NCSA Students Pushing Innovation Program Celebrates Success Amid COVID-19 June 15, 2021 Profiles Data AnalyticsStudentsVisualization Share this page: Twitter Facebook LinkedIn Email By Sophie Anh Bui The National Center for Supercomputing Applications’ Students Pushing INnovations (SPIN) internship program provides undergraduates at the University of Illinois Urbana-Champaign the opportunity to address fundamental challenges in high-performance computing, data analysis, visualization, cybersecurity and other areas of interest. Despite the COVID-19 pandemic challenges, SPIN interns adapted well to working remotely. They maintained high productivity levels, which contributed to great engagement and success in their program efforts. Students worked on various projects, including implementing machine learning for human nutrition research, and agricultural satellite data analysis and visualizing physics phenomena. From publishing papers to participating in conference, contests, SPIN interns worked on various outreach activities to share their research, including an award-winning exhibit at Illinois’ 2021 Engineering Open House. As the spring session concludes, we highlight notable SPIN projects, interns and recent UIUC graduates. MORE THAN A GUT FEELING: A BIOINFORMATICS APPROACH TO STUDYING THE IMPACT OF DIET ON THE GUT MICROBIOME AND METABOLIC HEALTH PROJECT Gut microbes aka bacteria, directly affect a person’s metabolism, immune system, and mental and physical health, making it a priority to understand how diet influences them. This project focuses on finding connections between the foods we eat and their impact on our gut. The team, led by Nutrition professor Hannah Holscher, included Aditya Mansharamani, a recent SPIN intern and Illinois grad, Statistics professor Ruoqing Zhu, and graduate student Leila Shinn. Together, they implemented machine-learning techniques, bioinformatics, and visualization to analyze changes in the gut microbiome and various health markers, like blood sugar and body weight. Holscher says, “Aditya has been an outstanding SPIN intern. His strengths in coding and analytics make him an invaluable member of our research team. We’re lucky to have him.” Mansharamani worked on data analysis and machine-learning processes by building statistical models to analyze dietary intake biomarkers that identify which microbes are explicitly affected by what foods. He also co-authored a paper with the research team published in Oxford Academic’s Journal of Nutrition earlier this year. “I have been working with the team on this project since my freshman year, and it has been gratifying. I learned a lot of technical skills outside of coursework and improved upon effective communication and scientific writing,” says Mansharamani. “As a computer scientist, I often find myself translating terms and concepts from the computer programming world to the biology world and vice-versa. Rarely, any job focuses solely on a single field in the real world—most areas are interdisciplinary, so being able to experience an environment like NCSA has been beneficial for my career and personal goals. Dr. Holscher, Dr. Zhu, and Leila helped me grow as a student, scientist, and coworker. My time at Illinois would not have been the same without them.” Mansharamani continues his studies in the Illinois Master’s of Computer Science program next year and plans to join the industry afterward as a software engineer. TEACHING EXPERIENCES AROUND CUTTING-EDGE VISUALIZATION OF MATERIALS SCIENCE DATA PROJECT Teaching computational materials science can be challenging. Research in this area often produces large amounts of static and time-dependent data, including atomic positions and electron densities rich in information. This project aims to enable an immersive teaching experience for materials science with virtual reality technology and collaboration. The team, led by Materials Science and Engineering Professor Andre Scheife, included two recent SPIN interns and recent Illinois grads, Zixuan Chen and Zhili Luo. Together, the team developed and enhanced MaterialsVR, a visualization tool that allows users to interact with electron-density data and molecular structures. Schleife says, “It has been great working with Zixuan, Zhili and NCSA SPIN on visualization and development. This year, we have created many compelling images that we have used in research presentations, videos, the MatSE department calendar, and the undergraduate image competition. The team has done an excellent job visualizing atoms and electron densities using Blender (a free, open-source modeling and animation tool).” Chen visualized isosurfaces of electron densities and created a laser plane effect, contributing to the tool’s purpose. His work won second place at UIUC’s 2021 Undergraduate Image of Research competition. “NCSA SPIN offers excellent opportunities for students to participate in research activities,” says Chen. “Although we worked remotely, Dr. Andre Schleife and I communicated smoothly and happily through Zoom and emails. He provided crucial guidance, patience and genuine interest when discussing the project with me. My main takeaway from the program is that curiosity is key to addressing research challenges. If you follow your interests and spend time patiently, you will find a solution.” Chen is actively exploring summer internship opportunities and plans to continue his studies as a graduate student at Illinois. Luo helped develop the tool, which contributed to its operation and functionality. He worked with the team to roll out the app on Steam, a well-known digital content distribution channel. “I believe NCSA SPIN brings together people of different backgrounds to collaborate. I appreciate their efforts in supporting international students,” says Luo. “I realized virtual reality’s potential in promoting curiosity and intuitive interaction. I also gained invaluable experience developing tools for a field that is unfamiliar to me. I met with Dr. Schleife on a biweekly basis, where we discussed where we are and what to do next. He gave me valuable feedback and valued my inputs. He provided the VR equipment and materials science-related resources for the project. Overall, the project could not have been completed without his effort and enthusiasm.” Luo is continuing his studies in the Illinois Master of Computer Science program. USING SATELLITE DATA FOR LARGE-SCALE CROP MONITORING PROJECT Sustainability, food security, and climate change are top concerns in supporting and maintaining the world’s growing populations. A project led by Blue Waters professor Kaiyu Guan focuses on processing extensive satellite data to generate insights into the environmental impact on global agriculture productivity, food production and security. Guan’s team included SPIN interns Melissa Chen, Dhruv Dahiya, Yihong Jian, Arjun Nair, John Walls, Trevor Wong, and Chenhui Zhang. Together, they leveraged high-performance computing to analyze satellite images of the Midwest to make crop monitoring and yield predictions more accurate. Nair, a recent Illinois grad, worked on bug fixes, information retrieval algorithms, collecting data from street-level images of farmland and developing a method to isolate fields from them. He is currently developing an algorithm that can detect tractor tire tracks in various imaging, so researchers better understand when farmers are planting their crops. “Senior members of the lab mostly mentored me, and they did a great job of advising me and giving me help when I needed it,” says Nair. “NCSA hosts a lot of outreach events, and the administration has done a great job of fostering an inclusive environment, even with everything being virtual this semester. My biggest takeaway from SPIN is that research careers can be exciting, meaningful, and accessible. My internship with NCSA has encouraged me to explore the possibility of pursuing a full-time research career in the future.” Nair has accepted a summer internship with SPIN and is continuing his studies at Yale University’s Master of Computer Science program next year. Chen helped research, build and assess the system that analyzes data for the sub-project Crop Field Grassway Segmentation. She worked with the team to determine grassways locations using satellite images of various resolutions. “I had an excellent experience working alongside my mentor, Yizhi Huang. He was always willing to answer questions, help me with my work, and provide guidance,” says Chen. “The most important takeaway for me was learning how research worked. I enjoyed the process of ideating, experimenting, iterating, building, and testing. It was amazing to build the unsupervised system by the end of my internship, and I hope to continue this work. I was fortunate to be able to be a part of the program this semester. There are many layers of support available to students throughout the program, and it’s easy to seek support. NCSA also has a lot of programs, events, and opportunities to support everyone of all backgrounds.” Chen is on track to graduate next May and plans to apply for PhD programs specializing in artificial intelligence and computer science. Jian worked on modeling data for two sub-projects, Grassed Waterway and Riparian Buffer Segmentation and Identifying Ponding Areas. He worked with the team to model various satellite imaging data to identify land features using multiple methods and techniques. Jian’s work won third place at the virtual 2020-21 SPIN Poster Session Competition. “My experience with my mentor and the team was great. We had regular meetings via Zoom, and everything worked well,” says Jian. “My main takeaway from the program is that parallelism is important. It saves a lot of time, especially on large projects such as this one. I believe NCSA SPIN is a great interdisciplinary opportunity that promotes diversity and collaboration. I knew a lot of students from different backgrounds who participated in this program. We are still working on identifying pond areas and hope to share results in the summer.” Jian is on track to graduate in 2023 and plans to continue his studies in a joint graduate program before joining the industry. Wong worked on two sub-projects, Normalized Difference Vegetation Index Data for Cover Crop Detection and Residual Neural Networks for Waterlogged Field Classification. He worked with the team to implement an algorithm that can predict whether cover crops were used in fields and create a neural network capable of classifying waterlogged and non-waterlogged areas while ignoring other water sources such as rivers and streams. Both sub-projects will provide Illinois farmers valuable data related to climate change and risk assessment. Wong’s work won second place at the virtual 2020-21 SPIN Poster Session Competition. “My experience with my mentors has been positive, and they consistently provide useful feedback,” says Wong. “I would like to thank Yaping Cai and Yizhi Huang, researchers part of Dr. Kaiyu Guan’s lab. They have helped me tremendously with my projects. Undergraduate research may seem daunting at first, as it did to me. However, the SPIN program has taught me that anyone can participate in research if they are a hard worker and intellectually curious. I believe that NCSA supports equal opportunities and an inclusive work environment.” Wong is on track to graduate in 2023 and has accepted a summer internship with 3M. Zhang worked on the Large-Scale Crop Monitoring in the Midwest sub-project. He worked with the team to preprocess data, design and run experiments, and select and finetune machine learning models. With his help, the team has one journal submission under peer review and two ongoing projects that could lead to publication. “Even though we were working remotely, my experience has been great,” says Zhang. “I learned that good communication is critical. It can save you a lot of time. Also, always take a careful look at your data carefully before applying any algorithm to it. The NCSA SPIN program helps students gain essential experience and skills through mentorship, especially those new to research. Programs like this are essential to bridging the gap of diversity and inclusion in STEM.” Zhang is on track to graduate in 2023 and plans to pursue a graduate or postdoctoral degree. NCSA SPIN welcomes all undergraduates in good academic standing, regardless of major, to apply. This program aims to create an inclusive and collaborative environment by pairing interns with field experts to enhance tech skills, gain valuable hands-on experience, and prepare them for the future. The SPIN program is directed and managed by NCSA Senior Research Coordinator Olena Kindratenko. I am impressed with our interns for being core contributors to this year’s SPIN projects. Their willingness to learn new tools and techniques helped move their projects forward and develop vital skills. From improving and adding new features to developing high-accuracy machine-learning models to improving user experiences of services to vulnerable populations, I feel confident that they are prepared to lead efforts in identifying and shaping research group decisions.Olena Kindratenko, NCSA Senior Research Coordinator Congratulations to all SPIN interns, mentors and recent Illinois graduates on completing the program’s spring 2021 term. Learn more about NCSA’s SPIN program and apply today! See below for additional program mentions and recognitions. The following SPIN students received letters of recognition signed by NCSA Director Bill Gropp: Saumya AgrawalBrain ChenZixuan ChenMohammed JamilAditya MansharamaniRuby Wang The following mentors received SPIN Outstanding Mentor certificates: Brian AllanHannah HolscherZeynep Madak-ErdoganRuby MendenhallTaras PogorelovAndre SchelifeAiman SolimanLiu Xin Winners of the virtual 2020-21 SPIN Poster Session Competition: 1st place and $300 Fiddler Innovation Award Winner: Sneh Pandya2nd place and $200 Fiddler Innovation Award Winner: Trevor Wong3rd place and $100 Fiddler Innovation Award Winner: Yihong JianHonorable Mentions: Keshav Gandhi and Sophia Torrellas ABOUT NCSA The National Center for Supercomputing Applications at the University of Illinois Urbana-Champaign provides supercomputing and advanced digital resources for the nation’s science enterprise. At NCSA, University of Illinois faculty, staff, students and collaborators from around the globe use these resources to address research challenges for the benefit of science and society. NCSA has been advancing many of the world’s industry giants for over 35 years by bringing industry, researchers and students together to solve grand challenges at rapid speed and scale.