CV

Jieke (Jack) Wu's academic CV — education, research experience, publications, awards, and skills.

Contact Information

Name Jieke (Jack) Wu
Professional Title Graduate Student
Email jieke.wu@kaust.edu.sa

Professional Summary

Graduate student at KAUST focusing on artificial intelligence, multi-agent systems, and AI for scientific discovery. Developing autonomous AI systems and self-improving multi-agent frameworks.

Experience

  • 2025 - Present

    Thuwal, Saudi Arabia

    Research Assistant
    KAUST, Prof. Basem Shihada
    • Research on AI Scientist, Self-Improving AI, and Multi-Agent RL
    • Exploring generative models for scientific discovery
    • Developing multi-agent systems for collaborative AI research
  • 2024 - 2025

    Shanghai, China

    Research Intern
    MoleculeMind
    • Designed and implemented an unconditional protein backbone generation model using SE(3) diffusion (DDPM on SO(3))
    • Developed an epitope-conditioned binder design framework via cross-attention over target structure features
    • Extended the SE3Diffusion Binder module to support multi-chain protein binder generation
    • Investigated Flow Matching on SE(3) as an alternative to diffusion, achieving faster convergence
    • Systematically analyzed iPAE and distogram metrics; deployed DiffAffinity online service with JAX compatibility
  • 2024 - 2025

    Remote (US)

    Research Assistant
    Simon Fraser University / Natera, Prof. Wuyang Chen & Dr. Zijun Zhang
    • Developed TEACUP framework for training-free evaluation of clinical AI systems
    • Achieved 90% reduction in computational costs
    • Implemented ensemble modeling for clinical decision-making
  • 2024 - 2024

    Remote (US)

    Research Assistant
    Northwestern University, Prof. Han Liu
    • Designed evaluation metrics for GenomeOcean DNA sequence generation model
    • Conducted comparative analysis of ORF length distributions
    • Analyzed codon bias patterns for biological realism assessment
  • 2023 - 2024

    Remote (Canada)

    Research Assistant
    UC Berkeley, Dr. Wuyang Chen
    • Developed training-free data augmentation design principles
    • Published findings in ICML 2024 Workshop AI4Science

Education

  • 2025 - Present

    Thuwal, Saudi Arabia

    MS/PhD
    King Abdullah University of Science and Technology (KAUST)
    Computer Science
    • Member of the Intelligent Systems Lab
    • Advisor - Prof. Basem Shihada
    • Research Focus - AI Scientist, Self-Improving AI, and Multi-Agent RL
    • Relevant Coursework - Deep Learning for Visual Computing, Scientific Visualization, Robotics
  • 2021 - 2025

    Hefei, China

    B.S.
    University of Science and Technology of China (USTC)
    Life Sciences (Biotechnology)
    • Department of Life Sciences and Medicine
    • Core Courses - Linear Algebra B1, Electromagnetism B, Undergraduate Research Project (A+)
    • Relevant Coursework - Molecular Biology, Biochemistry, Structural Biology, Bioinformatics, Probability & Statistics
    • Interdisciplinary background bridging wet-lab biology with computational modeling for AI-driven research

Publications

  • 2026
    D-DOIT: Training-free Adaptation of Discrete Diffusion via Doob's h-Transform

    First-author paper on training-free adaptation of discrete diffusion models using Doob’s h-transform.

  • 2024
    Training-free Design of Augmentations with Data-centric Principles

    First-author workshop paper on training-free data augmentation design.

  • 2026
    Annealed Co-Generation: Disentangling Variables via Progressive Pairwise Modeling
  • 2026
    AnchorGen: Anchored Optimization for Customizable Generative 3D Design
  • 2025
    GenomeOcean: Efficient Foundation Model for Genome Generation
  • 2024
    Training-free Design of Deep Networks as Ensembles of Clinical Experts

Awards

  • 2025
    Outstanding Graduate of USTC, Class of 2025
    USTC
  • 2024
    University-level Outstanding Project (Undergraduate Innovation and Entrepreneurship Training Program)
    USTC
  • 2023
    University-level Outstanding Project (College Student Research Program)
    USTC
  • 2023
    8th National College Student Life Science Competition, First Prize
    National Level
  • 2024
    Outstanding Student Scholarship
    USTC
  • 2023
    Outstanding Student Scholarship
    USTC
  • 2022
    Outstanding Student Scholarship
    USTC
  • 2021
    Outstanding Student Scholarship
    USTC

Skills

Programming Languages: Python (Advanced), C/C++ (Strong foundation), MATLAB (Experience in numerical computing)
AI/ML & Agent Frameworks: PyTorch, PyTorch Lightning, HuggingFace (transformers, diffusers, fine-tuning), JAX, LangChain, LangGraph, Pydantic AI, LoRA/PEFT
Research Areas: AI Scientist & Self-Improving AI, Multi-Agent RL, Generative Models (Diffusion, Flow Matching on SE(3)), Training-Free Methods, Geometric Deep Learning, Large Language Models (LLMs), Computational Biology
Dev Tools: Git, Linux/Bash, Docker, SLURM/HPC, LaTeX, Vibe-coding Tools (Cursor, Claude Code, OpenAI Codex)