Welcome to my personal website!

Hi, I’m Mohammed, a computational scientist, software engineer, and applied mathematician working at the intersection of artificial intelligence, molecular modeling, and drug delivery.

I currently conduct research in Prof. Yang Zhang’s lab at the National University of Singapore, where I develop computational models and AI-driven tools for drug discovery and delivery. My current work focuses on generative AI models, molecular representations, molecular dynamics simulations, and physics-informed machine learning, with a particular interest in designing and predicting the performance of lipid nanoparticles for RNA and drug delivery.

I completed my PhD at the University of California, Merced, in December 2024. My doctoral research focused on graph and geometric machine learning, constrained optimization, and the robustness of graph neural networks. I developed convex and non-convex optimization methods for attacking and defending GNNs, as well as optimization-based machine-learning approaches for applications in computer vision and bioinformatics.

I also hold a Master’s degree in Biomedical Data Science and Informatics from Clemson University, and a Master’s degree in Scientific Computing from An-Najah National University.

My interdisciplinary research combines applied mathematics, artificial intelligence, molecular simulation, and software development to build computational tools that advance scientific discovery and address real-world challenges.

Industrial & Academic Affiliations
Industrial & Academic Affiliations
National University of Singapore logo
Prior Affiliations
UC Merced logo Image 1 Image 2 Image 3 Image 4 Image 5 Image 6






————————————————————————————————————————————————————————————————-

News:


2026
  • September 2026: Submitted Mohammed Aburidi and Yang Zhang. LNPHub: A Multimodal Data Foundation for AI-Driven Lipid Nanoparticle Discovery in Nucleic Acid Therapeutics. Nature Communications.
  • September 2026: Code development update: lnphub, a Python package for lipid nanoparticles for mRNA drug delivery, is under active development.
  • September 2026: Code development update: LNPHub, a web app for lipid nanoparticles for mRNA drug delivery, is under active development.
  • 2026: Added publication: "Predicting Cancer Cell Line-Drug Responses over Signal Network Profiles via Optimal Transport" by A. Li, M. Aburidi, and R. Marcia, ICASSP 2026.
  • January 01, 2026: Started a new postdoctoral research position in Prof. Yang Zhang’s group at the National University of Singapore, focusing on AI-driven molecular modeling, lipid nanoparticle discovery, and drug delivery.
2025
2024
  • December 25, 2024: Excited to share that our new paper, "Contrastive Pre-Training and Multiple Instance Learning for Predicting Tumor Microsatellite Instability" has been published! [Online version] Co-authored with Rnold Nap and Prof. Roummel Marcia
  • December 25, 2024: Excited to share that our new paper, "Optimal Transport-Based Network Alignment: Graph Classification of Small Molecule Structure-Activity Relationships in Biology," has been published! [Online version] Co-authored with Prof. Roummel Marcia
  • December 25, 2024: Excited to share that our new paper, "Wasserstein-Based Similarity Constrained Matrix Factorization for Drug-Drug Interaction Prediction," has been published! [Online version] Co-authored Sarah Malone and Prof. Roummel Marcia
  • November 18, 2024: I am thrilled to share that I have successfully defended my Ph.D. dissertation, titled "Optimization for Robust and Interpretable Learning on Graphs and Images. Many thanks to my advisor Prof. Roummel Marcia , Prof. Arnold Kim (Applied Mathematics) and Prof. Shawn Newsam (EECS) for serving on my committee and for their invaluable support throughout this journey.
  • November 01, 2024: I am proud to announce the founding of LIOTECH Solutions in Merced, California. LioTech Solutions is dedicated to providing innovative software solutions, with a focus on developing cutting-edge technologies that empower businesses and drive growth [Online version]
  • October 05, 2024: Excited to share that our new journal paper, "Optimal Transport-Based Graph Kernels for Drug Property Prediction," has been published in the IEEE Open Journal of Engineering in Medicine and Biology! [Online version] Co-authored with Prof. Roummel Marcia
  • July 15, 2024: Thrilled to announce that I've been awarded the UC Merced Valley Institute for Sustainability, Technology, and Agriculture GSR Fellowship [Letter]
  • April 24, 2024: Thrilled to announce that I've been awarded Applied Math Summer Research Fellowship. [Letter]
  • April 18, 2024: Thrilled to announce that my paper "Optimal transport-based network alignment: Graph classification of small molecule structure-activity relationships in biology" is accepted for presentation at the [IEEE EMBC 2024]
  • April 18, 2024: Thrilled to announce that my paper "Contrastive pre-training and multiple instance learning for predicting tumor microsatellite instability" is accepted for presentation at the [IEEE EMBC 2024]
  • March 10, 2024: Thrilled to announce that my paper "Topological adversarial attacks on graph neural networks via projected meta learning" is accepted for presentation at the [IEEE EAIS 2024]
  • February 18, 2024: Thrilled to announce that my paper "Adversarial attack and training for graph convolutional networks using focal loss-projected momentum" is accepted for presentation at the [IEEE ICMI 2024]
  • January 14, 2024: Thrilled to announce that I've been awarded the AMAT Travel Award Fellowship
2023
  • December 05, 2023: Thrilled to announce that I've been awarded the Fall 2023 GSA Travel Award Fellowship [See here] for more details!
  • November 25, 2023: A paper is accepted for presentation at the [IEEE AIMHC 2024]
  • June 10, 2023: A paper is accepted for presentation at the [IEEE ICMLA 2023]
  • September 10, 2023: A paper is accepted for presentation at the [IEEE ICIP 2023]
  • May 06, 2023: Thrilled to announce that I've passed the Ph.D. qualifying exam at the Applied Math Program at University of California Merced
  • May 05, 2023: Thrilled to announce that I've been awarded the LNLL DSC Fellowship [See here] for more details!
  • April 05, 2023: Thrilled to announce that I've been awarded the UCM GSOP Fellowship [See here] for more details!
  • March 10, 2023: A paper is accepted for presentation at the [IEEE MeMeA 2023]

© 2023 Mohammed Aburidi.

All rights reserved