Machine learning-based interatomic potentials, such as those provided by neural networks, are increasingly important in molecular dynamics simulations. In the present work, we consider the applicability and robustness of machine learning molecular dynamics to predict the equation of state properties of methane by using high-dimensional neural network potentials (HDNNPs). We investigate two different strategies for generating training data: one strategy based upon bulk representations using periodic cells and another strategy based upon clusters of molecules. We assess the accuracy of the trained potentials by predicting the equilibrium mass density for a wide range of thermodynamic conditions to characterize the liquid phase, supercritical fluid, and gas phase, as well as the liquid-vapor coexistence curve. Our results show an excellent agreement with reference phase diagrams, with an average error below ∼2% for all studied phases. Moreover, we confirm the applicability of models trained on cluster data sets for producing accurate and reliable results.
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http://dx.doi.org/10.1021/acs.jctc.3c00469 | DOI Listing |
Stat Interface
January 2024
Purdue University, West Lafayette, IN 47907, United States of America.
Graphical models have long been studied in statistics as a tool for inferring conditional independence relationships among a large set of random variables. The most existing works in graphical modeling focus on the cases that the data are Gaussian or mixed and the variables are linearly dependent. In this paper, we propose a double regression method for learning graphical models under the high-dimensional nonlinear and non-Gaussian setting, and prove that the proposed method is consistent under mild conditions.
View Article and Find Full Text PDFNeuro Oncol
January 2025
Department of Neurosurgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg.
Background: Peripheral nerve sheath tumors (PNSTs) encompass entities with different cellular differentiation and degrees of malignancy. Spatial heterogeneity complicates diagnosis and grading of PNSTs in some cases. In malignant PNST (MPNST) for example, single cell sequencing data has shown dissimilar differentiation states of tumor cells.
View Article and Find Full Text PDFMethods
January 2025
School of Computer Science, Qufu Normal University, Rizhao 276826, China.
Brain imaging genetics aims to explore the association between genetic factors such as single nucleotide polymorphisms (SNPs) and brain imaging quantitative traits (QTs). However, most existing methods do not consider the nonlinear correlations between genotypic and phenotypic data, as well as potential higher-order relationships among subjects when identifying bi-multivariate associations. In this paper, a novel method called deep hyper-Laplacian regularized self-representation learning based structured association analysis (DHRSAA) is proposed which can learn genotype-phenotype associations and obtain relevant biomarkers.
View Article and Find Full Text PDFJ Acoust Soc Am
January 2025
Department of Electronics Engineering, Pusan National University, Busan, South Korea.
The amount of information contained in speech signals is a fundamental concern of speech-based technologies and is particularly relevant in speech perception. Measuring the mutual information of actual speech signals is non-trivial, and quantitative measurements have not been extensively conducted to date. Recent advancements in machine learning have made it possible to directly measure mutual information using data.
View Article and Find Full Text PDFMed Biol Eng Comput
January 2025
Radiol Dept, Jiangnan Univ, Affiliated Hosp, Wuxi, 214122, Jiangsu, People's Republic of China.
In computer-aided diagnosis systems, precise feature extraction from CT scans of colorectal cancer using deep learning is essential for effective prognosis. However, existing convolutional neural networks struggle to capture long-range dependencies and contextual information, resulting in incomplete CT feature extraction. To address this, the PEDRA-EFB0 architecture integrates patch embeddings and a dual residual attention mechanism for enhanced feature extraction and survival prediction in colorectal cancer CT scans.
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