Mohamed Tarek

Mohamed Tarek

Always learning.

Research and Teaching

  1. Preprints
  2. Conferences
  3. Journals
  4. Videos
  5. Workshops Taught

Preprints

  1. Nonconvex.jl: A Comprehensive Julia Package for Non-Convex Optimization. July 13, 2023.

  2. Earth Movers in The Big Data Era: A Review of Optimal Transport in Machine Learning. May 8, 2023.

  3. A Practitioner's Guide to Bayesian Inference in Pharmacometrics using Pumas. Mar 31, 2023.

  4. Preconditioners.jl: A Flexible and Extensible Framework for Preconditioning in Iterative Solvers. Feb 25, 2023.

  5. Accelerated Predictive Healthcare Analytics with Pumas, A High Performance Pharmaceutical Modeling and Simulation Platform. Mar 20, 2022.

  6. Bayesian Neural Ordinary Differential Equations. Feb 6, 2022.

  7. AbstractDifferentiation.jl: Backend-Agnostic Differentiable Programming in Julia. Feb 4, 2022.

  8. Simplifying deflation for non-convex optimization with applications in Bayesian inference and topology optimization. Jan 28, 2022.

  9. Some popular nonlinear programming algorithms. Oct 18, 2021.

  10. Approximation schemes for stochastic compliance-based topology optimization with many loading scenarios. Aug 8, 2021.

  11. Robust and stochastic compliance-based topology optimization with finitely many loading scenarios. Mar 8, 2021.

  12. DynamicPPL: Stan-like Speed for Dynamic Probabilistic Models. Feb 7, 2020.

Conferences

  1. DeepPumas for automatic discovery of individualizable functions governing longitudinal patient outcomes, Population Approach Group in Europe. Jun 27, 2023.

  2. Fast cross-validation for Bayesian inference using proposals on a linear subspace, Population Approach Group in Europe. Jun 27, 2023.

  3. Marginal No-U-Turn Sampler for Bayesian Analysis in Pharmacometrics, Population Approach Group in Europe. Jun 27, 2023.

  4. A Complete Bayesian Workflow in Pumas, Population Approach Group in Australia and New Zealand. Jan 20, 2023.

  5. ImplicitDifferentiation.jl: Differentiating Implicit Functions, JuliaCon. Jul 29, 2022.

  6. AbstractDifferentiation.jl: Backend-Agnostic Differentiable Programming in Julia, Differentiable Programming NeurIPS Workshop, Dec 13, 2021.

  7. Nonlinear mixed effects model based optimal design of experiments using mathematical programming in Pumas, American Conference on Pharmacometrics. Nov 9, 2021

  8. Non-Gaussian random effects in nonlinear mixed effects models in Pumas, American Conference on Pharmacometrics. Nov 9, 2021.

  9. Parallel hierarchical Gibbs-NUTS MCMC algorithm for Nonlinear Mixed Effects models in Pumas, American Conference on Pharmacometrics. Nov 9, 2021.

  10. Subspace MCMC algorithm for Bayesian parameter estimation of hierarchical PK/PD models in Pumas, Population Approach Group in Europe. Sep 7, 2021.

  11. Nonconvex.jl, JuMP-dev Workshop. Jul 30, 2021.

  12. TopOpt.jl: topology optimization done right, JuliaCon. Jul 29, 2021.

  13. TopOpt.jl: Truss and Continuum Topology Optimization - Interactive Visualization, Automatic Differentiation and More, World Congress of Structural and Multidisciplinary Optimization (WCSMO) 14. Jun 16, 2021.

  14. Bayesian Neural Ordinary Differential Equations, Languages for Inference (LAFI). Jan 15, 2021.

  15. Analysis of Laplace Approximation for Pharmaceutical Nonlinear Mixed Effects Models, Population Approach Group of Australia and New Zealand. Jan 7, 2021.

  16. DynamicPPL: Stan-like Speed for Dynamic Probabilistic Models, JuliaCon. Jul 31, 2020.

  17. AdvancedHMC.jl: A robust, modular and efficient implementation of advanced HMC algorithms, The International Conference on Probabilistic Programming (PROBPROG). Jan 1, 2020.

  18. DynamicPPL: Stan-like Speed for Dynamic Probabilistic Models, The International Conference on Probabilistic Programming (PROBPROG). Jan 1, 2020.

  19. AdvancedHMC.jl: A robust, modular and efficient implementation of advanced HMC algorithms, 2nd Symposium on Advances in Approximate Bayesian Inference. Jan 1, 2019.

  20. Bijectors.jl: Flexible transformations for probability distributions, 2nd Symposium on Advances in Approximate Bayesian Inference. Jan 1, 2019.

  21. TopOpt.jl: An efficient and high-performance package for topology optimization of continuum structures in the Julia programming language, The World Congress of Structural and Multidisciplinary Optimization (WCSMO) 13. Jan 1, 2019.

  22. Topology Optimization and JuMP, JuMP-dev Workshop. Jul 28, 2018.

Journals

  1. Scalable Optimal Transport Methods in Machine Learning: A Contemporary Survey, IEEE Transactions on Pattern Analysis and Machine Intelligence. Mar 20, 2024.

  2. Approximation schemes for stochastic compliance-based topology optimization with many loading scenarios, Structural and Multidisciplinary Optimization. Apr 13, 2022.

  3. Robust and stochastic compliance-based topology optimization with finitely many loading scenarios, Structural and Multidisciplinary Optimization. Sept 26, 2021.

  4. Adaptive continuation solid isotropic material with penalization for volume constrained compliance minimization, Computer Methods in Applied Mechanics and Engineering. May 1, 2020.

Videos

  1. Understanding automatic differentiation (in Julia). Dec 11, 2021.

  2. Nonconvex.jl, JuMP-dev Workshop. Jul 30, 2021.

  3. TopOpt.jl: topology optimization done right, JuliaCon. Jul 29, 2021.

  4. Setup, Reading and Developing Julia Packages, Canberra Julia Language Meetup. Apr 25, 2021.

  5. Pumas 2.0 Features: Beyond Gaussian Random Effects. Mar 30, 2021.

  6. DynamicPPL: Stan-like Speed for Dynamic Probabilistic Models, JuliaCon. Jul 31, 2020.

  7. Topology Optimization and JuMP, JuMP-dev Workshop. Jul 28, 2018.

Workshops Taught

CC BY-SA 4.0 Mohamed Tarek. Last modified: April 06, 2024. Website built with Franklin.jl and the Julia programming language.