Lizhi Liu's Personal Website

About Me

Lizhi Liu（刘砺志）

Email: liulizhi1996 [at] gmail.com

GitHub: https://github.com/liulizhi1996

LinkedIn: https://www.linkedin.com/in/砺志-刘-467649147/

Google Scholar: https://scholar.google.com/citations?user=c9ALKpAAAAAJ

Education

• School of Computer Science, Fudan University, Master, 2018 - 2021
• Studied at Shanghai Key Laboratory of Intelligent Information Processing under the supervision of Prof. Shanfeng Zhu.
• The slides for my master thesis defense are available here.
• Department of Computer Science, School of Information Science and Engineering, Xiamen University, Bachelor, 2014 - 2018
• Ranked 1st of the department (1/93)
• 2015 - 2018   Commissary in charge of studies   Class 1 of 2014, Department of Computer Science
• 2015 - 2016   Deputy director         Self-discipline Committee, Student Union of School of Information
• 2014 - 2015   Secretary           Dormitory Committee, Student Union of School of Information

Publications

• Lizhi Liu, Xiaodi Huang, Hiroshi Mamitsuka, Shanfeng Zhu, "HPOLabeler: improving prediction of human protein-phenotype associations by learning to rank", Bioinformatics, 2020, 36(14): 4180–4188. [link]
• The paper has been accepted as oral talk in the Function COSI at ISMB 2020. [Click to see the slides] [Watch talk video at YouTube] [Certificate]
• The paper has been accepted as highlight paper and oral talk in the venue of Transcriptome and Proteome at CBC 2020. [Click to see the slides]
• HPOLabeler (ZhuLab) achieved 1st place of F_max, 2nd place of S_min, and 2nd place of Averaged AUC in CAFA4 preliminary evaluation. [Result1] [Result2]
• Source code: https://github.com/liulizhi1996/HPOLabeler

• Lizhi Liu, Hiroshi Mamitsuka, Shanfeng Zhu, "HPOFiller: identifying missing protein-phenotype associations by graph convolutional network", Bioinformatics, 2021, 37(19): 3328-3336. [link]
• Source code: https://github.com/liulizhi1996/HPOFiller

• Lizhi Liu, Hiroshi Mamitsuka, Shanfeng Zhu, "HPODNets: deep graph convolutional networks for predicting human protein-phenotype associations", Bioinformatics, 2022, 38(3): 799–808. [link]
• Source code: https://github.com/liulizhi1996/HPODNets

• Lizhi Liu, Shanfeng Zhu, "Computational methods for prediction of human protein-phenotype associations: a review", Phenomics, 2021, 1: 171-185. [link]

• Junning Gao, Lizhi Liu, Shuwei Yao, Xiaodi Huang, Hiroshi Mamitsuka, Shanfeng Zhu, "HPOAnnotator: improving large-scale prediction of HPO annotations by low-rank approximation with HPO semantic similarities and multiple PPI networks", BMC Medical Genomics, 2019, 12(10): 187. [link]

• Lizhi Liu, "Prospects on Research of Human Protein-Phenotype Associations Prediction Algorithms" (人类蛋白质表型标注预测算法研究展望), 2021. [link]
• This is my review paper on the future prospects of research on prediction of human protein-phenotype associations written by Chinese. It was not published anywhere. I hope this review can provide insight into the development of Phenomics.

• Lizhi Liu, "TopoLink: Topology-enhanced Graph Transformer with Extended Persistent Homology For Link Prediction", IJCNN, 2025. [accepted]
• See the Leaderboard for ogbl-collab of Link Property Prediction task in the Stanford OGB Challenge.
• Source code: https://github.com/liulizhi1996/TopoLink

• Lizhi Liu, "Every Hop Etched in Memory: Tokenized Graph Mamba Meets Directed Graph Learning", IJCNN, 2025. [accepted]
• Source code: https://github.com/liulizhi1996/DIGRAM

Patents

• Lizhi Liu, Yu Wang, Haijian Jiang, Qing Min, "Entity tag association prediction method and device and computer readable storage medium" (一种实体标签关联预测方法、装置及计算机可读存储介质), 2021.11.26, China Patent No. CN114091614B; WIPO Patent No. WO2023093205A1; US Patent No. US-12327202-B2.
• Lizhi Liu, Yu Wang, Haijian Jiang, Qing Min, "An entity classification method, device, electronic equipment and storage medium" (一种实体分类方法、装置、电子设备及存储介质), 2022.09.16, China Patent No. CN115577283A.
• Lizhi Liu, Zhichen Tong, Haijian Jiang, Qing Min, "Entity tag association prediction method and device and computer readable storage medium" (一种实体标签关联预测方法、装置及计算机可读存储介质), 2023.04.23, China Patent No. CN116821822A.
• Lizhi Liu, Zhichen Tong, Haijian Jiang, Qing Min, Jia Li, Shuai Shang, "Enhanced payment verification method, device, server, system and medium" (支付增强验证的方法、装置、服务器、系统及介质), 2023.07.20, China Patent No. CN117132281A; Hong Kong Patent No. HK40102040; WIPO Patent No. WO2025015958A1; Taiwan Patent No. TW I888097B.
• Lizhi Liu, Zhichen Tong, Haijian Jiang, Qing Min, "A data clustering method, device and computer-readable storage medium" (一种数据聚类方法、装置及计算机可读存储介质), 2023.07.21, China Patent No. CN117034059A; WIPO Patent No. WO2025020590A1.
• Lizhi Liu, Zhichen Tong, Haijian Jiang, Qing Min, "A priority message queue implementation, device and computer-readable storage medium" (一种优先消息队列实现方法、装置及计算机可读存储介质), 2023.09.26, China Patent No. CN117435361A.
• Lizhi Liu, Zhichen Tong, Haijian Jiang, Qing Min, "An entity classification method, device and computer readable storage medium" (一种实体分类方法、装置及计算机可读存储介质), 2023.10.09, China Patent No. CN117290506A.
• Yuanyuan Niu, Weixing Zhao, Guanglu Huang, Qing Min, Lizhi Liu, "Interface update methods, devices, equipment, media and products" (界面更新方法、装置、设备、介质及产品), 2023.12.11, China Patent No. CN117908915A.
• Lizhi Liu, Zhichen Tong, Haijian Jiang, Qing Min, "Object classification method, model training method, device and equipment" (对象分类方法、模型训练方法、装置以及设备), 2024.03.25, China Patent No. CN118133125A.
• Lizhi Liu, Zhichen Tong, Haijian Jiang, Qing Min, "Product recommendation method, model training method, device and equipment" (商品推荐方法、模型训练方法、装置以及设备), 2024.03.25, China Patent No. CN118279017A; Hong Kong Patent No. HK40113099.
• Lizhi Liu, Zhichen Tong, Haijian Jiang, Qing Min, "Product recommendation method, model training method, device and equipment" (商品推荐方法、模型训练方法、装置及设备), 2024.07.08, China Patent No. CN118691377A; Hong Kong Patent No. HK40113568.
• Lizhi Liu, Zhichen Tong, Haijian Jiang, Qing Min, "Link prediction method, model training method, device and equipment" (链接预测方法、模型训练方法、装置以及设备), 2024.09.04, China Patent No. CN119179804A.
• Lizhi Liu, Xiaoqiang Yu, Zhichen Tong, Haijian Jiang, Qing Min, "Method, device, equipment, medium and program product for recommending commodity information" (商品信息的推荐方法、装置、设备、介质及程序产品), 2024.09.18, China Patent No. CN119130605A.

Honors and Awards

• Competitions
• 1st prize of the undergraduate group, Fujian Division, 2016 China Contemporary Undergraduate Mathematical Contest in Modeling (CUMCM)
• 3rd prize, 2017 "Huawei Cup" China Undergraduate Artificial Intelligent Design Competition
• 1st prize, South China Division, 2017 2nd National College Students Connected Smarter Systems Innovation Competition
• Scholarship
• National Scholarship, China Ministry of Education, 2014-2015 and 2016-2017
• China Construction Bank Scholarship, Xiamen University, 2017
• Academic Excellence Scholarship for Graduates (First Class), School of Information Science and Engineering, Xiamen University, 2018
• Academic Excellence Scholarship (First Class), School of Information Science and Engineering, Xiamen University, 2016
• Social Work Scholarship, School of Information Science and Engineering, Xiamen University, 2016
• Outstanding Academic Scholarship for Master Students (Second Class), Fudan University, 2019-2020
• Huawei Scholarship, Fudan University, 2020
• Honors
• Outstanding Graduates of Shanghai City, Shanghai Municipal Education Commission, 2021
• Outstanding Graduates, School of Information Science and Engineering, Xiamen University, 2018
• Merit Student, Xiamen University, 2016
• Dean's Honours List, School of Information Science and Engineering, Xiamen University, 2014-2015 and 2015-2016
• Advanced Individual of Summer Social Practice, Xiamen University, 2015
• Excellent League Member, School of Information Science and Engineering, Xiamen University, 2015-2016 and 2016-2017
• Advanced Individual of Academic Activities, School of Information Science and Engineering, Xiamen University, 2016-2017

Certificates

• Qualification of Computer and Software Professional (Ruan Kao), Database System Engineer, Intermediate Certification. Authorized by Ministry of Human Resources and Social Security & Ministry of Industry and Information Technology of the PRC.
• National Computer Rank Examination (NCRE), Java Programming, Certificate of Level 2 (Excellent). Authorized by National Education Examinations Authority, Ministry of Education of the PRC.
• National Computer Rank Examination (NCRE), Python Programming, Certificate of Level 2 (Excellent). Authorized by National Education Examinations Authority, Ministry of Education of the PRC.
• National Computer Rank Examination (NCRE), Database Technology, Certificate of Level 3 (Excellent). Authorized by National Education Examinations Authority, Ministry of Education of the PRC.
• National Computer Rank Examination (NCRE), Database Engineer, Certificate of Level 4 (Excellent). Authorized by National Education Examinations Authority, Ministry of Education of the PRC.