Hongye Liu

For More Information

• Hongye Liu's personal web site on Publish.
• Hongye Liu's research lab web site
• Hongye Liu's Siebel school faculty profile page

Biography

I joyfully joined the Illinois Department of Computer Science after years of research in Biomedical informatics all in the Boston Longwood Medical area including Harvard Medical School and its affiliated hospitals. There are two things that I feel very important in my career, one is I think learning is a lifelong journey, the other is there are always surprises and we must embrace changes. For example, when I received my B. E. in Precision Machinery and Instrumentation from the Univ. of Science and Technology of China, I did not expect at all I would get my PhD from MIT in the area of computer aided design for 3-D Printing because there was not even AutoCAD in my college years.

After my doctoral studies, I was drawn to the area of Biomedical research due to both my interest in helping cure diseases and my newfound faith. In the years I spent in Boston Longwood Area, I have done research in diverse Data Science related areas such as Bioinformatics, Computational Biology, Biostatistics, and Machine learning.

Over a 4-year period of encountering/interacting with students, reviewing academic works and college teaching, I discovered I feel happiest when I work with undergraduate students, and I enjoy teaching undergraduate students and training next generation of computer scientists and data-centered professionals. I am passionate about mentoring undergraduate students and helping undergraduate students do research. My research is focused on understanding the needs of students with disabilities and broadening the participation of students with disabilities. I have been PI of several projects at the Univ. of Illinois on helping students with disabilities and PI of a project on exploring UDL in teaching STEM courses, for example the SIIP project "UDL based best practices including utilizing Canvas for the needs of students with disability;" GIANT project "Developing tools to make Mathematics and other STEM contents more accessible in college engineering courses."

Other interests include Biomedical applications that involve large high dimensional data analysis and machine learning and data-driven educational improvement for undergraduate students. For more about me, please check my personal homepage: https://publish.illinois.edu/hongyeliu/

Professional Highlights

• I have been part of the faculty spotlight demonstrating active learning methods by the SIIP ENGINE projecthttps://publish.illinois.edu/siipcompendium/2021/10/11/faculty-spotlight-hongye-liu/
• I was featured in the article "The birth of a tumor" of The Boston Globe on Dec 4 2006 for my research on lung cancer. 

Resident Instruction

• Probability and Statistics for Computer Science (CS361)

Research Interests

• Machine Learning
• Bioinformatics; Large scale BioMedical data analysis
• Computer Science Education

Chapters in Books

• Kho A and Liu H. "Information Processing at the Genomics Level." Springer Handbook of Bio-/Neuroinformatics, pp. 43-55, 2014.

Selected Articles in Journals

• Deng J, Wang ES, Jenkins RW, Li S, Dries R, Yates K, Chhabra S, Huang W, Liu H, Aref AR, Ivanova E, Paweletz CP, Bowden M, Zhou CW, Herter-Sprie GS, Sorrentino JA, Bisi JE, Lizotte PH, Merlino AA, Quinn MM, Bufe LE, Yang A, Zhang Y, Zhang H, Gao P, Chen T, Cavanaugh ME, Rode AJ, Haines E, Roberts PJ, Strum JC, Richards WG, Lorch JH, Parangi S, Gunda V, Boland GM, Bueno R, Palakurthi S, Freeman GJ, Ritz J, Haining WN, Sharpless NE, Arthanari H, Shapiro GI, Barbie DA, Gray NS, Wong KK. "CDK4/6 Inhibition Augments Anti-Tumor Immunity by Enhancing T Cell Activation." Cancer Discovery, 8(2), pp. 216-233, 2018.
• Jenkins RW, Aref AR, Lizotte PH, Ivanova E, Stinson S, Zhou CW, Bowden M, Deng J, Liu H, Miao D, He MX, Walker W, Zhang G, Tian T, Cheng C, Wei Z, Palakurthi S, Bittinger M, Vitzthum H, Kim JW, Merlino A, Quinn M, Venkataramani C, Kaplan JA, Portell A, Gokhale PC, Phillips B, Smart A, Rotem A, Jones RE, Keogh L, Anguiano M, Stapleton L, Jia Z, Barzily-Rokni M, Cañadas I, Thai TC, Hammond MR, Vlahos R, Wang ES, Zhang H, Li S, Hanna GJ, Huang W, Hoang MP, Piris A, Eliane JP, Stemmer-Rachamimov AO, Cameron L, Su MJ, Shah P, Izar B, Thakuria M, LeBoeuf NR, Rabinowits G, Gunda V, Parangi S, Cleary JM, Miller BC, Kitajima S, Thummalapalli R, Miao B, Barbie TU, Sivathanu V, Wong J, Richards WG, Bueno R, Yoon CH, Miret J, Herlyn M, Garraway LA, Van Allen EM, Freeman GJ, Kirschmeier PT, Lorch JH, Ott PA, Hodi FS, Flaherty KT, Kamm RD, Boland GM, Wong KK, Dornan D, Paweletz CP, Barbie DA. "Ex Vivo Profiling of PD-1 Blockade Using Organotypic Tumor Spheroids." Cancer Discovery, 8(2), pp. 196-215, 2017.
• Hanna GJ, Liu H, Jones RE, Bacay AF, Lizotte PH, Ivanova EV, Bittinger MA, Cavanaugh ME, Rode AJ, Schoenfeld JD, Chau NG, Haddad RI, Lorch JH, Wong KK, Uppaluri R, Hammerman PS. "Defining an inflamed tumor immunophenotype in recurrent, metastatic squamous cell carcinoma of the head and neck." Oral Oncology, 67, pp. 61-69, 2017.
• Awad MM, Jones RE, Liu H, Lizotte PH, Ivanova EV, Kulkarni M, Herter-Sprie GS, Liao X, Santos AA, Bittinger MA, Keogh L, Koyama S, Almonte C, English JM, Barlow J, Richards WG, Barbie DA, Bass AJ, Rodig SJ, Hodi FS, Wucherpfennig KW, Jänne PA, Sholl LM, Hammerman PS, Wong KK, Bueno R. "Cytotoxic T Cells in PD-L1-Positive Malignant Pleural Mesotheliomas Are Counterbalanced by Distinct Immunosuppressive Factors." Cancer Immunology Research,4(12), pp. 1038-1048, 2016.
• Hirakawa M, Matos T, Liu H, Koreth J, Kim HT, Paul NE, Murase K, Whangbo J, Alho AC, Nikiforow S, Cutler C, Ho VT, Armand P, Alyea EP, Antin JH, Blazar BR, Lacerda JF, Soiffer RJ, Ritz J. "Low-dose IL-2 selectively activates subsets of CD4+ Tregs and NK cells." JCI Insight, 1(18), e89278, 2016.
• Lizotte PH, Ivanova EV, Awad MM, Jones RE, Keogh L, Liu H, Dries R, Almonte C, Herter-Sprie GS, Santos A, Feeney NB, Paweletz CP, Kulkarni MM, Bass AJ, Rustgi AK, Yuan GC, Kufe DW, Jnne PA, Hammerman PS, Sholl LM, Hodi FS, Richards WG, Bueno R, English JM, Bittinger MA, Wong KK. "Multiparametric profiling of non-small-cell lung cancers reveals distinct immunophenotypes." JCI Insight, 1(14), e89014, 2016.
• Lizotte PH, Jones RE, Keogh L, Ivanova E, Liu H, Awad MM, Hammerman PS, Gill RR, Richards WG, Barbie DA, Bass AJ, Bueno R, English JM, Bittinger M, Wong KK. "Fine needle aspirate flow cytometric phenotyping characterizes immunosuppressive nature of the methothelioma microenvionment." Scientific Reports, Vol. 6, Article: 31745, 2016.
• Rosen R, Amirault J, Liu H, Mitchell P, Hu L, Khatwa U, Onderdonk A. "Changes in gastric and lung microflora with acid suppression: acid suppression and bacterial growth." JAMA Pediatrics, 168(10), pp. 932-937, 2014.
• Fried AJ, Altrich ML, Liu H, Halsey JF, Bonilla FA. "Correlation of Pneumococcal Antibody Concentration and Avidity with Patient Clinical and Immunologic Characteristics." Journal of Clinical Immunology, 33(4), pp. 847-856, 2013. 
• Meijer DH, Kane MF, Mehta S, Liu H, Harrington E, Taylor CM, Stiles CD, Rowitch DH. "Separated at birth? The functional and molecular divergence of OLIG1 and OLIG2." Nature Reviews Neuroscience, 13(12), pp. 819-831, 2012.
• Liu H and Kohane IS. "Tissue and process specific microRNA-mRNA co-expression in mammalian development and malignancy." PLoS ONE 4(5): e5436, May 5, 2009.
• Ligon KL, Huillard E, Mehta S, Kesari S, Liu H, Alberta J A, Bachoo RM, Kane M, Louis DN, DePinho RA, Anderson DJ, Stiles CD, and Rowitch DH. "Olig2-Regulated Lineage-Restricted Pathway Controls Replication Competence in Neural Stem Cells and Malignant Glioma." Neuron, 53(4), 503-517, February 15, 2007.
• Liu H, Kho AT, Kohane IS, and Sun Y. "Predicting survival within the lung cancer histopathological hierarchy using a multi-scale genomic model of development." PLoS Medcine, 3(7):e232, 2006.
• Liu H, Maekawa T, Patrikalakis NM, Sachs EM, and Cho W. "Methods for Feature-Based Design of Heterogeneous Solids." Computer Aided Design. 36(12), 1141-1159, 2004.
• Jackson TR, Liu H, Patrikalakis NM, Sachs EM and Cima MJ. "Modeling and Designing Functionally Graded Material Components for Fabrication with Local Composition Control." Materials and Design. 20(2-3), 63-75, 1999.

Articles in Conference Proceedings

• Gelli, A., Tao, A., Zhang, G,,  Sundaram, N., Hogg, J.,Tamilarasan, S., Shao, Y., Vogiatzis, C., Robles-Granda, P., Angrave, L., Liu, H. "Identifying, categorizing, and evaluating the taxonomy of STEM content and the obstacles in converting handwritten lecture materials of engineering courses for improved accessibility." Proceedings of the ASEE Annual Conference, 2026. Accepted.
• Tao, A.,, Ding, X., Gelli, A., Sundaram, N., Zhang, G,, Hogg, J.,Tamilarasan, S., Shao, Y., Vogiatzis, C., Robles-Granda, P., Amos, J., Angrave, L., Liu, H. "Evaluating the perceived outcomes and understanding the needs of engineering and computing students in connection to the use of multi-modal mathematical lecture content." Proceedings of the ASEE Annual Conference, 2026. Accepted.
• Ding, X., Zhao, D., Tao, A., Gopannagari, M., Robles-Grandas, P., Shao, V., Vogiatzis, C., Fredricksen, A., Amos, J., Angrave, L., Liu, H. “Understanding the needs of students to make Mathematics and other STEM Contents more accessible in college Engineering courses.” Proceedings of the ASEE Annual Conference, no page numbers assigned, 2025.
• Asanaka, L., Zhao, D., Gopannagari, M., Tamilarasan, S., Tao, A., Zhang, N.Sletten, G., Solarman, A., Ding, X., Robles-Grandas, P., Shao, V., Vogiatzis, C., Angrave, L., Liu, H. “Improving the Accessibility of Mathematical and other STEM Content in Engineering courses through Machine Learning Models.” Proceedings of the ASEE Annual Conference, no page numbers assigned, 2025.
• Robles-Granda, P., Liu, H., Anwar C., Narang, S., Dalpiaz, D., Angrave, L. “Beyond Descriptive Statistics: Analysis of Time Series of Student Interactionsin Engineering Courses Through the Lens of Modern Mathematical Methods.” Proceedings of the ASEE Annual Conference, no page numbers assigned, 2025.
• Ding, X., Gopannagari, M., Sun, K., Tao, A., Zhao, D., Varadhan, S., Vogiatzis, C., Hardy, B., Dalpiaz, D., Angrave, L., and Liu, H. "Evaluation of LLMs and other machine learning methods in the analysis of qualitative survey responses for accessible engineering education research." Proceedings of the ASEE Annual Conference, no page numbers assigned, 2024.
• Zhao, D., Gopannagari, M., Ding, X., Tao, A., Varadhan, S., Dignan, B., Amos, J., Vogiatzis, C., Dalpiaz, D., Hardy, B., Angrave, L., and Liu, H. "Accessibility Nuggets, Video Vignettes, and other Instructor Development approaches to foster UDL adoption and Inclusive Engineering Education." Proceedings of the ASEE Annual Conference, no page numbers assigned, 2024.
• Ding X., Sun K., Xiao Z., Varadhan S., Li J., Gersich N., Agarwal A., Gopannagari M., Vogiatzis C., Dalpiaz D., Amos J., Angrave L., Liu H. "Evaluating the low-stakes assessment performance, student perceived accessibility, belongingness, and self-efficacy in connection to the use of digital notes in engineering and computing courses." Proceedings of the ASEE Annual Conference, no page numbers assigned, 2023.
• Varadhan S., Ding X., Zhao D., Agarwal A., Dalpiaz D., Vogiatzis C., Huang Y., Angrave L., Liu H. "Opportunities and Barriers to UDL-based Course Designs for Inclusive Learning in Undergraduate Engineering and other STEM courses." Proceedings of the ASEE Annual Conference, no page numbers assigned, 2023.
• Liu, H., Angrave, L., Amos, J., Dalpiaz, D., Vogiatzis, C., Xiao, Z.Y., Varadhan, S., Louie J. "A Digital Book-Based Pedagogy to Improve Course Content Accessibility for Students with and without Disabilities in Engineering and other STEM courses (WIP)." Proceedings of the ASEE Annual Conference, no page numbers assigned, 2022.
• Liu, H., Moparthi, D., Dalpiaz, D., Amos, J., Angrave, L., Vogiatzis, C., Reck, R., Varadhan, S., Huang Y. "Understanding the needs of students with and without disabilities for inclusive UDL-based design of Engineering courses through learning management systems." Proceedings of the ASEE Annual Conference, no page numbers assigned, 2022 .
• Amos, J.R., Zhang, Z., Angrave, L., Liu, H., Shen, Y., Vawani, K. "A UDL-based large-scale study on the needs of students with disabilities in engineering courses." Proceedings of the ASEE Annual Conference, no page numbers assigned, 2021.
• Vanwani, K, Zhang Z, Angrave L, Liu H, Amos JR, "Qualitative Analysis of college students' perception of multiple representations and modalities in courses." Proceedings of the ASEE Illinois-Indiana Regional Conference, no page numbers assigned, 2021.
• Angrave L., Jensen K., Zhang Z., Mahipal C., Mussulman M., Schmitz C., Baird R., Liu H., Sui R., Wu M., Kooper R. "Improving Student Accessibility, Equity, Course Performance, and Lab Skills: How Introduction of ClassTranscribe Is Changing Engineering Education at the University of Illinois." Proceedings of ASEE Annual Conference, no page numbers assigned, 2020.
• H. Liu, W. Cho, T. R. Jackson, N. M. Patrikalakis, and E. M. Sachs. "Algorithms for Design and Interrogation of Functionally Gradient Material Objects", Proceedings of 2000 ASME DETC/CIE, 26-th ASME Design Automation Conference September, 2000, Baltimore, Maryland, USA. p.141 and CDROM, NY:ASME, 2000.

Invited Lectures

• Improving Accessibility of STEM Content in Engineering courses with ML Models
• Understanding the needs of students to make Mathematics and other STEM Contents more accessible in college Engineering courses
• Evaluating the Low-Stakes Assessment Performance: Student-Perceived Accessibility, Belongingness, and Self-Efficacy in Connection to the Use of Digital Notes in Engineering and Computing Courses
• Opportunities and barriers in implementing UDL for accessibility - data from both students and faculty’s perspectives
• Utilizing Canvas to help teach a course with universal design of learning - a few practical strategies
• Universal design of learning and its practices - How to begin?
• Understanding the needs of students with disabilities based on Universal Design of Learning and some implementations
• A Digital Book-Based Pedagogy to Improve Course Content Accessibility for Students with and without Disabilities in Engineering and other STEM courses
• A UDL-based large-scale study on the needs of students with disabilities in engineering courses
• Understanding of the needs of students with disabilities-what does data in two semesters of covid19 tell us?
• Understanding of the needs of students with disabilities based on Universal Design of Learning principle

Conferences Organized or Chaired

• Organizer, Panel Discussion: "Understanding the Needs of Students with Disabilities based on Universal Design of Learning Principles," CMD-IT/ACM Richard Tapia Celebration of Diversity in Computing Conference (TAPIA), 2021

Presentations

• H. Liu, L. Angrave, "Opportunities and barriers in implementing UDL for accessibility-data from both students and faculty's perspectives." Accessing Higher Ground, Association on Higher Education And Disability (AHEAD), 2023
• H. Liu, "Understanding the needs of students with disabilities-what does data in two semesters of COVID 19 tell us?" Illinois Computer Science Summer Teaching Workshop, 2021

Other Scholarly Activities

• UDL and Accessbility Research Lab: https://publish.illinois.edu/udl-accessibility-group/

Professional Societies

• Reviewer for the American Society of Engineering Education, 2024-2025

Service on Department Committees

• Member, BPC Committee, SSCDS, University of Illinois Urbana-Champaign, 2022
• Member, Undergraduate Student Award Committee, 2019-Present

Service on College Committees

• Member, IDEA Institute, Grainger College of Engineering, University of Illinois Urbana-Champaign, 2021-Present
• Member, Anti-racism Task Force, Grainger College of Engineering, University of Illinois Urbana-Champaign, 2020

Service on Campus Committees

• Member, Senate Committee on Faculty and Academic Staff Benefits, University of Illinois Urbana-Champaign, 2026
• Member, University of Illinois Urbana-Champaign Senate, 2024-2026
• Member, Campus Canvas Transition Accessibility Team, University of Illinois Urbana-Champaign, 2021-2022
• Consultant, "Reimagine Our Future" Sustainability Competition, University of Illinois Urbana-Champaign, 2021
• Member, Initial Appointment of University Ombudsperson Committee, University of Illinois Urbana-Champaign, 2020

Honors

• 2nd Best DEI Paper Award, New Engineering Educators, ASEE, 2025
• Best DEI Paper Award, New Engineering Educators, ASEE, 2022 (6/23/2022)
• 2nd Best Diversity, Equity, and Inclusion Paper Award, New Engineering Educators, ASEE, 2021
• 3rd Best Paper Award, New Engineering Educators, ASEE, 2021 (6/21/2021)

Recent Courses Taught

• CS 361 (STAT 361) - Prob & Stat for Computer Sci