yupinglu89@gmail.com | YupingLu | @YupingLu | yupinglu | Dissertation

Education

University of Tennessee, Knoxville

• Research Interests: Machine Learning | Graph Algorithm | Bioinformatics
• PhD in Computer Science (August 2019) | GPA: 3.91
• Advisor: Dr. Michael A. Langston

Nanjing Agricultural University

• BEng in Computer Science (May 2011) | GPA: 3.64
• Advisor: Dr. Huanliang Xu

Technical Skills

• Programming languages: C/C++, Python, SQL, openCypher, R, PHP, HTML+CSS+Javascript
• Tools: PyTorch, LLM, PyG, DGL, Jupyter, NumPy, Pandas, Conda, Git, LaTeX
• Cloud Computing: AWS, GCP, Docker, Kubernetes
• HPC experience: ORNL CADES, LBNL NERSC, OpenMPI

Honors

• Klaus Halbach Award, ALS, Berkeley Lab (2021)
• GSS Travel Award, University of Tennessee, Knoxville (2018)
• Department Excellence Award, University of Tennessee, Knoxville (2013)
• Outstanding Graduate and Several Scholarships, Nanjing Agricultural University (2007-2011)

Ages ago, in another city, on another bus, I sat so at the windows, looking outward, investing for each flying face which trapped my brief attention some life, some destiny, in which I played a part.

Experience

Publications

Conference Papers

• Enhancing the MOGA Optimization Process at ALS-U with Machine Learning
  Yuping Lu, Simon C. Leemann, Changchun Sun, Michael P. Ehrlichman, Thorsten Hellert, Hiroshi Nishimura, Marco Venturini
  IPAC 21 (2021) | Paper | Web
• Clique Selection and its Effect on Paraclique Enrichment: An Experimental Study
  Yuping Lu, Charles A. Phillips, Elissa J. Chesler, Michael A. Langston
  Proceedings of the 12th International Conference on Bioinformatics and Computational Biology (2020) | Paper | Web
• Convolutional Neural Networks for Hydrometeor Classification using Dual Polarization Doppler Radars
  Yuping Lu, Jitendra Kumar
  Proceedings of the 2019 IEEE International Conference on Data Mining Workshops (ICDMW 2019) | Paper | Web
• Detecting Outliers in Streaming Time Series Data from ARM Distributed Sensors
  Yuping Lu, Jitendra Kumar, Nathan Collier, Bhargavi Krishna, Michael A. Langston
  Proceedings of the 2018 IEEE International Conference on Data Mining Workshops (ICDMW 2018) | Paper | Web

Journal Papers

• Demonstration of Machine Learning-enhanced Multiobjective Optimization of Ultrahigh-brightness Lattices for Fourth-generation Synchrotron Light Sources
  Yuping Lu, Simon C. Leemann, Changchun Sun, Michael P. Ehrlichman, Hiroshi Nishimura, Marco Venturini, Thorsten Hellert
  Nuclear Inst. and Methods in Physics Research, A — (2023): 168192 doi:10.1016/j.nima.2023.168192 | Paper | Web
• Biclique: Maximal Biclique Enumeration in Bipartite Graphs
  Yuping Lu, Charles A. Phillips, Michael A. Langston
  BMC Research Notes — 13, 88 (2020) doi:10.1186/s13104-020-04955-0 | Paper | Web
• A Robustness Metric for Biological Data Clustering Algorithms
  Yuping Lu, Charles A. Phillips, Michael A. Langston
  BMC Bioinformatics — 20, 503 (2019) doi:10.1186/s12859-019-3089-6 | Paper | Web
• Digital Gene Expression Profiling of the Phytophthora Sojae Transcriptome
  Wenwu Ye, Xiaoli Wang, Kai Tao, Yuping Lu, Tingting Dai, Suomeng Dong, Daolong Dou, Mark Gijzen, Yuanchao Wang
  Molecular Plant-Microbe Interactions — 24(12):1530–1539, December 2011 | Paper | Web

Posters & Short Papers

• Enhancing the MOGA Optimization Process at ALS-U with Machine Learning
  Yuping Lu, Simon C. Leemann, Changchun Sun, Michael P. Ehrlichman, Thorsten Hellert, Hiroshi Nishimura, Marco Venturini
  IPAC 21 — Campinas, Brazil, May 24, 2021 | Poster
• Improving Multi-objective Genetic Algorithm for Lattice Optimization with Machine Learning
  Yuping Lu, Changchun Sun, and Simon C. Leemann
  ALS User Meeting 2020 — Berkeley, California, August 25, 2020 | Poster
• Beam Based Optimization and Machine Learning for Synchrotrons
  Charles Nathan Melton, Yuping Lu, Shuai Liu, Hiroshi Nishimura, Matthew Marcus, Changchun Sun, Alexander Hexemer, Simon C. Leemann
  ALS User Meeting 2019 — Berkeley, California, October 1, 2019 | Poster
• Convolutional Neural Networks for Hydrometeor Classification Using Dual Polarization Doppler Radars
  Yuping Lu, Jitendra Kumar
  2019 ARM/ASR PI Meeting — Rockville, MD, June 11, 2019 | Poster
• Enrichment vs Robustness: A Comparison of Transcriptomic Data Clustering Metrics
  Yuping Lu, Charles A Phillips, Michael A Langston
  BMC Bioinformatics — 17(Suppl 10):P10, August 2016 | Paper | Web

Talks

• Deep Convolutional Neural Networks for Hydrometeor Classification using Dual Polarization Doppler Radars
  2019 ARM/ASR PI Meeting, Rockville, MD, June 10, 2019 | Slides
• A Robustness Metric for Biological Data Clustering Algorithms
  ISBRA 2018, Beijing, China, June 10, 2018 | Slides
• Outlier Detection for SGPMET Data
  Oak Ridge National Laboratory, April 04, 2018 | Slides

Professional Service

• Reviewer, Computational Biology and Bioinformatics, 2020-2022. | Web
• Reviewer, 10th International Workshop on Frontiers in Algorithmics, FAW 2016. | Web
• Reviewer, 9th International Workshop on Frontiers in Algorithmics, FAW 2015. | Paper | Web
• Reviewer, 9th International Workshop on Algorithms and Computation, WALCOM 2015. | Paper | Web
• Reviewer, 14th International Symposium on Algorithms and Data Structures, WADS 2015. | Web

Student Volunteer

• XSEDE14 : Atlanta, GA, USA. July 13-18, 2014 | Web