Browse
Submit Data
Databases
API
Help

Dataset Information

21 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Adaptive moving mesh algorithm based on local reaction rate.

ABSTRACT: An empirical mesh adaption algorithm is introduced for modeling one-dimensional reaction-diffusion systems with large moving gradients. Our new algorithm is based on the revelation, that in reaction-diffusion systems the high moving concentration gradients appear nearby to the region where the rate of reaction is maximal, thus the local reaction rate can be used to control the mesh adaption. We found, that the main advantage of such a method is its simplicity and easy implementation. As an example we study an acid-base diode, where large moving gradients appear. The mathematical model of the diode contains several parabolic PDEs, coupled with one elliptic PDE. An r-refinement technique is used and attached to the commercial finite element solver COMSOL. We investigated the time-dependent salt effects of the diode with our developed algorithm. Our mesh adaption method is advantageous for modeling of any reaction-diffusion systems with localized high concentration gradients.

SUBMITTER: Koncz V

PROVIDER: S-EPMC7820511 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Adaptive moving mesh algorithm based on local reaction rate.

Koncz Viktória V Izsák Ferenc F Noszticzius Zoltán Z Kály-Kullai Kristóf K

Heliyon 20210119 1

An empirical mesh adaption algorithm is introduced for modeling one-dimensional reaction-diffusion systems with large moving gradients. Our new algorithm is based on the revelation, that in reaction-diffusion systems the high moving concentration gradients appear nearby to the region where the rate of reaction is maximal, thus the local reaction rate can be used to control the mesh adaption. We found, that the main advantage of such a method is its simplicity and easy implementation. As an examp ...[more]

PMID: 33521342

Similar Datasets

A practical adaptive moving-mesh algorithm for solving unconfined seepage problem with Galerkin finite element method.

Project description:One of the great challenges of unconfined seepage through a dam lies in the accurate determination of free surface that depends on the complexity of the seepage model, especially if the model is characterized with complex geometry and sharp variations in permeability distribution. This study presents a practical methodology that combines the adaptive moving-mesh algorithm and the Galerkin finite element method (FEM) to solve an unconfined seepage problem with high efficiency and precision. The methodology employs a set of improvement terms, such as remainder factor, step-size parameter and termination condition, all of which guarantee that the simulation and the refinement fitting can be implemented efficiently until the free surface converges within a given allowable error. In particular, a specialized discussion is presented for the significant relation between the location of the exit point and the corresponding grid fineness. To validate the practicability of the proposed method, a series of examples are performed. Comparing the result with those of other numerical approaches, we conclude that even though the unconfined seepage model may be complicated with arbitrary complex geometry and sharp variations in permeability distribution, the proposed algorithm provides a great improvement in efficiency and accuracy in free-surface searching.

| S-EPMC6502791 | biostudies-literature

Implementing Contact Angle Hysteresis in Moving Mesh-Based Two-Phase Flow Numerical Simulations.

Project description:Contact angle hysteresis is a common phenomenon in nature, which also plays an important role in industrial applications. A numerical model based on the moving mesh two-phase flow method is presented for modeling contact angle hysteresis. The implementation includes a displacement-based penalty method and a state variable method. The pinning, moving, and repinning of the contact lines can be simulated. This method is robust considering both two-dimensional and three-dimensional geometries. To further demonstrate the performance of this method, a fluid-solid interaction model with a cylinder fluctuating on a water surface considering contact angle hysteresis is demonstrated.

| S-EPMC8717560 | biostudies-literature

Controlling the local false discovery rate in the adaptive Lasso.

Project description:The Lasso shrinkage procedure achieved its popularity, in part, by its tendency to shrink estimated coefficients to zero, and its ability to serve as a variable selection procedure. Using data-adaptive weights, the adaptive Lasso modified the original procedure to increase the penalty terms for those variables estimated to be less important by ordinary least squares. Although this modified procedure attained the oracle properties, the resulting models tend to include a large number of "false positives" in practice. Here, we adapt the concept of local false discovery rates (lFDRs) so that it applies to the sequence, λn, of smoothing parameters for the adaptive Lasso. We define the lFDR for a given λn to be the probability that the variable added to the model by decreasing λn to λn-δ is not associated with the outcome, where δ is a small value. We derive the relationship between the lFDR and λn, show lFDR =1 for traditional smoothing parameters, and show how to select λn so as to achieve a desired lFDR. We compare the smoothing parameters chosen to achieve a specified lFDR and those chosen to achieve the oracle properties, as well as their resulting estimates for model coefficients, with both simulation and an example from a genetic study of prostate specific antigen.

| S-EPMC3769997 | biostudies-literature

Path-oriented test cases generation based adaptive genetic algorithm.

Project description:The automatic generation of test cases oriented paths in an effective manner is a challenging problem for structural testing of software. The use of search-based optimization methods, such as genetic algorithms (GAs), has been proposed to handle this problem. This paper proposes an improved adaptive genetic algorithm (IAGA) for test cases generation by maintaining population diversity. It uses adaptive crossover rate and mutation rate in dynamic adjustment according to the differences between individual similarity and fitness values, which enhances the exploitation of searching global optimum. This novel approach is experimented and tested on a benchmark and six industrial programs. The experimental results confirm that the proposed method is efficient in generating test cases for path coverage.

| S-EPMC5685491 | biostudies-literature

Imaging-Based Algorithm for the Local Grading of Glioma.

Project description:Background and purposeGliomas are highly heterogeneous tumors, and optimal treatment depends on identifying and locating the highest grade disease present. Imaging techniques for doing so are generally not validated against the histopathologic criterion standard. The purpose of this work was to estimate the local glioma grade using a machine learning model trained on preoperative image data and spatially specific tumor samples. The value of imaging in patients with brain tumor can be enhanced if pathologic data can be estimated from imaging input using predictive models.Materials and methodsPatients with gliomas were enrolled in a prospective clinical imaging trial between 2013 and 2016. MR imaging was performed with anatomic, diffusion, permeability, and perfusion sequences, followed by image-guided stereotactic biopsy before resection. An imaging description was developed for each biopsy, and multiclass machine learning models were built to predict the World Health Organization grade. Models were assessed on classification accuracy, Cohen κ, precision, and recall.ResultsTwenty-three patients (with 7/9/7 grade II/III/IV gliomas) had analyzable imaging-pathologic pairs, yielding 52 biopsy sites. The random forest method was the best algorithm tested. Tumor grade was predicted at 96% accuracy (κ = 0.93) using 4 inputs (T2, ADC, CBV, and transfer constant from dynamic contrast-enhanced imaging). By means of the conventional imaging only, the overall accuracy decreased (89% overall, κ = 0.79) and 43% of high-grade samples were misclassified as lower-grade disease.ConclusionsWe found that local pathologic grade can be predicted with a high accuracy using clinical imaging data. Advanced imaging data improved this accuracy, adding value to conventional imaging. Confirmatory imaging trials are justified.

| S-EPMC7077885 | biostudies-literature

MeSHHeading2vec: a new method for representing MeSH headings as vectors based on graph embedding algorithm.

Project description:Effectively representing Medical Subject Headings (MeSH) headings (terms) such as disease and drug as discriminative vectors could greatly improve the performance of downstream computational prediction models. However, these terms are often abstract and difficult to quantify. In this paper, we converted the MeSH tree structure into a relationship network and applied several graph embedding algorithms on it to represent these terms. Specifically, the relationship network consisting of nodes (MeSH headings) and edges (relationships), which can be constructed by the tree num. Then, five graph embedding algorithms including DeepWalk, LINE, SDNE, LAP and HOPE were implemented on the relationship network to represent MeSH headings as vectors. In order to evaluate the performance of the proposed methods, we carried out the node classification and relationship prediction tasks. The results show that the MeSH headings characterized by graph embedding algorithms can not only be treated as an independent carrier for representation, but also can be utilized as additional information to enhance the representation ability of vectors. Thus, it can serve as an input and continue to play a significant role in any computational models related to disease, drug, microbe, etc. Besides, our method holds great hope to inspire relevant researchers to study the representation of terms in this network perspective.

| S-EPMC7986599 | biostudies-literature

PGAGP: Predicting pathogenic genes based on adaptive network embedding algorithm.

Project description:The study of disease-gene associations is an important topic in the field of computational biology. The accumulation of massive amounts of biomedical data provides new possibilities for exploring potential relations between diseases and genes through computational strategy, but how to extract valuable information from the data to predict pathogenic genes accurately and rapidly is currently a challenging and meaningful task. Therefore, we present a novel computational method called PGAGP for inferring potential pathogenic genes based on an adaptive network embedding algorithm. The PGAGP algorithm is to first extract initial features of nodes from a heterogeneous network of diseases and genes efficiently and effectively by Gaussian random projection and then optimize the features of nodes by an adaptive refining process. These low-dimensional features are used to improve the disease-gene heterogenous network, and we apply network propagation to the improved heterogenous network to predict pathogenic genes more effectively. By a series of experiments, we study the effect of PGAGP's parameters and integrated strategies on predictive performance and confirm that PGAGP is better than the state-of-the-art algorithms. Case studies show that many of the predicted candidate genes for specific diseases have been implied to be related to these diseases by literature verification and enrichment analysis, which further verifies the effectiveness of PGAGP. Overall, this work provides a useful solution for mining disease-gene heterogeneous network to predict pathogenic genes more effectively.

| S-EPMC9895109 | biostudies-literature

Moment feature based fast feature extraction algorithm for moving object detection using aerial images.

Project description:Fast and computationally less complex feature extraction for moving object detection using aerial images from unmanned aerial vehicles (UAVs) remains as an elusive goal in the field of computer vision research. The types of features used in current studies concerning moving object detection are typically chosen based on improving detection rate rather than on providing fast and computationally less complex feature extraction methods. Because moving object detection using aerial images from UAVs involves motion as seen from a certain altitude, effective and fast feature extraction is a vital issue for optimum detection performance. This research proposes a two-layer bucket approach based on a new feature extraction algorithm referred to as the moment-based feature extraction algorithm (MFEA). Because a moment represents the coherent intensity of pixels and motion estimation is a motion pixel intensity measurement, this research used this relation to develop the proposed algorithm. The experimental results reveal the successful performance of the proposed MFEA algorithm and the proposed methodology.

| S-EPMC4452346 | biostudies-literature

CRBA: A Competitive Rate-Based Algorithm Based on Competitive Spiking Neural Networks.

Project description:In this paper we present a Competitive Rate-Based Algorithm (CRBA) that approximates operation of a Competitive Spiking Neural Network (CSNN). CRBA is based on modeling of the competition between neurons during a sample presentation, which can be reduced to ranking of the neurons based on a dot product operation and the use of a discrete Expectation Maximization algorithm; the latter is equivalent to the spike time-dependent plasticity rule. CRBA's performance is compared with that of CSNN on the MNIST and Fashion-MNIST datasets. The results show that CRBA performs on par with CSNN, while using three orders of magnitude less computational time. Importantly, we show that the weights and firing thresholds learned by CRBA can be used to initialize CSNN's parameters that results in its much more efficient operation.

| S-EPMC8100331 | biostudies-literature

Local error estimates for adaptive simulation of the Reaction-Diffusion Master Equation via operator splitting.

Project description:The efficiency of exact simulation methods for the reaction-diffusion master equation (RDME) is severely limited by the large number of diffusion events if the mesh is fine or if diffusion constants are large. Furthermore, inherent properties of exact kinetic-Monte Carlo simulation methods limit the efficiency of parallel implementations. Several approximate and hybrid methods have appeared that enable more efficient simulation of the RDME. A common feature to most of them is that they rely on splitting the system into its reaction and diffusion parts and updating them sequentially over a discrete timestep. This use of operator splitting enables more efficient simulation but it comes at the price of a temporal discretization error that depends on the size of the timestep. So far, existing methods have not attempted to estimate or control this error in a systematic manner. This makes the solvers hard to use for practitioners since they must guess an appropriate timestep. It also makes the solvers potentially less efficient than if the timesteps are adapted to control the error. Here, we derive estimates of the local error and propose a strategy to adaptively select the timestep when the RDME is simulated via a first order operator splitting. While the strategy is general and applicable to a wide range of approximate and hybrid methods, we exemplify it here by extending a previously published approximate method, the Diffusive Finite-State Projection (DFSP) method, to incorporate temporal adaptivity.

| S-EPMC4746020 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data