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Researcher profile

Mohamed Tarek

Mohamed Tarek contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Machine LearningComputationComputational Engineering, Finance, and ScienceMathematical Softwaremath.OCMethodologyProgramming LanguagesSoftware Engineering

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Published work

6 published item(s)

preprint2026arXiv

Fitting Large Nonlinear Mixed Effects Models Using Variational Expectation Maximization

Nonlinear Mixed Effects models (NLME) models are widely used in pharmacometrics and related fields to analyze hierarchical and longitudinal data. However, as the number of parameters and random effects increases, traditional methods for maximizing the marginal likelihood become computationally expensive. This paper explores the Variational Expectation Maximization (VEM) algorithm, a scalable alternative for fitting NLME models. Originally introduced in the context of probabilistic graphical models and later popularized through variational autoencoders, VEM has not been extensively applied to NLME modeling. By leveraging flexible variational families and reverse-mode automatic differentiation, VEM can efficiently maximize the marginal likelihood, scaling to NLME models with over 15,000 population parameters. This work provides a detailed description of VEM, compares it to other NLME fitting algorithms, and highlights its scalability through computational experiments. Using the Pumas statistical software, we fit two test models: 1) a standard warfarin model, and 2) a DeepNLME Friberg model with 15,410 population parameters and 16 random effects. The warfarin model was fitted to completion to demonstrate the correctness of VEM, while the DeepNLME Friberg model was fitted for a limited number of iterations to measure the time per iteration and demonstrate VEM's scalability.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

AbstractDifferentiation.jl: Backend-Agnostic Differentiable Programming in Julia

No single Automatic Differentiation (AD) system is the optimal choice for all problems. This means informed selection of an AD system and combinations can be a problem-specific variable that can greatly impact performance. In the Julia programming language, the major AD systems target the same input and thus in theory can compose. Hitherto, switching between AD packages in the Julia Language required end-users to familiarize themselves with the user-facing API of the respective packages. Furthermore, implementing a new, usable AD package required AD package developers to write boilerplate code to define convenience API functions for end-users. As a response to these issues, we present AbstractDifferentiation.jl for the automatized generation of an extensive, unified, user-facing API for any AD package. By splitting the complexity between AD users and AD developers, AD package developers only need to implement one or two primitive definitions to support various utilities for AD users like Jacobians, Hessians and lazy product operators from native primitives such as pullbacks or pushforwards, thus removing tedious -- but so far inevitable -- boilerplate code, and enabling the easy switching and composing between AD implementations for end-users.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Bayesian Neural Ordinary Differential Equations

Recently, Neural Ordinary Differential Equations has emerged as a powerful framework for modeling physical simulations without explicitly defining the ODEs governing the system, but instead learning them via machine learning. However, the question: "Can Bayesian learning frameworks be integrated with Neural ODE's to robustly quantify the uncertainty in the weights of a Neural ODE?" remains unanswered. In an effort to address this question, we primarily evaluate the following categories of inference methods: (a) The No-U-Turn MCMC sampler (NUTS), (b) Stochastic Gradient Hamiltonian Monte Carlo (SGHMC) and (c) Stochastic Langevin Gradient Descent (SGLD). We demonstrate the successful integration of Neural ODEs with the above Bayesian inference frameworks on classical physical systems, as well as on standard machine learning datasets like MNIST, using GPU acceleration. On the MNIST dataset, we achieve a posterior sample accuracy of 98.5% on the test ensemble of 10,000 images. Subsequently, for the first time, we demonstrate the successful integration of variational inference with normalizing flows and Neural ODEs, leading to a powerful Bayesian Neural ODE object. Finally, considering a predator-prey model and an epidemiological system, we demonstrate the probabilistic identification of model specification in partially-described dynamical systems using universal ordinary differential equations. Together, this gives a scientific machine learning tool for probabilistic estimation of epistemic uncertainties.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Simplifying deflation for non-convex optimization with applications in Bayesian inference and topology optimization

Non-convex optimization problems have multiple local optimal solutions. Non-convex optimization problems are commonly found in numerous applications. One of the methods recently proposed to efficiently explore multiple local optimal solutions without random re-initialization relies on the concept of deflation. In this paper, different ways to use deflation in non-convex optimization and nonlinear system solving are discussed. A simple, general and novel deflation constraint is proposed to enable the use of deflation together with existing nonlinear programming solvers or nonlinear system solvers. The connection between the proposed deflation constraint and a minimum distance constraint is presented. Additionally, a number of variations of deflation constraints and their limitations are discussed. Finally, a number of applications of the proposed methodology in the fields of approximate Bayesian inference and topology optimization are presented.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

Approximation schemes for stochastic compliance-based topology optimization with many loading scenarios

In this paper, approximation schemes are proposed for handling load uncertainty in compliance-based topology optimization problems, where the uncertainty is described in the form of a set of finitely many loading scenarios. Efficient approximate methods are proposed to approximately evaluate and differentiate either 1) the mean compliance, or 2) a class of scalar-valued function of the individual load compliances such as the weighted sum of the mean and standard deviation. The computational time complexities of the proposed algorithms are analyzed, compared to the exact approaches and then experimentally verified. Finally, some mean compliance minimization problems and some risk-averse compliance minimization problems are solved for verification.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

DynamicPPL: Stan-like Speed for Dynamic Probabilistic Models

We present the preliminary high-level design and features of DynamicPPL.jl, a modular library providing a lightning-fast infrastructure for probabilistic programming. Besides a computational performance that is often close to or better than Stan, DynamicPPL provides an intuitive DSL that allows the rapid development of complex dynamic probabilistic programs. Being entirely written in Julia, a high-level dynamic programming language for numerical computing, DynamicPPL inherits a rich set of features available through the Julia ecosystem. Since DynamicPPL is a modular, stand-alone library, any probabilistic programming system written in Julia, such as Turing.jl, can use DynamicPPL to specify models and trace their model parameters. The main features of DynamicPPL are: 1) a meta-programming based DSL for specifying dynamic models using an intuitive tilde-based notation; 2) a tracing data-structure for tracking RVs in dynamic probabilistic models; 3) a rich contextual dispatch system allowing tailored behaviour during model execution; and 4) a user-friendly syntax for probabilistic queries. Finally, we show in a variety of experiments that DynamicPPL, in combination with Turing.jl, achieves computational performance that is often close to or better than Stan.

0 citations0 reviewsNo code linkedOpen access