U.S. Department of Energy

Pacific Northwest National Laboratory

SDI Publications

2016

A path towards uncertainty assignment in an operational could phase algorithm from ARM vertically pointing active sensors

Riihimaki LD, JM Comstock, KK Anderson, A Holmes, and E Luke. 2016. "A Path Towards Uncertainty Assignment in an Operational Cloud-Phase Algorithm from Arm Vertically Pointing Active Sensors." Adv. Stat. Clim. Meteorol. Oceanogr. 2(1):49-62. 10.5194/ascmo-2-49-2016.

2015

Standoff human identification using body shape

Matzner et al., 2015] Matzner, S., Heredia-Langner, A., Amidan, B., Boettcher, E., Lochtefeld, D., and Webb, T. (2015). Standoff human identification using body shape. In Technologies for Homeland Security (HST), 2015 IEEE International Symposium on, pages 1–6. http://dx.doi.org/10.1109/THS.2015.7225300 

Behavior Models as a Language to Express and Share Threat Information

Oehmen CS, ES Peterson, and A Cox.  2015.  "Behavior Models as a Language to Express and Share Threat Information."  PNNL-SA-110938, Pacific Northwest National Laboratory, Richland, WA. 

Comparative hazard analysis and predictive modeling of diverse nanomaterials using the embryonic zebrafish (EZ) metric of toxicity

Harper B, DG Thomas, S Chikkagoudar, NA Baker, K Tang, A Heredia-Langner, RD Lins, and S Harper.  2015.  "Comparative hazard analysis and predictive modeling of diverse nanomaterials using the embryonic zebrafish (EZ) metric of toxicity."  Nanotoxicology.  doi:10.1007/s11051-015-3051-0

A Stochastic Regression Based Approach for Improved Approximation of Graph Edit Distance

Best DM, PS Mackey, and SM Libby.  2015.  "A Stochastic Regression Based Approach for Improved Approximation of Graph Edit Distance."  PNNL-SA-110679, Pacific Northwest National Laboratory, Richland, WA. 

Review, Evaluation, and Discussion of the Challenges of Missing Value Imputation for Mass Spectrometry-Based Label-Free Global Proteomics

Webb-Robertson BJM, HK Wiberg, MM Matzke, JN Brown, J Wang, JE McDermott, RD Smith, KD Rodland, TO Metz, JG Pounds, and KM Waters.  2015.  "Review, Evaluation, and Discussion of the Challenges of Missing Value Imputation for Mass Spectrometry-Based Label-Free Global Proteomics."  Journal of Proteome Research 14(5):1993-2001.  doi:10.1021/pr501138h

2014

Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements

Webb-Robertson BJ, Matzke MM, Datta S, Payne SH, Kang J, Nicora CD, Shukla AK, Metz TO, Rodland KD, Smith RD, Tardiff MF, McDermott JE, Pounds JG, Waters KM. 2014. Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements. Molecular and Cellular Proteomics. 10.1074/mcp.O113.030932.

Discerning Viable from Nonviable Yersinia pestis pgm- and Bacillus anthracis Sterne using Propidium Monoazide in the Presence of White Powders

Hess BM, BLD Kaiser, MA Sydor, DS Wunschel, CJ Bruckner-Lea, and JR Hutchison.  2014.  "Discerning Viable from Nonviable Yersinia pestis pgm- and Bacillus anthracis Sterne using Propidium Monoazide in the Presence of White Powders."  PNNL-SA-107253, Pacific Northwest National Laboratory, Richland, WA.

The human is the loop: new directions for visual analytics

Endert A, MS Hossain, N Ramakrishnan, C North, P Fiaux, and C Andrews. 2014. The human is the loop: new directions for visual analytics. Journal of Intelligent Information Systems, 43(3), 411–435. doi:10.1007/s10844-014-0304-9

Optimization of an individual re-identification modeling process using biometric features

Heredia-Langner A, BG Amidan, S Matzner, and KH Jarman. 2014. Optimization of an individual re-identification modeling process using biometric features. In Proc DMIN’14. http://worldcomp-proceedings.com/proc/p2014/DMI.html

Signatures of Illicit Nuclear Procurement Networks: An Overview of Preliminary Approaches & Results

Webster JB, ZN Gastelum, DM Best, S Chikkagoudar, EA Hogan, VA Lewis, and JR Schweighardt.  2014.  "Signatures of Illicit Nuclear Procurement Networks: An Overview of Preliminary Approaches & Results."  Presented by Jennifer B. Webster (Invited Speaker) at Presentation to be given to SDI Mentor and his technical editors, Fort Meade, MD on May 23, 2014.  PNNL-SA-102882

Machine Learning and Compressive Sensing for Electron Microscopy

Stevens AJ.  2014.  "Machine Learning and Compressive Sensing for Electron Microscopy."  Abstract submitted to Imaging and Modeling in Electron Microscopy - Recent Advances, Banff, AB, Canada.  PNNL-SA-102375

Signatures of Illicit Nuclear Procurement Networks: An Overview of Preliminary Approaches & Results

Webster JB, LE Erikson, ZN Gastelum, V Lewis, DM Best, EA Hogan, and S Chikkagoudar. 2014."Signatures of Illicit Nuclear Procurement Networks: An Overview of Preliminary Approaches & Results." In INMM Information Analysis Technologies, Techniques and Methods for Safeguards, Nonproliferation and Arms Control Verification Workshop. PNNL-SA-102660, Pacific Northwest National Laboratory, Richland, WA. Proceeds available at https://www.inmm.org/.

Strategic Goods Testbed: A Data Library for Illicit Nuclear Trafficking

Webster JB, LE Erikson, C Toomey, and VA Lewis. 2014. PNNL Strategic Goods Testbed: A Data Library for Illicit Nuclear Trafficking. PNNL-SA-102611, Pacific Northwest National Laboratory, Richland, WA.

Optimizing Detection of RDX Vapors Using Designed Experiments for Remote Sensing.

Ewing RG, A Heredia-Langner, and MG Warner. 2014. "Optimizing Detection of RDX Vapors Using Designed Experiments for Remote Sensing." Analyst 139:2440-2448. doi: 10.1039/c4an00125g

Forensic signature detection of Yersinia pestis culturing practices across institutions using a Bayesian Network

Webb-Robertson BJ, CD Corley, LA McCue, BH Clowers, CP Dowling, KL Wahl, DS Wunshel and HW Kreuzer. 2014. Forensic signature detection of Yersinia pestis culturing practices across institutions using a Bayesian Network. Journal of Forensic Investigation, 2(1): 7.

Physicochemical Signatures of Nanoparticle-Dependent Complement Activation

Thomas DG, S Chikkagoudar, A Heredia-Langner, MF Tardiff, Z Xu, DE Hourcade, CTN Pham, GM Lanza, KQ Weinberger, and NA Baker. 2014. "Physicochemical Signatures of Nanoparticle-Dependent Complement Activation." Computational Science & Discovery 7:e015003. doi: 10.1088/1749-4699/7/1/015003

Signatures for Mass Spectrometry Data Quality

Amidan BG, DJ Orton, BL LaMarche, ME Monroe, RJ Moore, AM Venzin, DJ Smith, LH Sego, MF Tardiff, and SH Payne. 2014. Signatures for Mass Spectrometry Data Quality.  Journal of Proteome Research. 13(4), 2215-2222. dx.doi.org/10.1021/pr401143e

The Potential for Bayesian Compressive Sensing to Significantly Reduce Electron Dose in High-Resolution STEM Images

Stevens A, H Yang, L Carin, I Arslan, and ND Browning. 2014. "The Potential for Bayesian Compressive Sensing to Significantly Reduce Electron Dose in High-Resolution STEM Images." Microscopy 63(1):41-51. doi: 10.1093/jmicro/dft042

2013

A Decision Theoretic Approach to Evaluate Radiation Detection Algorithms

Nobles MA, LH Sego, SK Cooley, LJ Gosink, RM Anderson, SE Hays, and MF Tardiff. 2013. "A Decision Theoretic Approach to Evaluate Radiation Detection Algorithms". Proceedings of the 2013 IEEE International Conference on Technologies for Homeland Security. 683-686, November 12-14, 2013, pp. 683-686. Waltham, Massachusetts. doi: 10.1109/THS.2013.6699086

Assessing Performance and Tradeoffs of Bioforensic Signature Analysis

Watkins DM, LH Sego, AE Holmes, BM Webb-Robertson, AM White, DS Wunschel, HW Kreuzer, CD Corley, and MF Tardiff. 2013. "Assessing Performance and Tradeoffs of Bioforensic Signature Analysis." Proceedings of the 2013 IEEE International Conference on Technologies for Homeland Security. November 12-14, 2013, pp. 304-309. Waltham, Massachusetts. 

Domain-Specific Languages For Developing and Deploying Signature Discovery Workflows

Jacob F, AS Wynne, Y Liu, and J Gray.  2013.  "Domain-Specific Languages For Developing and Deploying Signature Discovery Workflows."  Computing in Science & Engineering 16(1):52-64. 

 

Order Theoretical Semantic Recommendation

Joslyn CA, E Hogan, P Paulson, E Peterson, E Stephan, and D Thomas. 2013. "Order Theoretical Semantic Recommendation", 2nd International Workshop on Ordering and Reasoning (OrdRing 2013).  

Ontology Metrics for Semantic Recommendation in Scientific Workflows

Joslyn CA, EA Hogan, PR Paulson, ES Peterson, EG Stephan, and DG Thomas. 2013. "Ontology Metrics for Semantic Recommendation in Scientific Workflows." In The 12th International Semantic Web Conference (ISWC 2013), 21-25 October 2013, Sydney, Australia.

Direct Real-Time Detection of Vapors from Explosive Compounds

Ewing RG, BH Clowers, and DA Atkinson.  2013.  "Direct Real-Time Detection of Vapors from Explosive Compounds."  Analytical Chemistry 85(22):10977-10983.  doi:10.1021/ac402513r

Trelliscope: A System for Detailed Visualization in the Deep Analysis of Large Complex Data

Hafen RP, LJ Gosink, WS Cleveland, JE McDermott, KD Rodland, and K Kleese van Dam. 2013. "Trelliscope: A System for Detailed Visualization in the Deep Analysis of Large Complex Data." In IEEE Symposium on Large-Scale Data Analysis and Visualization (LDAV 2013) , October 13-14, Atlanta, Georgia. doi:10.1109/LDAV.2013.6675164

Applications of Dictionary Learning

Stevens AJ.  2013.  "Applications of Dictionary Learning."  Presented by Andrew Stevens (Invited Speaker) at University of Utah SCI Institute Seminar Talk, Richland, WA on September 19, 2013.  PNNL-SA-98401.

A Semi-automated Framework for Integrating Expert Knowledge into Disease Marker Identification

Wang J, BJM Webb-Robertson, MM Matzke, SM Varnum, JN Brown, RM Riensche, JN Adkins, JM Jacobs, JR Hoidal, MB Scholand, JG Pounds, MR Blackburn, KD Rodland, and JE McDermott. 2013. "A Semi-automated Framework for Integrating Expert Knowledge into Disease Marker Identification." Disease Markers. 5(5): 513-523. doi:10.1155/2013/613529.

Novel Visual and Analytical Methods in Repurposing Legacy Scientific Code - A Case Study

Oehmen CS, DS Curtis, AR Phillips, and ES Peterson. 2013. "Novel Visual and Analytical Methods in Repurposing Legacy Scientific Code - A Case Study." In Proc 2013 Intl Conf Software Eng Res Practice (SERP 2013).

Genetic Algorithms and Classification Trees in Feature Discovery: Diabetes and the NHANES database

Heredia-Langner A, KH Jarman, BG Amidan, and JG Pounds. 2013. "Genetic Algorithms and Classification Trees in Feature Discovery: Diabetes and the NHANES database." In The 9th International Conference on Data Mining (DMIN’13), a joint conference with 2013 World Congress in Computer Science, Computer Engineering, and Applied Computing (WORLDCOMP'13) , July 22-25, 2013, Las Vegas, Nevada.

Beyond Control Panels: Direct Manipulation for Visual Analytics

Endert A, L Bradel, and C North. 2013. "Beyond Control Panels: Direct Manipulation for Visual Analytics." IEEE Computer Graphics and Applications 33(4):6-13. doi: 10.1109/MCG.2013.53.

Bayesian Model Development for Analysis of Open Source Information to Support the Assessment of Nuclear Programs

Gastelum ZN, PD Whitney, and AM White. 2013. "Bayesian Model Development for Analysis of Open Source Information to Support the Assessment of Nuclear Programs." In Proceedings of the Institute of Nuclear Materials Management Annual Meeting, July 14-18, 2013, Palm Desert, California.

Model Identification for Optimal Diesel Emissions Control

Stevens AJ, Y Sun, X Song, and G Parker. 2013. "Model Identification for Optimal Diesel Emissions Control." In JMLR Workshop and Conference Proceedings, Volume 28: Proceedings of the 30th International Conference on Machine Learning (ICML2013), June 16-21, 2013, Atlanta, Georgia.

Research towards a systematic signature discovery process

Baker NA, JL Barr, GT Bonheyo, CA Joslyn, K Krishnaswami, M Oxley, RW Quadrel, LH Sego, MF Tardiff, and AS Wynne. 2013. "Research towards a systematic signature discovery process." In IEEE International Conference on Intelligence and Security Informatics (ISI) , June 4-7, 2013, Seattle, Washington, pp. 301-308. Institute of Electrical and Electronics Engineers, Piscataway, NJ. doi: 10.1109/ISI.2013.6578848

A Generalized Bio-inspired Method for Discovering Sequence-based Signatures

Peterson ES, DS Curtis, AR Phillips, JR Teuton, and CS Oehmen. 2013. "A Generalized Bio-inspired Method for Discovering Sequence-based Signatures." In IEEE International Conference on Intelligence and Security Informatics (ISI), June 4-7, 2013, Seattle, Washington, pp. 330-332. Institute of Electrical and Electronics Engineers, Piscataway, NJ. doi: 10.1109/ISI.2013.6578853.

A Graph Analytic Metric for Mitigating Advanced Persistent Threat

Johnson JR, III, and EA Hogan.  2013.  "A Graph Analytic Metric for Mitigating Advanced Persistent Threat."  In IEEE International Conference on Intelligence and Security Informatics (ISI 2013), June 4-7, 2013, Seattle, Washington, pp. 129-133.  IEEE, Piscataway, NJ. doi: 10.1109/ISI.2013.6578801

Assessing the Quality of Bioforensic Signatures

Sego LH, AE Holmes, LJ Gosink, BJM Webb-Robertson, HW Kreuzer, RM Anderson, AJ Brothers, CD Corley, and MF Tardiff. 2013. "Assessing the Quality of Bioforensic Signatures." In IEEE International Conference on Intelligence and Security Informatics (ISI) , June 4-7, 2013, Seattle, Washington, pp. 346-351. doi: 10.1109/ISI.2013.6578856

Graph Analytics for Signature Discovery

Hogan EA, JR Johnson, III, M Halappanavar, and C Lo. 2013. "Graph Analytics for Signature Discovery." In IEEE International Conference on Intelligence and Security Informatics (ISI) , June 4-7, 2013, Seattle, Washington, pp. 315-320. Institute of Electrical and Electronics Engineers, Piscataway, NJ. doi:10.1109/ISI.2013.6578850.

The Lifecycle of Bayesian Network Models Developed for Multi-Source Signature Assessment of Nuclear Programs

Gastelum ZN, AM White, PD Whitney, LJ Gosink, and LH Sego. 2013. "The Lifecycle of Bayesian Network Models Developed for Multi-Source Signature Assessment of Nuclear Programs." ." In IEEE International Conference on Intelligence and Security Informatics (ISI) , June 4-7, 2013, Seattle, Washington, pp. 339-345. Institute of Electrical and Electronics Engineers, Piscataway, NJ. doi: 10.1109/ISI.2013.6578855.

Structured Random Nonnegative Matrix Factorization

Stevens, AJ. Structured Random Nonnegative Matrix Factorization. 2013. Presented by Andrew Stevens at International Conference on Machine Learning Workshop on Spectral Learning, Atlanta, GA on June 21, 2013.  PNNL-SA-96120

Reducing Dose in STEM Images with Bayesian Diction

Stevens AJ, H Yang,  L Carin, I Arslan, and ND Browning. 2013. "Reducing Dose in STEM Images with Bayesian Diction." Presented at the Advances in Structural Chemical Imaging Conference.

LINEBACkER: Bio-inspired Data Reduction Toward Real Time Network Traffic Anomaly Detection.” In 1st International Symposium on Resilient Cyber Systems

Teuton JR, ES Peterson, DJ Nordwall, BA Akyol, and CS Oehmen. 2013. "LINEBACkER: Bio-inspired Data Reduction Toward Real Time Network Traffic Anomaly Detection." In 1st International Symposium on Resilient Cyber Systems. PNNL-SA-95878. doi: 10.1109/ISRCS.2013.6623771                 

Posteriori Ontology Engineering for Data-Driven Science

Gessler DDG, CA Joslyn, and  KM Verspoor. 2013. "A Posteriori Ontology Engineering for Data-Driven Science", in Data Intensive Science, ed. K Kleese-van Dam, T Critchlow, pp. 215-244, CRC Press.

Structured Random Non-negative Matrix Factorization

Stevens AJ. 2013. "Structured Random Non-negative Matrix Factorization." International Conference on Machine Learning workshop on Spectral Learning. PNNL-SA-94560.

PCA for complex multivariate datasets with non-random missing values

Webb-Robertson BJ, MM Matzke, TO Metz, JE McDermott, KD Rodland, JG Pounds, and KM Waters. 2013. PCA for complex multivariate datasets with non-random missing values. BioTechniques 54(3):165-8.

Parameter Selection for Practical Sparse Coding

May CJ, AJ Stevens, Y Sun, and N Beagley. 2013. "Parameter Selection for Practical Sparse Coding." IEEE Transactions on Evolutionary Computation. PNNL-SA-94075.

An Approach for Assessing the Signature Quality of Various Chemical Assays when Predicting the Culture Media Used to Grow Microorganisms

Holmes AE, LH Sego, BJM Webb-Robertson, HW Kreuzer, RM Anderson, SD Unwin, MR Weimar, MF Tardiff, and CD Corley. 2013. An Approach for Assessing the Signature Quality of Various Chemical Assays when Predicting the Culture Media Used to Grow Microorganisms. PNNL-22126, Pacific Northwest National Laboratory, Richland, WA.

ScalaBLAST 2.0: Rapid and robust BLAST calculations on multiprocessor systems

Oehmen CS, and DJ Baxter. 2013. "ScalaBLAST 2.0: Rapid and robust BLAST calculations on multiprocessor systems." Bioinformatics 29(6):797-8. doi:10.1093/bioinformatics/btt013

Fusion of laboratory and textual data for investigative bioforensics

Webb-Robertson, BJ, C Corley, LA McCue, K Wahl and HW Kreuzer. 2013. "Fusion of laboratory and textual data for investigative bioforensics." Forensic Science International, 226(1): 118-124. http://dx.doi.org/10.1016/j.forsciint.2012.12.016

Graph Coarsening for Path Finding in Cybersecurity Graphs

Hogan EA, JR Johnson, III, and M Halappanavar. 2013. "Graph Coarsening for Path Finding in Cybersecurity Graphs." In Proceedings of the Eighth Annual Cyber Security and Information Intelligence Research Workshop (CSIIRW’13), January 8-10, Oak Ridge, Tennessee, Article No. 7. Association for Computing Machinery, New York, NY. doi:10.1145/2459976.2459984.

Pages

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