Citations of Scholarly Work—Division of Computing & Software Systems

Refereed Journal Articles

* indicates student-faculty research. Students in bold, faculty underlined  

  • C. Leonie(*), R. Angotti, and K. Sung, ”CourseExpo: An Immersive Collaborative Learning Ecosystem,” in  ACM Symposium on Virtual Reality Software and Technology (VRST 2022), Tsukuba, Japan, p. 1-2, Nov 2022. Available: https://doi.org/10.1145/3562939.3565646       Sung, K. (2022).  
  • J. Sung, K. Sung, “Integrating Videogames Development and Software Engineering in a College Senior Elective Course,” 14th Annual International Conference on Education and New Learning Technologies (EduLearn 2022), p. 4338-4345, July 2022. Available: http://dx.doi.org/10.21125/edulearn.2022.1035.    Sung, K. (2022). 
  • J. Chesnut(*) , K. Sung, “Interactable Topographical Map with Remote Cross Reality Collaboration Support,” IEEE International Conference on Computational Intelligence & Virtual Environments for Measurement Systems and Applications (CIVEMSA), p. 1-5, June 2022. Available: http://dx.doi.org/10.1109/CIVEMSA53371.2022.9853708.   Sung, K. (2022). 
  • Nostalgic Analysis of Location Based Tweets Gao, L., Hong, L., Mashhadi, A. (2022, October). In Proceedings of 13th International Conference of Social Informatics, SocInfo 2022, Glasgow, UK, October 19–21, 2022. (SocInfo22) Mashadi, A. (2022). 
  • Impact of Exogenous Biases of Instagram Posts on Park Visitation Estimation. Mashhadi, Afra, Sana Suse, Susan Ammiri, and Spencer Wood. In Proceedings of the 33rd ACM Conference on Hypertext and Social Media, pp. 203-208. 2022.(Hypertext22) Mashadi, A. (2022). 
  • Causal Impact Model to Evaluate the Diffusion Effect of Social Media Campaigns. Yu, X., Mashhadi, A., Boy, J., Nielsen, R. C., Hong, L. (2022). In Proceedings of 20th European Conference on Computer Supported Cooperative Work. European Society for Socially Embedded Technologies (EUSSET22). Mashadi, A. (2022). 
  • Multi-task Models for Multi-faceted Classification of Pandemic Information on Social Media. Yu, X., Xie, Z., Mashhadi, A., Hong, L. (2022, June). In 14th ACM Web Science Conference 2022 (pp. 327-335). (WebSci2022) Mashadi, A. (2022). 
  • A Case Study of Integrating Fairness Visualization Tools in Machine Learning Education. Jay Quedado, Anouska Zolyomi and Afra Mashhadi. In proceedings of the ACM CHI Conference on Human Factors in Computing Systems. (CHI2022). Mashadi, A. (2022). 
  • Y. Jia, N. McMichael, P. Mokarzel, B. Thompson, D. Si, and T. Humphries*, “Superiorization-inspired unrolled SART algorithm with U-Net generated perturbations for sparse-view and limited-angle CT reconstruction”, Physics in Medicine and Biology, 2022 Phys. Med. Biol. 67 245004 DOI: https://doi.org/10.1088/1361-6560/aca513. (Impact Factor 4.17) Si, D. (2022) 
  • N. Ranno, D. Si*, “Neural Representations of Cryo-EM Maps and a Graph-Based Interpretation”, BMC Bioinformatics 23 (Suppl 3), 397 (2022). https://doi.org/10.1186/s12859-022-04942-1. (Impact Factor 3.17) Si, D. (2022) 
  • F. Wang, C. H. Chan, V. Suciu, K. Mustafa, D. Si, A. Hochbaum, E. H. Egelman*, D. Bond, “Structure of Geobacter OmcZ filaments suggests extracellular cytochrome polymers evolved independently multiple times”, eLife 11:e81551. https://doi.org/10.7554/eLife.81551. (Impact Factor 8.71) Si, D. (2022) 
  • L. Chang, F. Wang*, K. Connolly, H. Meng, Z. Su, V. Cvirkaite-Krupovic, M. Krupovic, E. H. Egelman*, D. Si*, “DeepTracer-ID: De novo protein identification from cryo-EM maps”, Biophysical Journal – Cell Press, 2022, https://doi.org/10.1016/j.bpj.2022.06.025. (Impact Factor 4.03) Si, D. (2022) 
  • F. Wang, K. Mustafa, V. Suciu, K. Joshi, C.H. Chan, Z. Su, D. Si, A. I. Hochbaum*, E. H. Egelman*, D. R. Bond*. “Cryo-EM structure of an extracellular Geobacter OmcE cytochrome filament reveals tetrahaem packing”. Nature Microbiology, 2022 Jul 7. doi: 10.1038/s41564-022-01159-z. (Impact Factor 17.75) Si, D. (2022) 
  • Jeffy Jahfar Poozhithara, Hazeline U. Asuncion, Brent Lagesse. Keyword Extraction from Specification Documents for Planning Security Mechanisms. In the International Conference on Software Engineering (ICSE) 2023, to appear, 26% acceptance rate. Asuncion, H. (2022).  
  • Jeffy Jahfar Poozhithara, Hazeline U. Asuncion, Brent Lagesse. Towards Lightweight Detection of Design Patterns in Source Code. In the 34th International Conference on Software Engineering & Knowledge Engineering (SEKE). June 2022. Asuncion, H. (2022).  
  • Jeffy Jahfar Poozhithara, Hazeline Asuncion, and Brent Lagesse. Keyword Extraction From Specification Documents for Planning Security Mechanisms, IEEE/ACM International Conference on Software Engineering (ICSE), 2023. Lagesse, B. (2022).  
  • Vidushi Ojha, Christopher Perdriau, Brent Lagesse and Colleen M Lewis. Computing Specializations: Perceptions of AI and Cybersecurity Among CS Students, Technical Symposium on Computer Science Education (SIGCSE), 2023. Lagesse, B. (2022). 
  • Jeffy Jahfar Poozhithara, Hazeline Asuncion and Brent Lagesse. Towards Lightweight Detection of Design Patterns in Source Code, International Conference on Software Engineering and Knowledge Engineering (SEKE), 2022. Lagesse, B. (2022). 
  • Brent Lagesse, Shuoqi Wang, Timothy V. Larson, and Amy A. Kim. Performing Indoor PM2.5 Prediction with Low-cost Data and Machine Learning. Facilities Journal, 2022. Lagesse, B. (2022). 
  • Carl Mofjeld∗ , Yang Peng, and Hua Qin “A Joint Request Routing and Model Adaptation Scheme for Adaptive Acceleration of Inference Services at the Network Edge,” under Major Revision, Elsevier Pervasive and Mobile Computing, 2022 Peng, Y. (2022). 
  • Meenakshi Sethunath∗ and Yang Peng “A Joint Function Warm-up and Request Routing Scheme for Performing Confident Serverless Computing,” in Elsevier High-Confidence Computing, vol. 2, no. 3, pp. 100071, 2022. Peng, Y. (2022). 

Conference Presentations/Proceedings

* indicates student-faculty research. Students in bold, faculty underlined  

  • Vishnu Mohan, Anirduh Potturi, Munehiro Fukuda Automated Agent Migration over Distributed Data Structures In Proc. of the 15th International Conference on Agents and Artificial Intelligence pages 363-371, February 2023 Fukuda, M. (2022). 
  • Yang Hon, Munehiro Fukuda Pipelining Graph Construction and Agent-based Computation over Distributed Memory Ninth Int’l Workshop on Big Graphs at IEEE BigData’22, pages 4616-4624, December 2022 17. Daniel Blashaw, Munehiro Fukuda An Interactive E. Fukuda, M. (2022). 
  •  Sana Suse and Clark F. Olson. Classifying Urban Regions in Satellite Imagery Using the Bag of Words Methodology. Submitted for publication Olson, C. (2022). 
  • Hofman, D.C., P. Franks, M. Stiber, C. Rogers, and B. Hamidzadeh, “Panel Discussion: Time to Join ‘AAA’: Are you an AI-Aware Archivist?”, ARCHIVES*RECORDS 2022, Boston, MA, August 25–27, 2022. Stiber, M. (2022) 
  • Martinez Jordan, J.*, V. Salvatore *, B. Endicott-Popovsky, V. Gandhi *, C. O’Keefe *, M.S. Sotebeer, and M. Stiber, “Graph-Based Simulation of Emergency Services Communications Systems”, 2022 Annual Modeling and Simulation Conference, San Diego, CA, July 18–21, 2022. Stiber, M. (2022) 
  • Frontoni, E., M. Paolanti, T.P. Lauriault, M. Stiber, L. Duranti, and M. Abdul-Mageed, “Trusted Data Forever: Is AI the Answer?”, Workshop Proceedings of the EDBT/ICDT 2022 Joint Conference, Edinburgh, UK, March 29–April 1, 2022. Stiber, M. (2022) 
  • H. Guan, D. Si*, “DeepTracer-Denoising: Deep Learning for 3D Electron Density Map Denoising”, 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Las Vegas, NV, USA, 2022, pp. 2080-2087, doi: 10.1109/BIBM55620.2022.9994879. IEEE BIBM 2022 Student Travel Award Si, D. (2022).  
  • J. Lee, S. Kopelovich, S. Cheng, and D. Si*, “Psychosis iREACH: Reach for Psychosis Treatment using Artificial Intelligence”, 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Las Vegas, NV, USA, 2022, pp. 2913-2920, doi: 10.1109/BIBM55620.2022.9995430. Si, D. (2022). 
  • M. Rahbar, R. K. Chauhan, P. N. Shah, R. Cao, D. Si, J. Hou*, “Deep Graph Learning to Estimate Protein Model Quality Using Structural Constraints from Multiple Sequence Alignments”, In Proceedings of the 13th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB ’22). Association for Computing Machinery, New York, NY, USA, Article 21, 1–10. https://doi.org/10.1145/3535508.3545558 Si, D. (2022). 
  • Renaud, K., Dupuis, M., and Searle, R. (2022). Cybersecurity Regrets: I’ve had a few…. In Proceedings of 2022 New Security Paradigms Workshop, New Hampshire, USA, October 2022, (NSPW ’22), (17 pages).  Dupuis, M. (2022). 
  • Dupuis, M., Renaud, K., & Searle, R. (2022, September). Crowdsourcing Quality Concerns: An Examination of Amazon’s Mechanical Turk. In Proceedings of the 23rd Annual Conference on Information Technology Education (pp. 127-129). Dupuis, M. (2022). 
  • Crouse, L., & Dupuis, M. (2022, September). A Dangerous Infodemic: An Examination of the Impact Social Media Misinformation has on COVID-19 Vaccination Status. In Proceedings of the 23rd Annual Conference on Information Technology Education (pp. 37-43). Dupuis, M. (2022). 
  • Dupuis, M., Bee, J., & Wright-Mockler, A. (2022, September). Virtual Cybersecurity Camps: Lessons Learned. In Proceedings of the 23rd Annual Conference on Information Technology Education (pp. 130-133). Dupuis, M. (2022). 
  • Dupuis, M., Renaud, K., and Jennings, A.** (2022). Fear might motivate secure password choices in the short term, but at what cost? In The 55 th Hawaii International Conference on System Sciences (HICSS). Maui, Hawaii: IEEE. Dupuis, M. (2022). 
  • Mitchell Lee*, Chris Lee*, Sanjay V Penmetsa*, Min Chen, Mizuki Miyashita, and Naatosi Fish, “Reproducibility Companion Paper: MeTILDA – Platform for Melodic Transcription in Language Documentation and Application,” 2023 ACM International Conference on Multimedia Retrieval, accepted for publication. Chen, M. (2022).  
  • Junjie Liu* and Min Chen, “COVID-19 Fake News Detector,” 2023 IEEE International Conference on Computing, Networking and Communications, accepted for publication. Chen, M. (2022). 
  • Apoorva Bhatnagar* and Min Chen, “Improving GIF Image Accessibility on Web,” Proceedings of IEEE 23rd International Conference on Information Reuse and Integration for Data Science, pp. 190-191, 2022. Chen, M. (2022). 
  • Neha Kumari* and Min Chen, “Malware and Piracy Detection in Android Applications,” Proceedings of 2022 IEEE International Conference on Multimedia Information Processing and Retrieval, pp. 306-311, 2022. Chen, M. (2022). 
  • K. Sanyour∗ and W. Kim, Machine Learning Algorithms in Gene Editing, 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Las Vegas, Nevada, USA, December 6-8, 2022, pp. 799-802, doi:10.1109/BIBM55620.2022.9995135. Kim, W. (2022).  
  • Alex Xie∗ and Yang Peng “Improving the Quality of Inference for Applications using Chained DNN Models during Edge Server Handover,” to appear in The 3rd Workshop on Edge Computing and Communications (EdgeComm), Seattle, WA, December 5-8, 2022. Peng, Y. (2022). 
  • Carl Mofjeld∗ , Yang Peng, and Hua Qin “Adaptive Acceleration of Inference Services at the Network Edge,” in the 10th IEEE International Conference on Mobile Cloud Computing, Services, and Engineering (MobileCloud), San Francisco, California, August 15 – 22, 2022. Peng, Y. (2022). 
  • Manwaring⇤, G. Thamilarasu, “”Defense Guild: A Privacy-preserving Intrusion Detection System for Healthcare Data in Clouds”, accepted for publication in International Conference on Emerging Applications of Artificial Intelligence, Machine Learning and Cybersecurity, 2022 Thailmarasu, G. (2022). 
  • Rahmati⇤ G. Thamilarasu, “Federated learning based Anomaly Detection in Internet of Things, 9th Women in Cybersecurity Annual Conference (accepted for presentation), April 2022 Thailmarasu, G. (2022). 
  • Conference Panel Presentation: Lummi Nation: Panel Session Presenter: Building Native Nations Sovereignty: Vision for Moving the Lummi Nation Forward ; Presentation: The Tulalip Technology Project (2022) Erdly, B.(2022). 
  • C. Leonie(*), R. Angotti, and K. Sung,” CourseExpo: An Immersive Collaborative Learning Ecosystem,” Poster in ACM Symposium on Virtual Reality Software and Technology (VRST 2022), Tsukuba, Japan, Nov 2022. Sung, K. (2022).  
  • Rahmati⇤ G. Thamilarasu, “Federated learning-based Anomaly Detection in Internet of Things, 9th Women in Cybersecurity Annual Conference (accepted for presentation), April 2022 Thailmarasu, G. (2022). 

Published Book Chapters

* indicates student-faculty research. students in bold, faculty underlined  

  • Si*, H. Meng, J. Pfab, Y. Deng, Y. Xie, J. Tan, S. H. M. Chow, J. Chen, A. Jain. (2022). DeepTracer Web Service for Fast and Accurate De Novo Protein Complex Structure Prediction from Cryo-EM. Algorithms and Methods in Structural Bioinformatics. Computational Biology. Springer, Cham. https://doi.org/10.1007/978-3-031-05914-8_6    Si, D. (2022).  

Newly Funded External & Internal Grants

  • IEEE Computer Society Diversity and Inclusion Fund (with UW budget sharing) PI $5,234 (+ $1,333) 2022 Fukuda, M. (2022). 
  • Regular panel member, US National Science Foundation and US National Institutes of Health. Editor, special issue of BioSystems, 2022. Stiber, M. (2022). 
  • 2021–26 “Context and Provenance for Disaster Data” InterPARES Trust AI and the Social Sciences and Humanities Research Council of Canada, PI, with co-investigators: Erik Borglund (Mid Sweden University), Megan Cohen (University of British Columbia), Barbara Endicott-Popovsky (University of Washington), Arika Kaneko (University of British Columbia), Scott Sotebeer (USA Strategics), and Samuel Tweneboah-Koduah (Ghana Institute of Management and Public Administration). Stiber, M. (2022).  
  • 2020–23 “An Intelligent Testbed for Critical Infrastructure” National Security Agency, $299,945. Stiber, M. (2022).  
  • “Interactive Affordability Model for WSAC,” Washington Student Achievement Council, $70,031, Submitted, 2022-2023, PI: K. Sung, Co-PI: Jim Fridley. Sung, K. (2022).  
  • “Using Emerging Technologies to Create Common Learning Environments,” $30,000, UW Bothell Scholarship, Research, and Creative Practice (SRCP) Seed Grant Program, May 2022, PI: R. Angotti, Co-PI: K. Sung. Sung, K. (2022).  
  • Computing and Software Systems Division, University of Washington, Bothell, Research Assistant Support Sung, K. (2022). 
  • “Interactable Topographical Map,” Three academic quarters, 2022-2023, September, 2022. Sung, K. (2022). 
  • Computing and Software Systems Division, University of Washington, Bothell, Research Support “Reimagine the Classroom,” $5,000, March 2022 Sung, K. (2022). 
  • GRANTS 2022-2023 CSS graduate RA 2 Quarters (PI): A privacy preserving generative model for location traces. ($20,000) Mashadi, A. (2022).  
  • Co-PI September 2022-April 2024 Public lands in public hands Funded by CS4Env ($50,000) Mashadi, A. (2022).  
  • CoMotion Innovation Gap Fund Grant, UW, PI (Sole), $50,000 Si, D. (2022). 
  • DeepTracer Development” 2021-2022 
  • Scholarship, Research, and Creative Practice Grant, UWB, PI (Sole), $18,464  Si, D. (2022). -“Intelligent RNA and Ligand Involved SARS-CoV-2 Supramolecular Assembly Modeling from Cryo-EM” 2021-2022 
  • National Science Foundation Research Award, NSF, PI (sole), $200,000  Si, D. (2022). “Predicting All-atom Structure of SARS-CoV-2 Related Protein Complex from 3D Cryo-Electron Microscopy Data” 2020-2022 
  • PI, CSS Graduate Research Proposal, “CSS Research: Advancing Software and Data Provenance Research”, awarded Winter 2022. Asuncion, H. (2022).  
  • Virtual GenCyber Program for Teachers in Washington State, PI ($147,165) National Security Agency (NSA) Collaborators: Columbia Basin College and Pacific Northwest National Laboratories (PNNL), July 2022 – July 2024 Dupuis, M. (2022).  
  • GenCyber Capacity Building: Curriculum Development for Non-Profit Programs Serving Historically Underrepresented Individuals in Cybersecurity, PI ($95,886) National Security Agency (NSA) Collaborators: iUrban Teen, June 2022 – June 2024 Dupuis, M. (2022).  
  • PI, NSF BCS-2109654, “Collaborative Research: Prosodic Analysis and Visualization of Phonetic Samples for Improved Understanding of Stress and Intonation,” $140,351, 09/01/2021 – 02/28/2025.  Chen, M. (2022). 
  • PI, NSF IIS-2005422, “NSF Student Travel Support for ACM Special Interest Group of Management of Data (ACM SIGMOD),” $20,929, 3/1/2020 – 2/28/2023. Chen, M. (2022). 
  • PI, “Interpretable machine learning techniques to identify adaptive mutations in genomics data,” Computing and Software Systems Division, University of Washington, Graduate Research Program, Winter 2022, $5,000, Mar. 2022 Kim, W. (2022). 
  • PI, “Exploring interpretable machine learning in identifying adaptive mutations,” Computing and Software Systems Division, University of Washington, Research Assistant Support for three academic quarters AY2022-2023, Mar. 2022  Kim, W. (2022). 
  • National Security Agency (NSA). GenCyber Capacity Building: Curriculum Development for Non-Profit Programs Serving Historically Under-Represented Individuals in Cybersecurity, Co-PI, $95,886 (responsible for $47,943), 6/2022. Lagesse, B. (2022). 
  • Co-PI, Public lands in public hands: innovative technology and community science for parks and outdoor recreation, University of Washington, Computer Science for the Environment (CS4Env) Initiative, July 2022 – June 2023, $50000 Peng, Y. (2022). 
  • Co-PI, “Next-Generation Health Monitoring Systems – Devices, Novel Algorithms, and Secure Communication,” renewal submission to NSF Research Experiences for Undergraduates (REU), August 2022 (not funded) Thailmarasu, G. (2022). 
  • SEVA Grant Extensions – VisionVan and Cloud-based Technologies grants: Total funding = $175,000 Erdly, B. (2022).  
  • Munehiro Fukuda, IEEE CS Diversity & Inclusion Fund 2022 – A Summer High School Internship for BIPOC Students, Distributed Systems Laboratory, University of Washington Bothell, WA 98011, December 29, 2022. (Fukuda, M. (2022). 
  • Examining Emotional Stimuli Related to Cybersecurity in a Multi-Method Study, 2022-23 (2 quarters), ≈ $32,000 Dupuis, M. (2022).  
  • Adaptive Risk Assessment and Recommendation System / Student Exchange Grant Work, Autumn (2022), $5,000 Dupuis, M. (2022). 
  • Cyber Range for Research and Teaching Purposes, Winter (2022), $5,186 Dupuis, M. (2022). 
  • National Security Agency (NSA). GenCyber Capacity Building: Curriculum Development for Non-Profit Programs Serving Historically Under-Represented Individuals in Cybersecurity, Co-PI, $95,886 (responsible for $47,943), 6/2022. 2. National Science Foundation (NSF). Artificial Intelligence-Enhanced Lagesse, B. (2022). 
  • Fiscal Year 2022 Omnibus Appropriations Bill, funding for the Center for Biotech Innovation and Training, https://www.uwb.edu/stem-news/march-2022/funding-center-for-biotech-innovation-and-training, $750,000, 2022 Socha, D. (2022).