Integration of Normative Decision-Making and Batch Sampling for Global Metamodeling

2020 ◽  
Vol 142 (3) ◽  
Author(s):  
Anton van Beek ◽  
Siyu Tao ◽  
Matthew Plumlee ◽  
Daniel W. Apley ◽  
Wei Chen

Abstract The cost of adaptive sampling for global metamodeling depends on the total number of costly function evaluations and to which degree these evaluations are performed in parallel. Conventionally, samples are taken through a greedy sampling strategy that is optimal for either a single sample or a handful of samples. The limitation of such an approach is that they compromise optimality when more samples are taken. In this paper, we propose a thrifty adaptive batch sampling (TABS) approach that maximizes a multistage reward function to find an optimal sampling policy containing the total number of sampling stages, the number of samples per stage, and the spatial location of each sample. Consequently, the first batch identified by TABS is optimal with respect to all potential future samples, the available resources, and is consistent with a modeler’s preference and risk attitude. Moreover, we propose two heuristic-based strategies that reduce numerical complexity with a minimal reduction in optimality. Through numerical examples, we show that TABS outperforms or is comparable with greedy sampling strategies. In short, TABS provides modelers with a flexible adaptive sampling tool for global metamodeling that effectively reduces sampling costs while maintaining prediction accuracy.

Author(s):  
Anton van Beek ◽  
Siyu Tao ◽  
Wei Chen

Abstract We consider the problem of adaptive sampling for global emulation (metamodeling) with a finite budget. Conventionally this problem is tackled through a greedy sampling strategy, which is optimal for taking either a single sample or a handful of samples at a single sampling stage but neglects the influence of future samples. This raises the question: “Can we optimize the number of sampling stages as well as the number of samples at each stage?” The proposed thrifty adaptive batch sampling (TABS) approach addresses this challenge by adopting a normative decision-making perspective to determine the total number of required samples and maximize a multistage reward function with respect to the total number of stages and the batch size at each stage. To amend TABS’ numerical complexity we propose two heuristic-based strategies that significantly reduce computational time with minimal reduction of reward optimality. Through numerical examples, TABS is shown to outperform or at least be comparable to conventional greedy sampling techniques. In this fashion, TABS provides modelers a flexible adaptive sampling tool for global emulation, effectively reducing computational cost while maintaining prediction accuracy.


2021 ◽  
Author(s):  
Théo Jaffrelot Inizan ◽  
Frédéric Célerse ◽  
Olivier Adjoua ◽  
Dina El Ahdab ◽  
Luc-Henri Jolly ◽  
...  

We provide an unsupervised adaptive sampling strategy capable of producing μs-timescale molecular dynamics (MD) simulations of large biosystems using many-body polarizable force fields (PFFs).


2021 ◽  
Author(s):  
Fréderic Célerse ◽  
Theo Jaffrelot-Inizan ◽  
Louis Lagardère ◽  
Olivier Adjoua ◽  
Pierre Monmarché ◽  
...  

We detail a novel multi-level enhanced sampling strategy grounded on Gaussian accelerated Molecular Dynamics (GaMD). First, we propose a GaMD multi-GPUs-accelerated implementation within the Tinker-HP molecular dynamics package. We then introduce the new "dual-water" mode and its use with the flexible AMOEBA polarizable force field. By adding harmonic boosts to the water stretching and bonding terms, it accelerates the solvent-solute interactions while enabling speedups thanks to the use of fast multiple--timestep integrators. To further reduce time-to-solution, we couple GaMD to Umbrella Sampling (US). The GaMD—US/dual-water approach is tested on the 1D Potential of Mean Force (PMF) of the CD2-CD58 system (168000 atoms) allowing the AMOEBA PMF to converge within 1 kcal/mol of the experimental value. Finally, Adaptive Sampling (AS) is added enabling AS-GaMD capabilities but also the introduction of the new Adaptive Sampling--US--GaMD (ASUS--GaMD) scheme. The highly parallel ASUS--GaMD setup decreases time to convergence by respectively 10 and 20 compared to GaMD--US and US.


2021 ◽  
Author(s):  
Fréderic Célerse ◽  
Theo Jaffrelot-Inizan ◽  
Louis Lagardère ◽  
Olivier Adjoua ◽  
Pierre Monmarché ◽  
...  

We introduce a novel multi-level enhanced sampling strategy grounded on Gaussian accelerated Molecular Dynamics (GaMD). First, we propose a GaMD multi-GPUs -accelerated implementation within Tinker-HP. For the specific use with the flexible AMOEBA polarizable force field (PFF), we introduce the new "dual–water" GaMD mode. By adding harmonic boosts to the water stretching and bonding terms, it accelerates the solvent-solute interactions while enabling speedups with fast multiple–timestep integrators. To further reduce time-to-solution, we couple GaMD to Umbrella Sampling (US). The GaMD—US/dual–water approach is tested on the 1D Potential of Mean Force (PMF) of the CD2–CD58 system (168000 atoms) allowing the AMOEBA PMF to converge within 1 kcal/mol of the experimental value. Finally, Adaptive Sampling (AS) is added enabling AS–GaMD capabilities but also the introduction of the new Adaptive Sampling–US–GaMD (ASUS–GaMD) scheme. The highly parallel ASUS–GaMD setup decreases time to convergence by respectively 10 and 20 compared to GaMD–US and US.


Author(s):  
Charles Nyakito ◽  
Catherine Amimo ◽  
Vencie B. Allida

In this 21st century, educational institutions the world over are faced with increasing demand from society to transform from analogue practices to digital systems using technology. This study investigated the challenges experienced by teacher education college lecturers in their quest to integrate ICT in teacher training practices. The study was qualitative, using focus group discussions, interview and observation with 10 college lecturers from each of the 4 colleges and 4 Principals, one from each college. Snowball purposive sampling strategy was used to draw the participants. The findings revealed a host of challenges, despite a high level of appreciation among college lecturers on the importance of ICT integration into classroom instructional practices. Several debilitating factors evolved including, lack of experience and skills in using ICT, lack of ICT curriculum for the teachers' colleges, lack of clear government policy on the teaching of ICT in the teachers' college curriculum, inadequate ICT resources, obsolete ICT hardware and soft wares, intensive teaching programs due to examination pressures, overcrowded classrooms, lack of time, heavy workload, slow internet connectivity, intermittent electricity supply and, attitudinal barriers from the relatively older lecturers with technophobia. The researchers therefore, recommended government intervention with a clear policy on ICT inclusion in the curriculum, equipping the colleges with adequate and up-to-date equipment, regular training opportunities for the lecturers, provision of alternative and affordable source of power, recruiting more human resource in the colleges to reduce the workload for the lecturers and government subsidizing on the cost of internet connectivity.


2018 ◽  
Vol 14 (11) ◽  
pp. 5459-5475 ◽  
Author(s):  
Maxwell I. Zimmerman ◽  
Justin R. Porter ◽  
Xianqiang Sun ◽  
Roseane R. Silva ◽  
Gregory R. Bowman

Author(s):  
Sayan Ghosh ◽  
Jesper Kristensen ◽  
Yiming Zhang ◽  
Waad Subber ◽  
Liping Wang

Abstract Multi-fidelity Gaussian process (GP) modeling is a common approach to employ in resource-expensive computationally demanding algorithms such as optimization, calibration and uncertainty quantification where multiple datasets of varying fidelities are encountered. Briefly, in its simplest form, a multi-fidelity GP is trained on two separate sources of datasets each with its own fidelity level, e.g., a software code/simulator for the low-fidelity source and real-world experiments for the high-fidelity source. Adaptive sampling for multi-fidelity Gaussian processes is a challenging task since we not only seek to estimate the next sampling location of the design variable, but also account for the data fidelities. This issue is often addressed by including the cost of the data sources as an another element in the search criterion in conjunction with an uncertainty reduction metric. In this work, we extent the traditional design of experiment framework for multi-fidelity GPs by partitioning the prediction uncertainty based on the fidelity level and the associated cost of execution. In addition, we utilize the concept of a meta-model believer which quantifies the effect of adding an exploratory design point on the GP uncertainty prediction. We demonstrate the framework using academic examples as well as an industrial application of a steady-state thermodynamic operation point of a fluidized bed process.


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