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Search · four archives
12 papers · ranked by Valyu relevance
Máté Mohácsi, Márk Patrik Török, Sára Sáray, Luca Tar + 1 more
Finding optimal parameters for detailed neuronal models is a ubiquitous challenge in neuroscientific research. Recently, manual model tuning has been replaced by automated parameter search using a variety of different tools and methods. However, using most of these software tools and choosing the most appropriate…
Authors not listed
With the ever-increasing demand for atomistic structures representative of real-life systems as well as the ad-vent of exascale computers, it has now become necessary and possible to use advanced global optimization (GO) techniques to intelligently sample the potential energy surface (PES). Given the previous studies…
Prasad U. Bandodkar, Razeen R. Shaikh, Gregory T. Reeves
Model development is essential to gain a mathematical understanding of the underlying phenomena in systems biology. In most models, it is typically hard to estimate the values of the biophysical/phenomenological parameters that characterize the model. The parameters are estimated by minimizing a function that reduces a…
Daniel Gaissmaier, Matthias van den Borg, Donato Fantauzzi, Timo Jacob
In this work, we demonstrate the superior exploration capabilities of the population-based methods over the sequential one-parameter parabolic interpolation (SOPPI) approach to optimise ReaxFF force field parameters. Evolutionary algorithms (EAs) are heuristic-based approaches using a population of concurrent models in…
Changin Oh, Kathleen P. Wilkie
We present the Toroidal Search Algorithm (TSA), a novel population-based metaheuristic optimization method inspired by the topology of a torus. Conventional metaheuristics frequently suffer from boundary stagnation, a phenomenon that severely degrades performance in bounded and high-dimensional search spaces. TSA…
Robert Arbon, Yanchen Zhu, Antonia S. J. S. Mey
Markov state models (MSM) are a popular statistical method for analyzing the conformational dynamics of proteins, including protein folding. With all statistical and machine learning (ML) models choices must be made about the modeling pipeline that cannot be directly learned from the data. These choices, or…
Lijuan Wang, Yuze Wang, Chen Qiu, Liwei Xiao + 2 more
Protein sequence design for tailored functional properties is a fundamental task in protein engineering, with critical applications in drug discovery and therapeutic development. Efficient navigation of the combinatorial vastness of protein sequence space to identify functional variants remains a formidable challenge.…
Yifan Wu, Aron Walsh, Alex Ganose
What is the minimum number of experiments, or calculations, required to find an optimal solution? Relevant chemical problems range from identifying a compound with target functionality within a given phase space to controlling materials synthesis and device fabrication conditions. A common feature in this application…
Sumedh S Nagrale, Alik S Widge
The use of Deep Brain Stimulation (DBS) on the ventral capsule/ventral striatum (VCVS) has therapeutic potential for patients with refractory psychiatric disorders, but clinical success is impeded by the need for a time-consuming and trial-and-error process when setting the parameters, this process relying on…
Authors not listed
Optimizing the synthesis conditions of advanced materials is challenging, especially when outcomes are subject to inherent experimental uncertainties. Bayesian optimization is a popular tool for accelerating materials discovery, but its standard risk-neutral framework overlooks the variability of outcomes under…
Sterling Baird, Jason R. Hall, Taylor D. Sparks
Would you rather search for a line inside a cube or a point inside a square? Physics-based simulations and wet-lab experiments often have symmetries (degeneracies) that allow reducing problem dimensionality or search space, but constraining these degeneracies is often unsupported or difficult to implement in many…
Authors not listed
Experimental design plays an important role in efficiently acquiring informative data for system characterization and deriving robust conclusions under resource limitations. Recent advancements in high-throughput experimentation coupled with machine learning have notably improved experimental procedures. While Bayesian…