Juexiao Zhou 周觉晓, Joshua Chou

Ph.D. Candidate working with Prof. Xin Gao

Structural and Functional Bioinformatics (SFB) Group

Computational Bioscience Research Center (CBRC)

King Abdullah University of Science and Technology (KAUST)

Email: juexiao.zhou@kaust.edu.sa, juexiao.zhou@gmail.com

Office: Building 3, Level 4, Sea Side, 4216-WS23, KAUST

CV (last update: Apr 2024) | Github | Linkedln | ORCID | Google Scholar

Recent News:

• Apr 2024, Global incidence, prevalence, YLDs, DALYs, and HALE paper is accept by The Lancet (IF=168.9)
• Apr 2024, Causes of Death paper is accept by The Lancet (IF=168.9)
• Mar 2024, Global fertility paper is accept by The Lancet (IF=168.9)
• Mar 2024, Patient privacy paper is accept by Trends in Genetics (IF=11.4)
• Mar 2024, Demographics paper is accept by The Lancet (IF=168.9)
• Feb 2024, invited to the TV show “Investing Now for Future in Hong Kong and the Middle East：New Cradle of Innovation” by RTHK 香港電台
• Dec 2023, PPML-Omics is accepted by Science Advances (IF=15.4).
• Dec 2023, PPPML-HMI is accepted by Computers in Biology and Medicine (IF=7.7).
• Nov 2023, invited to give a talk to the Saudi Olympiad Elite Camp.
• Oct 2023, AFS is accepted by Nature Communications (IF=17).
• Sep 2023, passed my Ph.D. proposal titled “Towards Privacy-preserving Artificial General Intelligence (PAGI) for Healthcare and Bioinformatics”.
• Jun 2023, COVID-19 paper is accepted by Nature Communications (IF=17).
• Mar 2023, spatial transcriptomics paper is accepted by Nature Communications (IF=17).
• Feb 2023, invited to give a talk at Rising Stars in AI Symposium 2023 at KAUST.
• Oct 2022, DeeReCT-TSS paper is accepted by Genomics, Proteomics & Bioinformatics (IF=10.1).
• May 2022, COVID-19 paper is accepted by Nature Machine Intelligence (IF=27.2).

​ [Past news]

Short Bio

He is a Ph.D. Candidate in Computer Science at King Abdullah University of Science and Technology under the supervision of Prof. Xin Gao from Dec 2021 - Present.

He got the Master of Science degree, M.S. in Computer Science at King Abdullah University of Science and Technology under the supervision of Prof. Xin Gao in Dec 2021.

He got the Bachelor of Science degree, B.S. (Honored) in Bioinformatics at Southern University of Science and Technology under the supervision of Prof. Wei Chen in Jun 2020.

He was born on Jan 20, 1999 in Hunan, China.

Research Interests

• Intelligent Healthcare: develop machine learning (ML) / deep learning (DL) techniques for healthcare, including disease detection, risk assessment, etc.

• Bioinformatics: develop new methods for bioinformatics tasks, including gene regulation understanding, system biology, etc.

• Privacy and Security

• Artificial General Intelligence (AGI)

• Large Language Model (LLM)

  

Selected Publications [Full list]

(# equal contribution, * corresponding author)

1. A unified method to revoke the private data of patients in intelligent healthcare with audit to forget. Juexiao Zhou#, Haoyang Li#, Xingyu Liao, Bin Zhang, Wenjia He, Zhongxiao Li, Longxi Zhou, Xin Gao* Nature Communications DOI: 10.1038/s41467-023-41703-x Access: online, pdf Press: KAUST Discovery, Enerzine




2. PPML-Omics: A privacy-preserving federated machine learning method protects patients’ privacy in omic data. Juexiao Zhou#, Siyuan Chen#, Yulian Wu#, Haoyang Li, Bin Zhang, Longxi Zhou, Yan Hu, Zihang Xiang, Zhongxiao Li, Ningning Chen, Wenkai Han, Di Wang and Xin Gao*. Science Advances DOI: 10.1126/sciadv.adh8601 Access: online, pdf Press: Inside Precision Medicine, Today Headline, Tech Xplore, ScienMag, Bioengineer.org, Newswise, EurekAlert, Biocompare, nabd.ws




3. Patient privacy in AI-driven omics methods. Juexiao Zhou, Chao Huang, Xin Gao Trends in Genetics DOI: https://doi.org/10.1016/j.tig.2024.03.004 Access: online, pdf




4. Annotating TSSs in Multiple Cell Types Based on DNA Sequences and RNA-seq Data via DeeReCT-TSS. Juexiao Zhou#, Bin Zhang#, Haoyang Li, Longxi Zhou, Zhongxiao Li, Yongkang Long, Wenkai Han, Mengran Wang, Huanhuan Cui, Wei Chen, Xin Gao*. Genomics, Proteomics & Bioinformatics DOI: 10.1016/j.gpb.2022.11.010 Access: online, pdf




5. Personalized and privacy-preserving federated heterogeneous medical image analysis with PPPML-HMI. Juexiao Zhou#, Longxi Zhou#, Di Wang, Xiaopeng Xu, Haoyang Li, Yuetan Chu, Wenkai Han, Xin Gao* Computers in Biology and Medicine DOI: 10.1016/j.compbiomed.2023.107861 Access: online, pdf




6. SkinGPT-4: An Interactive Dermatology Diagnostic System with Visual Large Language Model. Juexiao Zhou#, Xiaonan He#, Liyuan Sun#, Jiannan Xu, Xiuying Chen, Yuetan Chu, Longxi Zhou, Xingyu Liao, Bin Zhang, Xin Gao* under review. Access: arXiv



7. Path to Medical AGI: Unify Domain-specific Medical LLMs with the Lowest Cost.
   Juexiao Zhou#, Xiuying Chen#, Xin Gao*
   under review.
   Access: arXiv


8. Automated Bioinformatics Analysis via AutoBA.
   Juexiao Zhou#, Bin Zhang#, Xiuying Chen, Haoyang Li, Xiaopeng Xu, Siyuan Chen, Xin Gao*
   under review.
   Access: arXiv
   Press: CBIRT news, Medium


9. A comprehensive benchmarking with practical guidelines for cellular deconvolution of spatial transcriptomics.
   Haoyang Li#, Juexiao Zhou#, Zhongxiao Li, Siyuan Chen, Xingyu Liao, Bin Zhang, Ruochi Zhang, Yu Wang, Shiwei Sun, Xin Gao*
   Nature Communications
   DOI: 10.1038/s41467-023-37168-7
   Access: online, pdf
   Press: BioMed, CBIRT news, KAUST news
   Chosen as Editors’ Highlights in Nature Communications


10. An Interpretable Deep Learning Workflow for Discovering Sub-Visual Abnormalities in CT Scans of COVID-19 Inpatients and Survivors.
    Longxi Zhou#, Xianglin Meng#, Yuxin Huang#, Kai Kang#, Juexiao Zhou, Yuetan Chu, Haoyang Li, Dexuan Xie, Jiannan Zhang, Weizhen Yang, Na Bai, Yi Zhao, Mingyan Zhao, Guohua Wang, Lawrence Carin, Xigang Xiao, Kaijiang Yu, Zhaowen Qiu, Xin Gao*.
    Nature Machine Intelligence
    DOI: 10.1038/s42256-022-00483-7
    Access: online, pdf


11. Predicting the antigenic evolution of SARS-COV-2 with deep learning.
    Wenkai Han#, NingNing Chen#, Xinzhou Xu#, Adil Salhi, Juexiao Zhou, Zhongxiao Li, Huawen Zhong, Elva Gao, Ruochi Zhang, Yu Wang, Shiwei Sun*, Peter Cheung*, Xin Gao*
    Nature Communications
    DOI: 10.1038/s41467-023-39199-6
    Access: online, pdf

Working Experience

• Student Ambassador, CEMSE, King Abdullah University of Science and Technology, Dec 2021 - Present

Teaching Experience

• CS220, Data Analytics - AI Camp for Ministry of Interior, Saudi Arabia, Fall 2023/2024, KAUST

  • Cooperated with Prof. Xin Gao

  • Position: Senior Teaching Assistant

• CS220, Data Analytics, Fall 2022/2023, KAUST

  • Cooperated with Prof. Xin Gao
  • Position: Teaching Assistant

• BioE 201/230 Foundations of Bioengineering, Fall 2022/2023, KAUST

  • Cooperated with Prof. Xin Gao
  • Position: Guest Lecturer, Building 9 Room 4225
  • Contents:
    • Lab 1. Genome data analysis, 2022.08.30, colab
      • Python basics
      • D/RNA sequence analysis
      • Biopython
      • BLAST
      • Reference genome
    • Lab 2. Protein sequence analysis, 2022.09.06, colab
      • Protein sequence analysis
      • MSA
      • PDB
      • PyMOL
      • Secondary structure prediction
    • Lab 3. Protein structure and function, 2022.09.13, colab
      • Ab initio with PyRosetta
      • AlphaFold2
      • NucleicNet
      • Docking with Smina
      • Pfam annotation with deep learning

• CS398 Graduate Seminar, Spring 2022, KAUST

  • Cooperated with Prof. Dominik Michels
  • Position: Teaching Assistant

Awards

King Abdullah University of Science and Technology

KAUST, 2021-Present

PhD, Computer Science

GPA: 4.00 / 4.00

• CEMSE Dean’s List Award, 2023
• KAUST AII’s NeurIPS travel grant, 2022
• CEMSE Dean’s List Award, 2022
• Excellent Research Award, CEMSE, 2021

King Abdullah University of Science and Technology

KAUST, 2020-2021

Master of Science, Computer Science

GPA: 3.95 / 4.00

• Student ambassador, CEMSE, 2021
• Yearly best student award, CEMSE, 2021
• Full scholarship for MS/PhD study, 2020

Southern University of Science and Technology

SUSTech, 2016-2020

Bachelor of Science, Bioinformatics, Biology

GPA: 3.92 / 4.00 (Top 0.1%), Core GPA: 3.94/4.00

• Outstanding graduate of SUSTech, 2020.
• Cum Laude Graduate of the Department of Biology (Top 1/10), 2020.
• The Guinness world record for “the most vows received by a single civilized act activity”, 2019
• Candidate for 2019 National Scholarship, 2019
• Summer social practice excellent experience Award, 2018
• Excellent Student, The First Prize Scholarship, 2018
• Outstanding volunteer for the 12th CBIS Biennial Meeting, Shenzhen, China, 2018
• Candidate for 2018 National Scholarship, 2018
• Outstanding Volunteer of the 3rd Shenzhen International Life Science & Health Industry Summit (2016) Excellent Student, The First Prize Scholarship, 2017
• Dean scholarship, The First Prize Scholarship, 2017
• Excellent Student Cadre, 2017
• Outstanding Volunteer of 2017 Shenzhen International Precision Medicine Summit, 2017
• Alma mater practice excellent team, 2017
• National Literary Creation Award, 2016
• Excellent Student, The Second Prize Scholarship, 2016

Memberships

• Chinese Association for Artificial Intelligence (CAAI) Member
• The international Asia-Pacific Bioinformatics Network (APBioNET) Member
• Global Burden of Disease (GBD) Collaborator Network Member

Selected Press Coverage [Full list]

• PPML-Omics protects patients’ privacy in omic data was covered by:
  • Algorithm Proposed to Protect Patient Privacy, Inside Precision Medicine
  • An integrated shuffler optimizes the privacy of personal genomic data used for machine learning, Today Headline
  • An integrated shuffler optimizes the privacy of personal genomic data used for machine learning, Tech Xplore
  • Shuffling the deck for privacy, ScienMag
  • Shuffling the deck for privacy, Bioengineer.org
  • Shuffling the deck for privacy, Newswise
  • Shuffling the deck for privacy, EurekAlert
  • Novel Privacy-Preserving Machine-Learning Method Developed for Genomics Data, Biocompare
  • نهج ثوري يحافظ على خصوصية البيانات الطبية, nabd.ws
  • Revolutionizing Healthcare: Secure Multi-Party Computation and Privacy-Preserving Machine Learning, BNN Breaking
  • An integrated shuffler optimizes the privacy of personal genomic data used for machine learning, Microsoft Start
  • Shuffling The Deck For Privacy, Eurasia Review
• Audit to forget was covered by:
  • Un logiciel pour garantir le droit à l’oubli des patients dans l’IA en milieu de santé, Enerzine
  • Safeguarding the right to be forgotten, KAUST Discovery

Invited Talks

• [2023/11/22] Introduction to ChatGPT and Application of GPT in Healthcare.
  • Oral. Saudi Olympiad Elite Camp, King Abdullah University of Science and Technology, Saudi Arabia
• [2023/09/20] A Unified Method to Revoke the Private Data of Patients in Intelligent Healthcare with Audit to Forget.
  • Oral. CBRC Seminar, King Abdullah University of Science and Technology, Saudi Arabia
• [2023/06/12] SkinGPT-4: An Interactive Dermatology Diagnostic System with Visual Large Language Model.
  • Oral. Unlocking the Power of “ChatGPT”, King Abdullah University of Science and Technology, Saudi Arabia
• [2023/03/02] Audit to Forget: A Unified Method to Revoke Patients’ Private Data in Intelligent Healthcare.
  • Poster. CBRC session, KAUST Research Open Week, Saudi Arabia
• [2023/02/02] Audit to Forget: A Unified Method to Revoke Patients’ Private Data in Intelligent Healthcare.
  • Oral & Poster. Spotlight, Rising Stars in AI Symposium 2023 at KAUST, Saudi Arabia
• [2022/11/10] Privacy in Bioinformatics and Intelligent Healthcare.
  • Poster. Smart-Health Student Research Symposium, KAUST, Saudi Arabia
• [2022/03/29] PPML-Omics: a Privacy-Preserving federated Machine Learning system protects patients’ privacy from omic data
  • Oral. CBRC Dual Seminar, King Abdullah University of Science and Technology, Saudi Arabia
• [2022/03/09] PPML-Omics: a Privacy-Preserving federated Machine Learning system protects patients’ privacy from omic data
  • Oral. BDAI重点实验室研究生沙龙第19期, 中国人民大学高瓴人工智能学院，中国北京

Academic Services

Reviewer

Journal/Conference	# Paper Reviewed
AI4D3 @ NeurIPS 2023	1
Computers in Biology and Medicine	17
Genome Biology	1
Genome Research	2
Heliyon	1
IJCAI-ECAI 2022	1
ICONIP 2020	1
ICMLA 2021	1
IEEE Transactions on Knowledge and Data Engineering	1
Journal of Bioinformatics and Computational Biology	1
Medical Image Analysis	1
MICCAI 2020	1
MICCAI 2024	4
Multimedia Systems	1
SIGKDD 2022	2

Conference Administrator

• The 21st International Conference on Bioinformatics (InCoB2022), Administrator, certificate