Yanqing Ji

Research

Research Interest

Parallel and Cloud Computing

Data Mining

Multi-Agent System

Their Biomedical Applications

 

Research Group Members/Collaborators

Yanqing Ji, PhD, Associate Professor in Department of Electrical and Computer Engineering at Gonzaga University, Spokane WA

Yun Tian, PhD, Assistant Professor in Department of Computer Science at Eastern Washington University, Spokane WA

John Tran, MD, Medical Director in Frontier Behavioral Health, Spokane WA

Hao Ying, PhD, Professor in Department of Electrical and Computer Engineering at Wayne State University, Detroit MI

Michael Massanari, MD, Director of Research for the Critical Junctures Institute, Bellingham WA

Peter Dews, MD, Vice President in St. Mary Mercy Hospital (Trinity Health), Livonia MI

Fangyang Shen, PhD, Associate Professor in Department of Computer Systems Technology at New York City College of Technology, Brooklyn NY

See-Yan Lau, PharmD, Pharmacist in Department of Medicine in Albertsons, Spokane WA

Xiandong Meng, PhD, Senior Software Developer in Department of Genomics in Lawrence Berkeley National Lab, Berkeley CA

 

Current Research: Leveraging Cloud Computing to Mine Biomedical Associations

          We currently work on cloud computing algorithms to efficiently extract biomedically meaningful associations from big biomedical data using Amazon’s cloud computing and storage services.

Biomedical researchers and healthcare providers publish a large volume of clinical and research articles each year. Most of these articles are available online, which provide an important source of information that not only enables researchers to discover in-depth knowledge about biological systems, but also helps healthcare professionals do evidence-based medicine in clinical settings. However, investigating and analyzing these data is often both data-intensive and computation-intensive. In this project, we investigate how to utilize Amazon’s cloud computing and storage services to efficiently mine the associations between biomedical concepts from a large set of biomedical articles. Association extraction represents a very important category of knowledge discovery in biomedical domain since finding the relationships among biomedical concepts or entities (e.g. genes and diseases, drugs and adverse events, etc.) is often a fundamental objective for biological and medical researchers. At this stage, we conduct our research using a collection of 162,259 full-text articles from TREC (Text REtrieval Conference) 2006 Genomics Track.

We have done a pilot study supported by Gonzaga University under an internal research grant. The preliminary results based on 3,610 biomedical articles have been published in the 12th International Conference on Information Technology: New Generations (ITNG 2015). Our long-term goal is to develop cloud-hosted services and related software tools to help biomedical researchers and healthcare professionals find interesting biomedical associations based on all the articles in PubMed. PubMed represents the most influential online database in the biomedical field. It currently contains more than 24 million articles and approximately 10,000 articles are added to the database every week.

 

Professional Services

Editorial Services:

Editor of Journal of Digital Signal Processing since April 2013

Editorial Board Member of Biomedical Engineering Research (BER) since May 2013.

Program Committee Members:

Program Committee for the 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2015), Washington D.C., November 9-12, 2015.

Technical Program Committee for the 12th International Conference on Information Technology: New Generations (ITNG 2015), Las Vegas, Nevada, April 13-15, 2015.

Program Committee for the 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2014), Belfast, UK, November 2-5, 2014.

Technical Program Committee for the 11th International Conference on Information Technology: New Generations (ITNG 2014), Las Vegas, Nevada, April 7-9, 2014.

Program Committee for the 2013 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2013), Shanghai, China, December 18-21, 2013.

Technical Program Committee for the 10th International Conference on Information Technology: New Generations (ITNG 2013), Las Vegas, Nevada, April 15-17, 2013.

Technical Program Committee for the 2012 International Workshop on GPU Computing in Clouds (GPU-Cloud 2012), Taipei, Taiwan, December 03-06, 2012.

IEEE CIS FML (Functional Markup Language) Subcommittee of the Standards Committee (2012 - present).

Technical Program Committee for the 9th International Conference on Information Technology: New Generations (ITNG 2012), Las Vegas, Nevada, April 16-18, 2012.

Competition Task Force of the IEEE Computational Intelligence Society's Fuzzy Systems Technical Committee, Taipei, Taiwan, June 27-30, 2011.

Program Committee for the 24th IEEE International Conference on Advanced Information Networking and Application (AINA 2010), Perth, Australia, April 20-23, 2010.

Program Committee  for the 2009 International Workshop on GPU Technologies and Applications (GPUTA 2009), held with the 10th International Symposium on Pervasive Systems, Algorithms and Networks (I-Span2009), Kaohsiung, Taiwan, R.O.C., December 14-16, 2009.

Program Committee for the 23rd IEEE International Conference on Advanced Information Networking and Application (AINA 2009), Bradford, UK, May 26-29, 2009.

 

Publications

Peer-reviewed Journal Publications

[1]   Yanqing Ji, Yun Tian, Fangyang Shen, John Tran “Leveraging MapReduce to Efficiently Extract Associations between Biomedical Concepts from Large Text Data,Journal of Microprocessors and Microsystems, vol.46 (Part B), pp. 202-210, 2016. DOI: 10.1016/j.micpro.2016.03.003

[2]   Yanqing Ji, Hao Ying, John Tran, Peter Dews, R. Michael Massanari, “Integrating Unified Medical Language System and Association Mining Techniques into Relevance Feedback for Biomedical Literature Search,BMC Bioinformatics, vol.17 (Suppl 9):264, 12 pages, 2016. DOI:  10.1186/s12859-016-1129-z

[3]   Yanqing Ji, Hao Ying, John Tran, Peter Dews, See-Yan Lau, Richard E. Miller, R. Michael Massanari, “A Functional Temporal Association Mining Approach for Screening Potential Drug-Drug Interactions from Electronic Patient Databases,” Informatics for Health & Social Care, vol.41 (4), pp. 387-404, 2016. DOI: 10.3109/17538157.2015.1064427

[4]   Yanqing Ji, Fangyang Shen, See Yan Lau, John Tran “A Multi-Agent System for Reporting Suspected Adverse Drug Reactions,Online Journal of Public Health Informatics, vol.6 (3), 19 pages, 2014. DOI: 10.5210/ojphi.v6i3.5579

[5]   Yanqing Ji, Hao Ying, Peter Dews, John Tran, Ayman Mansour, Richard E. Miller, R. Michael Massanari, “A Method for Mining Infrequent Causal Associations and Its Application in Finding Adverse Drug Reaction Signal Pairs,IEEE Transactions on Knowledge and Data Engineering, vol.25(4), pp.721-733,  2013. DOI: 10.1109/TKDE.2012.28

[6]   Xiandong Meng, Yanqing Ji, "Modern Computational Techniques for the HMMER Sequence Analysis," ISRN Bioinformatics, vol. 2013, Article ID 252183, 13 pages, 2013. DOI: 10.1155/2013/252183

[7]   Yanqing Ji, Hai Jiang, Vipin Chaudhary, “A Heuristic Checkpoint Placement Algorithm for Adaptive Application-Level Checkpointing,, vol. 1(6), pp. 50-61, 2011.

[8]   Yanqing Ji, Hao Ying, Peter Dews, Ayman Mansour, Margo S. Farber, John Tran, Richard E. Miller, R. Michael Massanari,A Potential Causal Association Mining Algorithm for Screening Adverse Drug Reactions in Postmarketing Surveillance,” IEEE Transactions on Information Technology in Biomedicine, vol. 15(3), pp. 428-437, 2011. DOI: 10.1109/TITB.2011.2131669

[9] Yanqing Ji, Hao Ying, Margo S. Farber, John Yen, Peter Dews, Richard E. Miller, R. Michael    Massanari, “A Distributed, Collaborative Intelligent Agent System Approach for Proactive Postmarketing Drug Safety Surveillance,” IEEE Transactions on Information Technology in Biomedicine, vol. 14 (3), pp. 826-837, 2010. DOI: 10.1109/TITB.2009.2037007

[10] Xiandong Meng, Yanqing Ji, Hai Jiang, “Advanced Acceleration Technologies for Biological Sequence Analysis,” Journal of Current Bioinformatics, vol. 5 (3), pp. 176-194, 2010. DOI: 10.2174/157489310792006738

[11] Yanqing Ji, R. Michael Massanari, Joel Ager, John Yen, Richard E. Miller, and Hao Ying "A Fuzzy Logic-Based Computational Recognition-Primed Decision Model," Information Sciences, vol. 177(20), pp. 4338-4353, 2007. DOI: 10.1016/j.ins.2007.02.026

[12] Yanqing Ji, Hao Ying, John Yen, Shizhuo Zhu, Daniel C. Barth-Jones, Richard E. Miller,  R. Michael Massanari, “A Distributed Adverse Drug Reaction Detection System Using Intelligent Agents with Fuzzy Recognition-Primed Decision Model,” International Journal of Intelligent Systems, vol. 22(8), pp. 827-845, 2007. DOI: 10.1002/int.20230

[13] Yanqing Ji, Yongming Zhang, Xianbin Du, Ruishen Wu, Shixing Liu “Software Design of New-style Nuclear Gauge System,” Nuclear Electronics & Detection Technology (in Chinese), Vol. 22 (6), pp. 541-544, 2002.

[14] Shixing Liu, Yongming Zhang, Ying Yang, Ruisheng Wu, Xianbin Du, Yanqing Ji “A Microcomputerized Nuclear Gauge System with High Sensitivity and Low Radiation,” Nuclear Electronics & Detection Technology (in Chinese), Vol. 22 (3), pp. 265-267, 2002.

[15]  Yanqing Ji, Yongming Zhang, Ruisheng Wu, Shixing Liu, Ying Yang “Multichannel Data Acquisition and Control Interface in Microcomputer Nuclear Gauge System,” Nuclear Electronics & Detection Technology (in Chinese), Vol. 21 (3), pp. 239-244, 2001.

Peer-reviewed Conference Proceedings Publications

[1]    Yanqing Ji, Hao Ying, John Tran, Peter Dews, R. Michael Massanari, “Integrating Association Mining into Relevance Feedback for Biomedical Literature Search,” 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2015), 6 pages, Washington D.C., November 9-12, 2015.

[2]    Yun Tian, Bojian Xu, Yanqing Ji, Jesse Scholer, “CloudTree: A Library to Extend Cloud Services for Trees”, IEEE BigData Congress 2015, 5 pages, New York, June 27-July 2, 2015.

[3]    Yanqing Ji, Yun Tian, Fangyang Shen, John Tran, “High-Performance Biomedical Association Mining with MapReduce”, 12th International Conference on Information Technology: New Generations (ITNG 2015), 6 pages, Las Vegas, Nevada, April 13-15, 2015.

[4]    Yun Tian, Yanqing Ji “A Prototype Spatio-temporal Database Built on Top of Relational Database”, 12th International Conference on Information Technology: New Generations (ITNG 2015), 6 pages, Las Vegas, Nevada, April 13-15, 2015.

[5]    Yanqing Ji, Hao Ying, John Tran, Peter Dews, Ayman Mansour, R. Michael Massanari, “A Temporal Interestingness Measure for Drug Interaction Signal Detection in Post-marketing Surveillance,” 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, pp. 2722 - 2725, Chicago, Illinois, August 26-30, 2014.

[6]    Yanqing Ji, Fangyang Shen, John Tran, “A Multi-Relational Association Mining Algorithm for Screening Suspected Adverse Drug Reactions”, 11th International Conference on Information Technology: New Generations (ITNG 2014), pp. 407 – 412, Las Vegas, Nevada, April 7-9, 2014.

[7]    Yanqing Ji, Hao Ying, John Tran, Peter Dews, Ayman Mansour, See Yan Lau, R. Michael Massanari, “A Temporal Association Mining Method for Signaling Drug-Drug Interactions”, 2nd Workshop on Data Mining for Medicine and Healthcare in 2013 SIAM International Conference on Data Mining, 9 pages, Austin, Texas, May 2-4, 2013.

[8]    Ayman Mansour, Hao Ying, Peter Dews, Yanqing Ji, R. Michael Massanari, "Identifying Adverse Drug Reaction Signal Pairs by a Multi-Agent Intelligent System with Fuzzy Decision Model," Proceedings of the 31st North American Fuzzy Information Processing Society Conference, pp. 1-6, Berkeley, CA, August 6-8, 2012.

[9]    Yanqing Ji, Fangyang Shen, John Tran ," A High Performance Agent-Based System for Reporting Suspected Adverse Drug Reactions," 9th International Conference on Information Technology: New Generations (ITNG 2012), pp. 490-495,  Las Vegas, Nevada, April 16-18, 2012.

[10]  Yanqing Ji, Hao Ying, John Tran, Peter Dews, Ayman Mansour, R. Michael Massanari, "Mining Infrequent Causal Associations in Electronic Health Databases,"  2011 IEEE 11th International Conference on Data Mining Workshops, pp. 421-428, Vancouver, Canada, December 11-14, 2011.

[11] Yanqing Ji, Hao Ying, Peter Dews, John Tran, Ayman Mansour, Richard E. Miller, R. Michael Massanari, "An Exclusive Causal-Leverage Measure for Detecting Adverse Drug Reactions from Electronic Medical Records," Proceedings of the 30th North American Fuzzy Information Processing Society Conference, pp. 1-6, El Paso, TX, March 18-20, 2011.

[12] Ayman Mansour, Hao Ying, Peter Dews, Yanqing Ji, John Yen, Richard E. Miller, R. Michael Massanari, "Finding Similar Patients in a Multi-Agent Environment," Proceedings of the 30th North American Fuzzy Information Processing Society Conference, pp. 1-6, El Paso, TX, March 18-20, 2011.

[13] Yanqing Ji, Hao Ying, Margo S. Farber, Peter Dews, Ayman Mansour, John Tran, Richard E. Miller, R. Michael Massanari,  A Fuzzy Recognition-Primed Decision Model-Based Causal Association Mining Algorithm for Detecting Adverse Drug Reactions in Postmarketing Surveillance”, 2010 IEEE World Congress on Computational Intelligence (WCCI 2010), pp.1-8, Barcelona, Spain, July 18-23, 2010.

[14] Ayman Mansour, Hao Ying, Peter Dews, Yanqing Ji, Margo S. Farber, John Yen, Richard E. Miller, R. Michael Massanari, “A Multi-Agent System for Detecting Adverse Drug Reactions,” 29th North American Fuzzy Information Processing Society Annual Conference (NAFIPS10), pp. 1-6 Toronto, Canada, July 12-14, 2010.

[15] Kiatisak Wongsopanakul, Yanqing Ji, Xinyu Du, Feng Lin, Hao Ying, “Application of the Extended Fuzzy Discrete Systems Theory to HIV/AIDS Treatment Regimen Selection”, 28th North American Fuzzy Information Processing Society Annual Conference (NAFIPS09), pp. 1-6, Cincinnati, Ohio, June 14-17, 2009.