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Xiaopeng Xu, Ph.D.

Research Scientist @ KAUST · Agentic AI for scientific discovery, protein design & synthetic biology

Recent News

  • Sep 23, 2026, my Co-I Shaheen III Grand Challenge Project proposal on “Multi-Scale AI-MD-QM/MM Platform for Next-Generation Biologics Design” was appproved on Shaheen III GPU! Cheers!
  • Aug 2, 2026, my Co-I Translational Research Grants (TRG2026) on AI-based protein design solutions for industrial biologics and medical applications was funded by KAUST! ~1 million USD fund to support our research! Cheers!
  • Jun 23, 2026, started as a Research Scientist at SFB@KAUST.
  • Jun 8, 2026, Mater-trends — to track researches on material science — up and alive.
  • Jun 3, 2026, AI-trends — to track research trends on artificial intelligence — and Bio-trends — to track researches on bioscience — up and alive.
  • Mar 25, 2026, the first tool buddle in MacromNex, ProteinMCP — an agentic AI framework for autonomous protein engineering, published in Protein Science!
  • Mar 24, 2026, SegDesign — a framework for protein segment engineering — published in Protein Science.
  • Jan 22, 2025, AggNet — a Deep Learning method for protein aggregation prediction — published in Protein Science.
  • Oct 3, 2024, AutoBA — for multi-omics analysis with Agentic AI — published in Advanced Science.
  • Jul 18, 2024, SANTO — a method for alignment and stitching in spatial omics — published in Nature Communications.
  • Jun 12, 2024, HELM-GPT — de novo macrocyclic peptide design — published in Bioinformatics!
  • Jun 23, 2024, started as a Postdoctorate Research Fellow at SFB@KAUST.
  • May 13, 2024, my Co-I Shaheen III proposal on “Molecular dynamics simulations-enhanced AI for enzyme design and optimization” was appproved on Shaheen III CPU! Cheers!
  • May 5, 2024, defended my Ph.D Dissertation — “A ChatGPT-like solution for protein design: combining generative and predictive AI to design functional proteins”! Cheers!
  • Jun 28, 2023, SGPT-RL — for chemical drug design with GPT and RL — published in F1000Research!
  • Feb 20, 2023, AB-Gen — for antibody with GPT and RL — published in Genomics, Proteomics & Bioinformatics!
  • Nov 11, 2021, an AI guided review of 17 000 studies in COVID-19 computational research published in Briefings in Bioinformatics

Recent Notes

疫苗设计

背景

  1. 背景:

    1. 我们已经和利雅得的医院合作,获取到病人的康复期血液。包括血清和其中的血细胞 PBMC。

    2. 目前已经和剑桥合作开发mRNA疫苗,对方已经开发了两年,并且有相关得技术积累。

AB-Gen 抗体设计

今天给大家介绍的文章是来自沙特阿卜杜拉国王科技大学 (KAUST) 高欣教授课题组 (http://cemse.kaust.edu.sa/sfb) 和中科院福建物质结构研究所张璐研究员团队开发的基于生成式预训练 Transformer (GPT) 和强化学习设计抗体库的方法,AB-Gen,于近日发表在《Genomics, Proteomics & Bioinformatics》上 ,文章的第一作者是KAUST的博士生徐晓鹏。

Pytorch HPO 超参优化

超参优化是深度学习中的常见问题,有好多工具用于解决相关问题。其中,有一些博客对其做了比较好的综述,见这里:https://neptune.ai/blog/best-tools-for-model-tuning-and-hyperparameter-optimization。

总结如下: