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Zhi Huang ORCID iD icon

Ph.D. Candidate, ECE, Purdue University
Email: huang898@purdue.edu
IEEE student member '16
IEEE young professionals '16

Google Scholar Github

I am a Ph.D. candidate at Purdue University, majoring in Electrical and Computer Engineering (ECE), with the area of CNSIP (Communications, Networking, Signal and Image Processing). My background is in the area of Machine and Deep Learning, Bioinformatics, Computational Biology, and Healthcare.

My research resides at the intersection of computer vision, deep learning, and bioinformatics, with a focus on image processing and computational biology. I am working with Prof. Kun Huang and Prof. Paul Salama as a 4th year Ph.D. candidate. Prior to that, I worked with Prof. Li Shen at Indiana University Center for Neuroimaging in 2017. I received an M.S. in ECE (Computer Engineering) degree from the Purdue School of Electrical and Computer Engineering, IUPUI in December 2016 and a B.S. in ECE degree from Xi'an Jiaotong University (西安交通大学) (BS-MS straight entrance class) in June 2015. I exchanged to the University of Michigan - Dearborn during my senior year.

From May 2019 to August 2019, I was at Philips Research North America as a Research Intern.

Softwares

TSUNAMI TSUNAMI: Translational Bioinformatics Tool SUite for Network Analysis and MIning

lmQCM lmQCM: R package for Gene Co-Expression Network Analysis

SALMON: Survival Analysis Learning with Multi-Omics Neural Networks

biolearns Biolearns: Computational Biology and Bioinformatics Toolbox in Python

Publications

Journals

TSUNAMI: Translational Bioinformatics Tool Suite for Network Analysis and Mining [preprint] [github] [software]
Zhi Huang, Zhi Han, Tongxin Wang, Wei Shao, Shunian Xiang, Paul Salama, Maher Rizkalla, Kun Huang, and Jie Zhang
Genomics, Proteomics and Bioinformatics (2019) (Accepted, in press).

SALMON: Survival Analysis Learning with Multi-Omics Neural Networks on Breast Cancer [paper] [github]
Zhi Huang, Xiaohui Zhan, Shunian Xiang, Travis Johnson, Bryan Helm, Christina Yu, Jie Zhang, Paul Salama, Maher Rizkalla, Zhi Han, and Kun Huang
Frontiers in genetics 10 (2019): 166.

Deep Learning-based Cancer Survival Prognosis from RNA-seq Data: Approaches and Evaluations [paper]
Zhi Huang, Travis S. Johnson, Zhi Han, Bryan Helm, Sha Cao, Chi Zhang, Paul Salama, Maher Rizkalla, Christina Y. Yu, Jun Cheng, Shunian Xiang, Xiaohui Zhan, Jie Zhang, and Kun Huang
BMC medical genomics 13, no. 5 (2020): 1-12.

Brain-wide structural connectivity alterations under the control of Alzheimer risk genes
Jingwen Yan, V. Vinesh Raja, Zhi Huang, Enrico Amico, Kwangsik Nho, Shiaofen Fang, Olaf Sporns, Yu-chien Wu, Andrew Saykin, Joaquín Goñi, and Li Shen
International Journal of Computational Biology and Drug Design 13, no. 1 (2020): 58-70.

Acidic leucine-rich nuclear phosphoprotein-32A expression contributes to adverse outcome in acute myeloid leukemia
Sai Huang, Zhi Huang, Chao Ma, Lan Luo, Yan-Fen Li, Yong-Li Wu, Yuan Ren, Cong Feng
Annals of Translational Medicine 8, no. 6 (2020)

Correlation analysis of histopathology and proteogenomics data for breast cancer
Xiaohui Zhan, Jun Cheng, Zhi Huang, Zhi Han, Bryan Helm, Xiaowen Liu, Jie Zhang, Tian-Fu Wang, Dong Ni, and Kun Huang
Molecular & Cellular Proteomics 18, no. 8 suppl 1 (2019): S37-S51.

Gene Co-expression Network and Copy Number Variation Analyses Identify Transcription Factors Involved in Multiple Myeloma Progression
Christina Y Yu, Shunian Xiang, Zhi Huang, Travis S Johnson, Xiaohui Zhan, Zhi Han, Mohammad Issam Abu Zaid, and Kun Huang
Frontiers in genetics 10 (2019): 468.

PseudoFuN: Deriving functional potentials of pseudogenes from integrative relationships with genes and miRNAs across 32 cancers
Travis S. Johnson, Sihong Li, Eric Franz, Zhi Huang, Shuyu Dan Li, Moray J. Campbell, Kun Huang, and Yan Zhang
GigaScience 8, no. 5 (2019): giz046.

LAmbDA: Label Ambiguous Domain Adaption Dataset Integration Reduces Batch Effects and Improves Subtype Detection
Travis Johnson, Tongxin Wang, Zhi Huang, Christina Yu, Yi Wu, Yatong Han, Kun Huang, and Jie Zhang
Bioinformatics 35, no. 22 (2019): 4696-4706.

Condition-specific Gene Co-expression Network Mining Identify Key Pathways and Regulators in Alzheimer’s Disease
Shunian Xiang, Zhi Huang, Zhi Han, Tianfu Wang, Dong Ni, Kun Huang, and Jie Zhang
BMC medical genomics 11, no. 6 (2018): 115.

Identification of potential key genes associated with severe pneumonia using mRNA‑seq
Cong Feng, He Huang, Sai Huang, Yong‑Zhi Zhai, Jing Dong, Li Chen, Zhi Huang, Xuan Zhou, Bei Li, Li‑Li Wang, Wei Chen, Fa‑Qin Lv, and Tan‑Shi Li
Experimental and therapeutic medicine 16, no. 2 (2018): 758-766.

Molecular Mechanisms of Mild and Severe Pneumonia: Insights from RNA Sequencing
Sai Huang, Cong Feng, Li Chen, Zhi Huang, Xuan Zhou, Bei Li, Li-li Wang, Wei Chen, Fa-qin Lv, and Tan-shi Li
Medical science monitor: international medical journal of experimental and clinical research 23 (2017): 1662.

Prognostic Significance of Mixed-Lineage Leukemia (MLL) Gene Detected by Real-Time Fluorescence Quantitative PCR Assay in Acute Myeloid Leukemia
Sai Huang, Hua Yang, Yan Li, Cong Feng, Li Gao, Guo-feng Chen, Hong-hao Gao, Zhi Huang, Yong-hui Li, and Li Yu
Medical science monitor: international medical journal of experimental and clinical research 22 (2016): 3009.

Identification of Potential Key Long Non-Coding RNAs and Target Genes Associated with Pneumonia Using Long Non-Coding RNA Sequencing (lncRNA-Seq): A Preliminary Study
Sai Huang, Cong Feng, Li Chen, Zhi Huang, Xuan Zhou, Bei Li, Li-li Wang, Wei Chen, Fa-qin Lv, and Tan-shi Li
Medical science monitor: international medical journal of experimental and clinical research 22 (2016): 3394.

Conferences

Diagnosis-Guided Multi-modal Feature Selection for Prognosis Prediction of Lung Squamous Cell Carcinoma
Wei Shao, Tongxin Wang, Zhi Huang, Jun Cheng, Zhi Han, Daoqiang Zhang, and Kun Huang
International Conference on Medical Image Computing and Computer-Assisted Intervention, pp. 113-121. Springer, Cham, 2019.

Deep Learning-based Cancer Survival Prognosis from RNA-seq Data: Approaches and Evaluations
Zhi Huang, Travis S. Johnson, Zhi Han, Bryan Helm, Sha Cao, Chi Zhang, Paul Salama, Maher Rizkalla, Christina Y. Yu, Jun Cheng, Shunian Xiang, Xiaohui Zhan, Jie Zhang, and Kun Huang
ICIBM’19: Int. Conf. on Intelligent Biology and Medicine, Columbus, OH, USA, June 9-11, 2019. (Oral Presentation and Travel Award)

Brain-wide structural connectivity alterations under the control of Alzheimer risk genes
Jingwen Yan, V. Vinesh Raja, Zhi Huang, Enrico Amico, Kwangsik Nho, Shiaofen Fang, Olaf Sporns, Yu-chien Wu, Andrew Saykin, Joaquín Goñi, and Li Shen
ICIBM’18: Int. Conf. on Intelligent Biology and Medicine, Los Angeles, CA, USA, June 10-12, 2018.

A Hierarchical Clustering Analysis (HCA) in Automatic Driving Regarding to Vehicle-to-Vehicle Pedestrian Position Identification
Jie Xue, Zhi Huang, Jue Zhou, Yaobin Chen, and Stanley Chien
25th International Technical Conference on the Enhanced Safety of Vehicles (ESV) National Highway Traffic Safety Administration. 2017.

Pedestrian protection using the integration of V2V and the Pedestrian Automatic Emergency Braking System
Bo Tang, Stanley Chien, Zhi Huang, Yaobin Chen
Intelligent Transportation Systems (ITSC), 2016 IEEE 19th International Conference on. IEEE, 2016.

Abstracts

Identifying hard-tissue conditions from dental images using convolutional neural network
Qing Sun, Zhi Huang, Mansu Kim, Anderson Hara, Gerardo Maupomé, Li Shen
ISBI’20: IEEE International Symposium on Biomedical Imaging in Iowa City, Iowa, USA, April 3-7, 2020.

Machine-learning identification of dental hard-tissue conditions through fully convolutional neural networks
Anderson Hara, Zhi Huang, Qing Sun, Gerardo Maupomé, Li Shen
APHA’19: American Public Health Association Annual Meeting and Expo in Philadelphia, USA, November 2-6, 2019.

Artificial Intelligence Driven Neoadjuvant Chemotherapy Response Prediction in Triple Negative Breast Cancer (TNBC) Unveils Non-linear Feature Interactions
Zhi Huang, Zhi Han, Anil V. Parwani, Kun Huang, Zaibo Li
United States & Canadian Academy of Pathology (USCAP) 2020 Annual Meeting Abstracts in Los Angeles, CA, USA, March 1-5, 2020.

AI-Driven Forecasting of Mean Pulmonary Artery Pressure for the Management of Cardiac Patients
Zhi Huang, Kristen Tgavalekos, Claire Zhao
Society of Critical Care Medicine's (SCCM) 49th Critical Care Congress in Orlando, Florida, USA, February 16-19, 2020.

Predicting response to neoadjuvant chemotherapy in HER2-positive breast cancer using machine learning models with combined tissue imaging and clinical features
Zhi Huang, Zhi Han, Anil V. Parwani, Kun Huang, Zaibo Li
United States & Canadian Academy of Pathology (USCAP) 2019 Annual Meeting Abstracts in National Harbor, Maryland, USA, March 16-21, 2019. (Platform Presentation)

Patents

A pointing mouse [Google patent] [School] [Wanfang]
Zhi Huang, Xinzhu Bei, Kewen Huang, Kun Qian, Anxue Zhang
CN103257723B CN Grant, 2016


Awards

Federally funded ICIBM 2019 Travel Award

Personal biography

Zhi Huang was born in Hefei, China in 1994. In June 2011, he received his high school diploma from Beijing Bayi High School. In June 2015, he received his Bachelor of Science degree in Automation (BS-MS straight entrance class) from Xi'an Jiaotong University School of Electronic and Information Engineering. He was an exchange student in the University of Michigan - Dearborn School of Electrical and Computer Engineering in his senior year (August 2014 - May 2015).

In December 2016, he received his Master of Science degree in Computer Engineering from the Purdue School of Electrical and Computer Engineering, Indiana University - Purdue University Indianapolis, Indiana, USA.

His Ph.D. program is at Purdue University, West Lafayette, Indiana, USA, with the major of Electrical and Computer Engineering, and the area of Communications, Networking, Signal and Image Processing. His current research interests include machine and deep learning, matrix factorization, survival analysis, bioinformatics, and computational biology. He is a research assistant at Indiana University School of Medicine. He is a student member of the IEEE and the IEEE Young Professionals since 2016. He has served as a reviewer since 2017 for Scientific Report (2020), Medical Science Monitor (2019), the International Conference on Intelligent Biology and Medicine (ICIBM) (2019), the Medical Image Computing and Computer Assisted Intervention (MICCAI) (2017, 2018, 2020), the AMIA Annual Symposium (2020), and ACM SIGKDD Conference on Knowledge Discovery and Data Mining (2020).

From May 2019 to August 2019, he was at Philips Research North America, Cambridge, Massachusetts, USA as a Research Intern. He has published over 20 journal and conference publications. He also held a Chinese invention patent and a Chinese utility model patent.


Miscellaneous

Before I pursue for my Ph.D. degree, I was a good photographer...
Here are some of my works: I am also an amateur chef ...