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Measures of uncertainty of pharmacokinetic and pharmacodynamic parameter estimates: a new computerized algorithm.

Numerous algorithms exist to fit data to nonlinear models of the type used in chemistry, pharmacology, physiology, etc. Most include modules that provide some measure of the reliability of the estimated model parameters. The variance-covariance matrix (VCM) is the common tabulation of information that is used to quantify the parameter uncertainty as well as correlations between parameters. The VCM has its mathematical foundation in the linear regression world, where the dependent variable is a linear function of the parameters. However, when the model is not linear in its parameters, then the VCM is no longer an absolute quantitative measure of reliability of the parameter estimates and should be interpreted with caution. If the goal is to obtain a realistic and quantitative rather than a qualitative measurement of the parameter reliability, then it is necessary to have an alternative approach to describe the parameter likelihood region. We present a computerized algorithm that fills that need, and we compare its performance with the traditional VCM approach for different data sets. We also discuss criteria that may be used to determine when the VCM approach should and should not be used.

Algorithms↗

Robust parameter estimation techniques for stochastic within-host macroparasite models.

We present a stochastic model of the within-host population dynamics of lymphatic filariasis, and use a simulated goodness-of-fit (GOF) method to estimate immunological parameters and their confidence intervals from experimental data. A variety of deterministic moment closure approximations to the stochastic system are explored and compared with simulation results. For the maximum GOF parameter estimates, none of the methods of closure accurately reproduce the behaviour of the stochastic model. However, direct analysis of the stochastic model demonstrates that the high levels of variation observed in the data can be reproduced without requiring parameters to vary between hosts. This indicates that the observed aggregation of parasite load may be dynamically generated by random variation in the development of an effective immune response against parasite larvae.

Animals↗

Identification of insulin receptor systems: assessing the impact of model selection and measurement error on precision of parameter estimates using Monte Carlo study.

An extensive Monte Carlo study has been carried out in order to study the effect of measurement error on the precision of parameter estimates of an insulin binding system. Hypothetical radioimmunoassay experiments were generated for insulin binding to erythrocytes. The design of experiments followed strictly the protocol of real experiments. Randomly generated error was added to the synthetic data. The standard technique, a weighted non-linear regression analysis, was employed to re-estimate parameters of a model of two receptor sites and a model of negative co-operativity. As the original parameter values were known, the differences between original and estimated values was studied for (a) measurement error in the range from 0-17%, (b) random initial estimates and (c) error-free non-specific binding. In addition, analytical estimates of parameter precision were compared with the true between-experiment variation of parameter estimates. At the measurement error of 12%, a one site model is recommended to estimate the high affinity population of the two sites model. Plausible results can be expected in 90% of experiments, the between-experiment variation being approximately 30%. The model of two receptor sites gives approximately two thirds of plausible results. The high affinity population can be estimated with the between-experiment variation of 40%, the low affinity population is virtually unidentifiable with the between-experiment variation of approximately 100% and parameter estimates biased to higher values. Only half of the results obtained from the model of negative co-operativity are plausible, the variation in parameter estimates ranges from 90-150% and estimates are biased to higher values. At the level of 12% measurement error, random initial estimates do not significantly affect the estimation process, provided initial estimates are selected from a feasible range. At the same measurement error, the error-free non-specific binding does not improve the results, indicating that the mean of six replicates may be taken as a reliable estimate of non-specific binding. The analytical estimates of the coefficient of variation systematically underestimates the true between-experiments coefficient of variation, the difference has been found to be about 50%.

Erythrocytes↗

Data reconciliation and parameter estimation in flux-balance analysis.

Flux blance analysis (FBA) has been shown to be a very effective tool to interpret and predict the metabolism of various microorganisms when the set of available measurements is not sufficient to determine the fluxes within the cell. In this methodology, an underdetermined stoichiometric model is solved using a linear programming (LP) approach. The predictions of FBA models can be improved if noisy measurements are checked for consistency, and these in turn are used to estimate model parameters. In this work, a formal methodology for data reconciliation and parameter estimation with underdetermined stoichiometric models is developed and assessed. The procedure is formulated as a nonlinear optimization problem, where the LP is transformed into a set of nonlinear constraints. However, some of these constraints violate standard regularity conditions, making the direct numerical solution very difficult. Hence, a barrier formulation is used to represent these constraints, and an iterative procedure is defined that allows solving the problem to the desired degree of convergence. This methodology is assessed using a stoichiometric yeast model. The procedure is used for data reconciliation where more reliable estimations of noisy measurements are computed. On the other hand, assuming unknown biomass composition, the procedure is applied for simultaneous data reconciliation and biomass composition estimation. In both cases it is verified that the f measurements required to get unbiased and reliable estimations is reduced if the LP approach is included as additional constraints in the optimization.

Acetates↗

Improved parameter estimation for variance-stabilizing transformation of gene-expression microarray data.

A gene-expression microarray datum is modeled as an exponential expression signal (log-normal distribution) and additive noise. Variance-stabilizing transformation based on this model is useful for improving the uniformity of variance, which is often assumed for conventional statistical analysis methods. However, the existing method of estimating transformation parameters may not be perfect because of poor management of outliers. By employing an information normalization technique, we have developed an improved parameter estimation method, which enables statistically more straightforward outlier exclusion and works well even in the case of small sample size. Validation of this method with experimental data has suggested that it is superior to the conventional method.

Algorithms↗

Usefulness of subjective ovine milk scores: II. Genetic parameter estimates.

Genetic parameters for a subjective milk score given to ewes within 24 h of parturition were estimated to determine the usefulness of milk score as a selection trait to improve milk production, which influences total litter weight weaned. Heritability of milk score and the genetic correlation of milk score with litter weight weaned were estimated by REML separately for four sheep breeds, Rambouillet (n = 1,731), Targhee (n = 1,638), Columbia (n = 1,731), and Polypay (n = 1,129). Litter weight weaned was the total weight of lambs weaned at approximately 120 d of age under a western range production system. Observed heritability estimates for milk score at first parity were moderate and similar among breeds, ranging from 0.18 to 0.32. Heritability estimates adjusted for a binomial distribution of milk scores at first parity were high (Columbia, 0.43; Polypay, 0.35; Rambouillet, 0.50; Targhee, 0.84). Estimates of observed heritability for second-parity milk score were moderate to high, ranging from 0.23 to 0.46. Milk score at first or second parity was genetically correlated with milk score records at maturity (third parity and greater), with estimates ranging from 0.69 to 1.00. Milk score and litter weight weaned were genetically correlated at first or second parity in Rambouillet (r(g) = 1.00) and Targhee breeds (r(g) = 1.00 and 0.61, respectively), but not in the Columbia and Polypay breeds. Estimates of heritability for lifetime records for milk score ranged from 0.16 to 0.26 across breeds. Estimates of genetic correlations of annual lifetime milk score records with litter weight weaned were high (Columbia, 1.00; Polypay, 0.81; Rambouillet, 1.00; and Targhee, 0.77). Repeatability estimates for milk score were similar across breeds, 0.23 for Columbia, Rambouillet, and Targhee ewes and 0.28 for Polypay ewes. Milk score measured at first or second parity may be a good predictor of future potential milking ability. Further, milk score can be used as a selection trait to improve maternal ability for increasing litter weight weaned. The need for increasing ewe milking performance and lamb growth rate at first parity in commercial range sheep production systems may be addressed by selection for milk score at first parity.

Animals↗

Jackknife estimators of variance for parameter estimates from estimating equations with applications to clustered survival data.

An estimate of a parameter vector beta is often obtained by setting a "score" vector equal to zero and solving for beta. Estimating equations of this type include maximum likelihood, quasi-likelihood (McCullagh, 1983, Annals of Statistics 11, 59-67), and generalized estimating equations (Liang and Zeger, 1986, Biometrika 73, 13-22). White (1982, Econometrica 50, 1-26) proposed a variance estimator for beta that is robust to model misspecification. We show that a "one-step" jackknife estimator of variance is asymptotically equivalent to the variance estimator proposed by White. The one-step variance estimator may be preferred when the appropriate computer packages are not available to compute White's estimator directly. This jackknife estimator is very useful in our example with clustered survival data.

Analysis of Variance↗

Experimental design and efficient parameter estimation in preclinical pharmacokinetic studies.

Monte Carlo simulation technique used to evaluate the effect of the arrangement of concentrations on the efficiency of estimation of population pharmacokinetic parameters in the preclinical setting is described. Although the simulations were restricted to the one compartment model with intravenous bolus input, they provide the basis of discussing some structural aspects involved in designing a destructive ("quantic") preclinical population pharmacokinetic study with a fixed sample size as is usually the case in such studies. The efficiency of parameter estimation obtained with sampling strategies based on the three and four time point designs were evaluated in terms of the percent prediction error, design number, individual and joint confidence intervals coverage for parameter estimates approaches, and correlation analysis. The data sets contained random terms for both inter- and residual intra-animal variability. The results showed that the typical population parameter estimates for clearance and volume were efficiently (accurately and precisely) estimated for both designs, while interanimal variability (the only random effect parameter that could be estimated) was inefficiently (inaccurately and imprecisely) estimated with most sampling schedules of the two designs. The exact location of the third and fourth time point for the three and four time point designs, respectively, was not critical to the efficiency of overall estimation of all population parameters of the model. However, some individual population pharmacokinetic parameters were sensitive to the location of these times.

Animals↗

Parameter estimation: local identifiability of parameters.

For biological systems one often cannot set up experiments to measure all of the state variables. If only a subset of the state variables can be measured, it is possible that some of the system parameters cannot influence the measured state variables or that they do so in combinations that do not define the parameters' effects separately. Such parameters are unidentifiable and are in theory unestimable. Given a model of the system, linear or nonlinear, and initial estimates of the values of all parameters, we exhibit a simple theory and describe a program for checking the local identifiability of the parameters at the initial estimates for given experiments on the model. The program, IDENT, is available from the authors.

Animals↗

Nonlinear parameter estimation for solution-diffusion models of membrane pervaporation.

An optimization-based procedure for estimating unknown parameters in solution-diffusion models of membrane pervaporation is presented. Permeation of two components through a polymer membrane is described by distinct solution and diffusion models. The solution model is based on a modified form of Flory-Huggins theory that accounts for interactions between the two penetrants. The diffusion model is derived from Fick's law, where the diffusion coefficients are allowed to depend on the local concentration of each component in the membrane. A phenomenologic relation is used to account for the effect of temperature on the component fluxes. The solution and diffusion models, as well as the temperature-flux relation, contain parameters that are not directly measurable. It is shown that these parameters can be estimated effectively from sorption and flux data by the solution of suitably formulated nonlinear optimization problems. The separation of styrene and ethylbenzene with a polyurethane membrane is used to illustrate the parameter estimation procedure.

Chemistry↗

libSRES: a C library for stochastic ranking evolution strategy for parameter estimation.

SUMMARY: Estimation of kinetic parameters in a biochemical pathway or network represents a common problem in systems studies of biological processes. We have implemented a C library, named libSRES, to facilitate a fast implementation of computer software for study of non-linear biochemical pathways. This library implements a (mu, lambda)-ES evolutionary optimization algorithm that uses stochastic ranking as the constraint handling technique. Considering the amount of computing time it might require to solve a parameter-estimation problem, an MPI version of libSRES is provided for parallel implementation, as well as a simple user interface. libSRES is freely available and could be used directly in any C program as a library function. We have extensively tested the performance of libSRES on various pathway parameter-estimation problems and found its performance to be satisfactory. AVAILABILITY: The source code (in C) is free for academic users at http://csbl.bmb.uga.edu/~jix/science/libSRES/

Algorithms↗

Robust parameter estimation of intensity distributions for brain magnetic resonance images.

This paper presents two new methods for robust parameter estimation of mixtures in the context of magnetic resonance (MR) data segmentation. The head is constituted of different types of tissue that can be modeled by a finite mixture of multivariate Gaussian distributions. Our goal is to estimate accurately the statistics of desired tissues in presence of other ones of lesser interest. These latter can be considered as outliers and can severely bias the estimates of the former. For this purpose, we introduce a first method, which is an extension of the expectation-maximization (EM) algorithm, that estimates parameters of Gaussian mixtures but incorporates an outlier rejection scheme which allows to compute the properties of the desired tissues in presence of atypical data. The second method is based on genetic algorithms and is well suited for estimating the parameters of mixtures of different kind of distributions. We use this property by adding a uniform distribution to the Gaussian mixture for modeling the outliers. The proposed genetic algorithm can efficiently estimate the parameters of this extended mixture for various initial settings. Also, by changing the minimization criterion, estimates of the parameters can be obtained by histogram fitting which considerably reduces the computational cost. Experiments on synthetic and real MR data show that accurate estimates of the gray and white matters parameters are computed.

Adolescent↗

Estimating recharge rates with analytic element models and parameter estimation.

Quantifying the spatial and temporal distribution of recharge is usually a prerequisite for effective ground water flow modeling. In this study, an analytic element (AE) code (GFLOW) was used with a nonlinear parameter estimation code (UCODE) to quantify the spatial and temporal distribution of recharge using measured base flows as calibration targets. The ease and flexibility of AE model construction and evaluation make this approach well suited for recharge estimation. An AE flow model of an undeveloped watershed in northern Wisconsin was optimized to match median annual base flows at four stream gages for 1996 to 2000 to demonstrate the approach. Initial optimizations that assumed a constant distributed recharge rate provided good matches (within 5%) to most of the annual base flow estimates, but discrepancies of >12% at certain gages suggested that a single value of recharge for the entire watershed is inappropriate. Subsequent optimizations that allowed for spatially distributed recharge zones based on the distribution of vegetation types improved the fit and confirmed that vegetation can influence spatial recharge variability in this watershed. Temporally, the annual recharge values varied >2.5-fold between 1996 and 2000 during which there was an observed 1.7-fold difference in annual precipitation, underscoring the influence of nonclimatic factors on interannual recharge variability for regional flow modeling. The final recharge values compared favorably with more labor-intensive field measurements of recharge and results from studies, supporting the utility of using linked AE-parameter estimation codes for recharge estimation.

Ecosystem↗

Estimation in regression models with externally estimated parameters.

In many regression applications, some of the model parameters are estimated from separate data sources. Typically, these estimates are plugged into the regression model and the remainder of the parameters is estimated from the primary data source. This situation arises frequently in compartment modeling when there is an external input function to the system. This paper provides asymptotic and bootstrap-based approaches for accounting for all sources of variability when computing standard errors for estimated regression model parameters. Examples and simulations are provided to motivate and illustrate the ideas.

Algorithms↗

Pharmacokinetic parameter estimations by minimum relative entropy method.

For estimating pharmacokinetic parameters, we introduce the minimum relative entropy (MRE) method and compare its performance with least squares methods. There are several variants of least squares, such as ordinary least squares (OLS), weighted least squares, and iteratively reweighted least squares. In addition to these traditional methods, even extended least squares (ELS), a relatively new approach to nonlinear regression analysis, can be regarded as a variant of least squares. These methods are different from each other in their manner of handling weights. It has been recognized that least squares methods with an inadequate weighting scheme may cause misleading results (the "choice of weights" problem). Although least squares with uniform weights, i.e., OLS, is rarely used in pharmacokinetic analysis, it offers the principle of least squares. The objective function of OLS can be regarded as a distance between observed and theoretical pharmacokinetic values on the Euclidean space RN, where N is the number of observations. Thus OLS produces its estimates by minimizing the Euclidean distance. On the other hand, MRE works by minimizing the relative entropy which expresses discrepancy between two probability densities. Because pharmacokinetic functions are not density function in general, we use a particular form of the relative entropy whose domain is extended to the space of all positive functions. MRE never assumes any distribution of errors involved in observations. Thus, it can be a possible solution to the choice of weights problem. Moreover, since the mathematical form of the relative entropy, i.e., an expectation of the log-ratio of two probability density functions, is different from that of a usual Euclidean distance, the behavior of MRE may be different from those of least squares methods. To clarify the behavior of MRE, we have compared the performance of MRE with those of ELS and OLS by carrying out an intensive simulation study, where four pharmaco-kinetic models (mono- or biexponential, Bateman, Michaelis-Menten) and several variance models for distribution of observation errors are employed. The relative precision of each method was investigated by examining the absolute deviation of each individual parameter estimate from the known value. OLS is the best method and MRE is not a good one when the actual observation error magnitude conforms to the assumption of OLS, that is, error variance is constant, but OLS always behaves poorly with the other variance models. On the other hand, MRE performs better than ELS and OLS when the variance of observation is proportional to its mean. In contrast, ELS is superior to MRE and OLS when the standard deviation of observation is proportional to its mean. In either case the difference between MRE and ELS is relatively small. Generally, the performance of MRE is comparable to that of ELS. Thus MRE provides as reliable a method as ELS for estimating pharmacokinetic parameters.

Humans↗

An iterative curve stripping technique for pharmacokinetic parameter estimation.

Non-linear least-squares regression is commonly used for pharmacokinetic parameter estimation. Initial parameter estimates are required as a prelude to non-linear least-squares and the quality of the final parameter estimates may depend on these initial values. Polyexponential curve stripping is frequently used for the provision of initial estimates. It is demonstrated that under certain conditions conventional curve stripping yields biased estimates. A new iterative curve stripping technique is developed and is shown to be free of such bias. The two methods are compared using both simulated and real pharmacokinetic data.

Administration, Oral↗

Simulation-based parameter estimation for complex models: a breast cancer natural history modelling illustration.

Simulation-based parameter estimation offers a powerful means of estimating parameters in complex stochastic models. We illustrate the application of these ideas in the setting of a natural history model for breast cancer. Our model assumes that the tumor growth process follows a geometric Brownian motion; parameters are estimated from the SEER registry. Our discussion focuses on the use of simulation for computing the maximum likelihood estimator for this class of models. The analysis shows that simulation provides a straightforward means of computing such estimators for models of substantial complexity.

Algorithms↗

Parameter estimation in a crossbridge muscle model.

Models of muscle crossbridge dynamics have great potential for understanding muscle contraction and having a wide range of application. However, the estimation of many model parameters, most of which are difficult to measure, limits their applicability. This study developed a method of estimating parameters in the Distribution Moment crossbridge model from measurements of force-length and force-velocity relationships in cat soleus single muscle fibers. Analysis of the parameter estimates showed that the detachment rate parameters had more uncertainty than the attachment rate parameter, which could reflect physiological variations in the contractile protein content and in the response of muscle to lengthenings.

Animals↗