Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Nonlinear Calibration Model Choice between the Four and Five-Parameter Logistic Models.

ABSTRACT: Both the four-parameter logistic (4PL) and the five-parameter logistic (5PL) models are widely used in nonlinear calibration. In this paper, we study the choice between 5PL and 4PL both by the accuracy and precision of the estimated concentrations and by the power to detect an association between a binary disease outcome and the estimated concentrations. Our results show that when the true curve is symmetric around its inflection point, the efficiency loss from using 5PL is negligible under the prevalent experimental design. When the true curve is asymmetric, 4PL may sometimes offer better performance due to bias-variance trade-off. We provide a practical guideline for choosing between 5PL and 4PL and illustrate its application with a real dataset from the HIV Vaccine Trials Network laboratory.

SUBMITTER: Cumberland WN

PROVIDER: S-EPMC4263697 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Nonlinear Calibration Model Choice between the Four and Five-Parameter Logistic Models.

Cumberland William N WN Fong Youyi Y Yu Xuesong X Defawe Olivier O Frahm Nicole N De Rosa Stephen S

Journal of biopharmaceutical statistics 20140611 5

Both the four-parameter logistic (4PL) and the five-parameter logistic (5PL) models are widely used in nonlinear calibration. In this paper, we study the choice between 5PL and 4PL both by the accuracy and precision of the estimated concentrations and by the power to detect an association between a binary disease outcome and the estimated concentrations. Our results show that when the true curve is symmetric around its inflection point, the efficiency loss from using 5PL is negligible under the ...[more]

PMID: 24918306

Similar Datasets

An Optimized Bayesian Hierarchical Two-Parameter Logistic Model for Small-Sample Item Calibration.

Project description:Accurate item calibration in models of item response theory (IRT) requires rather large samples. For instance, N>500 respondents are typically recommended for the two-parameter logistic (2PL) model. Hence, this model is considered a large-scale application, and its use in small-sample contexts is limited. Hierarchical Bayesian approaches are frequently proposed to reduce the sample size requirements of the 2PL. This study compared the small-sample performance of an optimized Bayesian hierarchical 2PL (H2PL) model to its standard inverse Wishart specification, its nonhierarchical counterpart, and both unweighted and weighted least squares estimators (ULSMV and WLSMV) in terms of sampling efficiency and accuracy of estimation of the item parameters and their variance components. To alleviate shortcomings of hierarchical models, the optimized H2PL (a) was reparametrized to simplify the sampling process, (b) a strategy was used to separate item parameter covariances and their variance components, and (c) the variance components were given Cauchy and exponential hyperprior distributions. Results show that when combining these elements in the optimized H2PL, accurate item parameter estimates and trait scores are obtained even in sample sizes as small as N=100 . This indicates that the 2PL can also be applied to smaller sample sizes encountered in practice. The results of this study are discussed in the context of a recently proposed multiple imputation method to account for item calibration error in trait estimation.

| S-EPMC7262992 | biostudies-literature

Gibbs-Slice Sampling Algorithm for Estimating the Four-Parameter Logistic Model

Project description:The four-parameter logistic (4PL) model has recently attracted much interest in educational testing and psychological measurement. This paper develops a new Gibbs-slice sampling algorithm for estimating the 4PL model parameters in a fully Bayesian framework. Here, the Gibbs algorithm is employed to improve the sampling efficiency by using the conjugate prior distributions in updating asymptote parameters. A slice sampling algorithm is used to update the 2PL model parameters, which overcomes the dependence of the Metropolis–Hastings algorithm on the proposal distribution (tuning parameters). In fact, the Gibbs-slice sampling algorithm not only improves the accuracy of parameter estimation, but also enhances sampling efficiency. Simulation studies are conducted to show the good performance of the proposed Gibbs-slice sampling algorithm and to investigate the impact of different choices of prior distribution on the accuracy of parameter estimation. Based on Markov chain Monte Carlo samples from the posterior distributions, the deviance information criterion and the logarithm of the pseudomarginal likelihood are considered to assess the model fittings. Moreover, a detailed analysis of PISA data is carried out to illustrate the proposed methodology.

| S-EPMC7530206 | biostudies-literature

A Two-Parameter Logistic Extension Model: <i>An Efficient Variant of the Three-Parameter Logistic Model</i>.

Project description:A three-parameter logistic (3PL) model variant, named the two-parameter logistic extension (2PLE) model, was developed. This new model employs a function that integrates item features according to an examinee's ability level instead of a fixed guessing parameter used in the 3PL model to quantify guessing behavior. Correct response probabilities from a solution behavior and guessing behavior increase as the level of ability increases. At extreme cases in which the level of ability is close to negative infinity, the 2PLE model degenerates into a 3PL model with a guessing probability at chance level (i.e., 1/m, where m is the number of options). The properties of the 2PLE model were described and compared with those of other guessing models. Then, a simulation study comparing the performance of the 2PLE model with that of the 3PL model under three scenarios was conducted. Results showed that the 2PLE model generally outperforms the 3PL model. Finally, the application of the new model in comparison with several existing models was demonstrated by using two real data sets.

| S-EPMC6696869 | biostudies-literature

Neural parameter calibration for large-scale multiagent models.

Project description:Computational models have become a powerful tool in the quantitative sciences to understand the behavior of complex systems that evolve in time. However, they often contain a potentially large number of free parameters whose values cannot be obtained from theory but need to be inferred from data. This is especially the case for models in the social sciences, economics, or computational epidemiology. Yet, many current parameter estimation methods are mathematically involved and computationally slow to run. In this paper, we present a computationally simple and fast method to retrieve accurate probability densities for model parameters using neural differential equations. We present a pipeline comprising multiagent models acting as forward solvers for systems of ordinary or stochastic differential equations and a neural network to then extract parameters from the data generated by the model. The two combined create a powerful tool that can quickly estimate densities on model parameters, even for very large systems. We demonstrate the method on synthetic time series data of the SIR model of the spread of infection and perform an in-depth analysis of the Harris-Wilson model of economic activity on a network, representing a nonconvex problem. For the latter, we apply our method both to synthetic data and to data of economic activity across Greater London. We find that our method calibrates the model orders of magnitude more accurately than a previous study of the same dataset using classical techniques, while running between 195 and 390 times faster.

| S-EPMC9963791 | biostudies-literature

The robust estimation of examinee ability based on the four-parameter logistic model when guessing and carelessness responses exist.

Project description:The three-parameter Logistic model (3PLM) and the four-parameter Logistic model (4PLM) have been proposed to reduce biases in cases of response disturbances, including random guessing and carelessness. However, they could also influence the examinees who do not guess or make careless errors. This paper proposes a new approach to solve this problem, which is a robust estimation based on the 4PLM (4PLM-Robust), involving a critical-probability guessing parameter and a carelessness parameter. This approach is compared with the 2PLM-MLE(two-parameter Logistic model and a maximum likelihood estimator), the 3PLM-MLE, the 4PLM-MLE, the Biweight estimation and the Huber estimation in terms of bias using an example and three simulation studies. The results show that the 4PLM-Robust is an effective method for robust estimation, and its calculation is simpler than the Biweight estimation and the Huber estimation.

| S-EPMC8084210 | biostudies-literature

Inference-based assessment of parameter identifiability in nonlinear biological models.

Project description:As systems approaches to the development of biological models become more mature, attention is increasingly focusing on the problem of inferring parameter values within those models from experimental data. However, particularly for nonlinear models, it is not obvious, either from inspection of the model or from the experimental data, that the inverse problem of parameter fitting will have a unique solution, or even a non-unique solution that constrains the parameters to lie within a plausible physiological range. Where parameters cannot be constrained they are termed 'unidentifiable'. We focus on gaining insight into the causes of unidentifiability using inference-based methods, and compare a recently developed measure-theoretic approach to inverse sensitivity analysis to the popular Markov chain Monte Carlo and approximate Bayesian computation techniques for Bayesian inference. All three approaches map the uncertainty in quantities of interest in the output space to the probability of sets of parameters in the input space. The geometry of these sets demonstrates how unidentifiability can be caused by parameter compensation and provides an intuitive approach to inference-based experimental design.

| S-EPMC6073654 | biostudies-literature

A robust bayesian random effects model for nonlinear calibration problems.

Project description:In the context of a bioassay or an immunoassay, calibration means fitting a curve, usually nonlinear, through the observations collected on a set of samples containing known concentrations of a target substance, and then using the fitted curve and observations collected on samples of interest to predict the concentrations of the target substance in these samples. Recent technological advances have greatly improved our ability to quantify minute amounts of substance from a tiny volume of biological sample. This has in turn led to a need to improve statistical methods for calibration. In this article, we focus on developing calibration methods robust to dependent outliers. We introduce a novel normal mixture model with dependent error terms to model the experimental noise. In addition, we propose a reparameterization of the five parameter logistic nonlinear regression model that allows us to better incorporate prior information. We examine the performance of our methods with simulation studies and show that they lead to a substantial increase in performance measured in terms of mean squared error of estimation and a measure of the average prediction accuracy. A real data example from the HIV Vaccine Trials Network Laboratory is used to illustrate the methods.

| S-EPMC3897249 | biostudies-literature

Optimal control methods for nonlinear parameter estimation in biophysical neuron models.

Project description:Functional forms of biophysically-realistic neuron models are constrained by neurobiological and anatomical considerations, such as cell morphologies and the presence of known ion channels. Despite these constraints, neuron models still contain unknown static parameters which must be inferred from experiment. This inference task is most readily cast into the framework of state-space models, which systematically takes into account partial observability and measurement noise. Inferring only dynamical state variables such as membrane voltages is a well-studied problem, and has been approached with a wide range of techniques beginning with the well-known Kalman filter. Inferring both states and fixed parameters, on the other hand, is less straightforward. Here, we develop a method for joint parameter and state inference that combines traditional state space modeling with chaotic synchronization and optimal control. Our methods are tailored particularly to situations with considerable measurement noise, sparse observability, very nonlinear or chaotic dynamics, and highly uninformed priors. We illustrate our approach both in a canonical chaotic model and in a phenomenological neuron model, showing that many unknown parameters can be uncovered reliably and accurately from short and noisy observed time traces. Our method holds promise for estimation in larger-scale systems, given ongoing improvements in calcium reporters and genetically-encoded voltage indicators.

| S-EPMC9514669 | biostudies-literature

Analysis of schizophrenia data using a nonlinear threshold index logistic model.

Project description:Genetic information, such as single nucleotide polymorphism (SNP) data, has been widely recognized as useful in prediction of disease risk. However, how to model the genetic data that is often categorical in disease class prediction is complex and challenging. In this paper, we propose a novel class of nonlinear threshold index logistic models to deal with the complex, nonlinear effects of categorical/discrete SNP covariates for Schizophrenia class prediction. A maximum likelihood methodology is suggested to estimate the unknown parameters in the models. Simulation studies demonstrate that the proposed methodology works viably well for moderate-size samples. The suggested approach is therefore applied to the analysis of the Schizophrenia classification by using a real set of SNP data from Western Australian Family Study of Schizophrenia (WAFSS). Our empirical findings provide evidence that the proposed nonlinear models well outperform the widely used linear and tree based logistic regression models in class prediction of schizophrenia risk with SNP data in terms of both Types I/II error rates and ROC curves.

| S-EPMC4201476 | biostudies-literature

Calibration of Multi-Parameter Models of Avascular Tumor Growth Using Time Resolved Microscopy Data.

Project description:Two of the central challenges of using mathematical models for predicting the spatiotemporal development of tumors is the lack of appropriate data to calibrate the parameters of the model, and quantitative characterization of the uncertainties in both the experimental data and the modeling process itself. We present a sequence of experiments, with increasing complexity, designed to systematically calibrate the rates of apoptosis, proliferation, and necrosis, as well as mobility, within a phase-field tumor growth model. The in vitro experiments characterize the proliferation and death of human liver carcinoma cells under different initial cell concentrations, nutrient availabilities, and treatment conditions. A Bayesian framework is employed to quantify the uncertainties in model parameters. The average difference between the calibration and the data, across all time points is between 11.54% and 14.04% for the apoptosis experiments, 7.33% and 23.30% for the proliferation experiments, and 8.12% and 31.55% for the necrosis experiments. The results indicate the proposed experiment-computational approach is generalizable and appropriate for step-by-step calibration of multi-parameter models, yielding accurate estimations of model parameters related to rates of proliferation, apoptosis, and necrosis.

| S-EPMC6162291 | 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