Related papers: Multi-Layer Free Energy Perturbation
Mixed effects (ME) models inform a vast array of problems in the physical and social sciences, and are pervasive in meta-analysis. We consider ME models where the random effects component is linear. We then develop an efficient approach for…
Exploring the free-energy landscape along reaction coordinates or system parameters $\lambda$ is central to many studies of high-dimensional model systems in physics, e.g. large molecules or spin glasses. In simulations this usually…
For decades, it was unknown how electron bifurcating systems in Nature prevented energy-wasting short-circuiting reactions that have large driving forces, so synthetic electron bifurcating molecular machines could not be designed and built.…
In this paper, we address the performance degradation of efficient diffusion models by introducing Multi-architecturE Multi-Expert diffusion models (MEME). We identify the need for tailored operations at different time-steps in diffusion…
Electromigration (EM) is one of the major concerns in the reliability analysis of very large scale integration (VLSI) systems due to the continuous technology scaling. Accurately predicting the time-to-failure of integrated circuits (IC)…
Free-energy differences between pairs of end-states can be estimated based on molecular dynamics (MD) simulations using standard pathway-dependent methods such as thermodynamic integration (TI), free-energy perturbation, or Bennett's…
In this PhD thesis, we explore and apply methods inspired by the free energy principle to two important areas in machine learning and neuroscience. The free energy principle is a general mathematical theory of the necessary…
Linear Mixed-Effects (LME) models are a fundamental tool for modeling correlated data, including cohort studies, longitudinal data analysis, and meta-analysis. Design and analysis of variable selection methods for LMEs is more difficult…
We perform an extrapolative analysis of "fast-growth" free-energy-difference (DF) estimates of a computer-modeled, fully-solvated ethane<->methanol transformation. The results suggest that extrapolation can greatly reduce the systematic…
Resampling algorithms are a useful approach to deal with imbalanced learning in multilabel scenarios. These methods have to deal with singularities in the multilabel data, such as the occurrence of frequent and infrequent labels in the same…
This paper proposes a methodology to estimate stress in the subsurface by a hybrid method combining finite element modeling and neural networks. This methodology exploits the idea of obtaining a multi-frequency solution in the numerical…
Nonequilibrium, ``fast switching'' estimates of equilibrium free energy differences, Delta F, are often plagued by poor convergence due to dissipation. We propose a method to improve these estimates by generating trajectories with reduced…
Rearranging the six-dimensional phase space of particles in plasma can release energy. The rearrangement may happen through the application of electric and magnetic fields, subject to various constraints. The maximum energy that can be…
Mixed-effects regression models represent a useful subclass of regression models for grouped data; the introduction of random effects allows for the correlation between observations within each group to be conveniently captured when…
Electronic stopping (ES) of energetic atoms is not taken care of by the interatomic potentials used in molecular dynamics (MD) simulations when simulating collision cascades. The Lindhard-Scharff (LS) formula for electronic stopping is…
We study the problem of finding efficient sampling policies in an edge-based feedback system, where sensor samples are offloaded to a back-end server that processes them and generates feedback to a user. Sampling the system at maximum…
An important goal of environmental health research is to assess the health risks posed by mixtures of multiple environmental exposures. In these mixtures analyses, flexible models like Bayesian kernel machine regression and multiple index…
The relative energies of different phases or polymorphs of molecular solids can be small, less than a kiloJoule/mol. Reliable description of such energy differences requires high quality treatment of electron correlations, typically beyond…
A simple method to reduce the numerical cost in free electron laser (FEL) simulations is presented, which is based on retrieving a spatially-coherent component of microbunching to suppress artifact effects that can potentially overestimate…
There have been a lot of methods aimed at studying the limiting free energy per particle (LFEPP) for 3-dimensional (3D) Ising model in absence of an external magnetic field. These methods are elegant, but most of them are complicated and…