material Microstructures Using Conditional GANs for Advanced Manufacturing." Abstract submitted to Artificial Intelligence in Materials and Manufacturing, Pittsburgh, Pennsylvania.
- Wight C.L., S.M. Akers, W. Choi, T.H. Emerson, L.J. Gosink, E.R. Jurrus, and K.S. Kappagantula, et al. 04/01/2022. "DeepTemp: Predicting Material Processing Conditions with Artificial Intelligence." Presented by C.L. Wight at Artificial Intelligence in Materials and Manufacturing 2022, Pittsburgh, Pennsylvania. PNNL-SA-171530
- Drgona J., S.E. Skomski, S.S. Vasisht, A.R. Tuor, and D.L. Vrabie. 09/08/2021. "Data Science Challenges and Opportunities in Building Energy Automation." Presented by J. Drgona at IEEE SERVICES 2021, Online Conference, United States. PNNL-SA-166340
- Kumar N. 12/01/2021. "Predicting Properties of Metabolic Reactions Using Quantum Mechanics." Virtual, Washington. PNNL-SA-168445
- Visweswara Sathanur A. 12/17/2021. "Scalable Approaches to Selecting Key Entities in Networked Infrastructure Systems." Presented by A. Visweswara Sathanur at IEEE Big Data Conference 2021, Online, Washington. PNNL-SA-168734
- Courts N.C., and H.J. Kvinge. 12/09/2021. "Bundle Networks: Fiber Bundles, Local Trivializations, and a Generative Approach to Exploring Many-to-one Maps." Virtual, Colorado. PNNL-SA-168890.
- Tipireddy R., S. Chatterjee, and N. Sharma. 07/25/2021. "Reinforcement Learning-Driven Adaptive Mesh Refinement for Second-Order Elliptic Boundary Value Problems." Abstract submitted to 16th U.S. National Congress on Computational Mechanics, Chicago, Illinois. PNNL-SA-159625
- Wilson B.A., K.R. Duskin, R. Goychayev, M. Subramanian, and A.F. Michel Zuniga. 01/20/2022. "Artificial Judgement Assistance from teXt (AJAX): Applying Open Domain Question Answering to Nuclear Non-proliferation Analysis." Presented by M. Subramanian, A.F. Michel Zuniga at UW eScience Institute Data Science Seminar, Online Conference, Washington. PNNL-SA-169596
- Chiang T.Y., J.E. Flores, A.W. Engel, R.T. Cannon, J. Irvahn, and A.D. Sarwate. 12/06/2021. "SIGNAL-Briefing-061221." Seattle, Washington. PNNL-SA-169376
- Visweswara Sathanur A., A. Dutta, M. Jain, and M.H. Khan. 05/11/2022. "A Virtual Testbed for the Development of AI Solutions to Boost Operational Efficiency in Road Transportation Networks." Online Conference, Washington. PNNL-SA-172513.
- Vasisht S.S., W.E. Shaw Cortez, J. Drgona, A.R. Tuor, and D.L. Vrabie. 06/09/2022. "Domain-aware AI for Robotics." Richland, Washington. PNNL-SA-173969
- Subramanian M., A.F. Michel Zuniga, and B.A. Wilson. 06/17/2022. "Artificial Judgment Assistance from teXt (AJAX)." Presented by M. Subramanian at CSIS PONI Mid-Career Cadre - FlashTalks, PNNL, Friday June 17th, Online Conference, Washington. PNNL-SA-174028