相关论文: Metabolic Flux Analysis in Isotope Labeling Experi…

This paper presents a novel symbolic algorithm for the Maximal End Component (MEC) decomposition of a Markov Decision Process (MDP). The key idea behind our algorithm INTERLEAVE is to interleave the computation of Strongly Connected…

Searching for potential active compounds in large databases is a necessary step to reduce time and costs in modern drug discovery pipelines. Such virtual screening methods seek to provide predictions that allow the search space to be…

In this work we present an efficient numerical algorithm for the solution of interfacial statistical associating fluid theory (iSAFT) in cylindrical geometry to facilitate the study of inhomogeneous fluids having curvatures. The new…

Uncertainty quantification and sensitivity analyses are a vital component for predictive modeling in the sciences and engineering. The adjoint approach to sensitivity analysis requires solving a primary system of equations and a…

Calibrating mathematical models of biological processes is essential for achieving predictive accuracy and gaining mechanistic insight. However, this task remains challenging due to limited and noisy data, significant biological…

Target trial emulation (TTE) enables causal questions to be studied with observational data when randomized controlled trials (RCTs) are infeasible. Yet treatment-effect methods often address causal estimation, missingness, and temporal…

We discuss certain basic features of the equation-free (EF) approach to modeling and computation for complex/multiscale systems. We focus on links between the equation-free approach and tools from systems and control theory (design of…

Variational inference methods have been shown to lead to significant improvements in the computational efficiency of approximate Bayesian inference in mixed multinomial logit models when compared to standard Markov-chain Monte Carlo (MCMC)…

In silico tools are important for generating novel hypotheses and exploring alternatives in de novo metabolic pathway design. However, while many computational frameworks have been proposed for retrobiosynthesis, few successful examples of…

Untargeted metabolomic studies are revealing large numbers of naturally occurring metabolites that cannot be characterized because their chemical structures and MS/MS spectra are not available in databases. Here we present iMet, a…

With the maturation of metabolomics science and proliferation of biobanks, clinical metabolic profiling is an increasingly opportunistic frontier for advancing translational clinical research. Automated Machine Learning (AutoML) approaches…

We propose a novel approach to the estimation of multiple Graphical Models to analyse temporal patterns of association among a set of metabolites over different groups of patients. Our motivating application is the Southall And Brent…

This article focuses on covariance estimation for multi-study data. Popular approaches employ factor-analytic terms with shared and study-specific loadings that decompose the variance into (i) a shared low-rank component, (ii)…

Federated learning (FL) is a promising paradigm to enable privacy-preserving deep learning from distributed data. Most previous works are based on federated average (FedAvg), which, however, faces several critical issues, including a high…

Thermodynamic and flash equilibrium calculations are the cornerstones of simulation process calculations. The iterative approach, a widely used nonlinear problem-solving technique, relies on derivative calculations throughout the procedure…

Diffusion is the macroscopic manifestation of disordered molecular motion. Mathematically, diffusion equations are partial differential equations describing the fluid-like large-scale dynamics of parcels of molecules. Spatially…

In this paper we present a topology optimization technique applicable to a broad range of flow design problems. We propose also a discrete adjoint formulation effective for a wide class of Lattice Boltzmann Methods (LBM). This adjoint…

Controlling generative models is computationally expensive. This is because optimal alignment with a reward function--whether via inference-time steering or fine-tuning--requires estimating the value function. This task demands access to…

The complexity of linear mixed-effects (LME) models means that traditional diagnostics are rendered less effective. This is due to a breakdown of asymptotic results, boundary issues, and visible patterns in residual plots that are…

In this paper, we develop a class of interacting particle Langevin algorithms to solve inverse problems for partial differential equations (PDEs). In particular, we leverage the statistical finite elements (statFEM) formulation to obtain a…