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Comparing Eight Parameter Estimation Methods for the Ratcliff Diffusion Model Using Free Software.

ABSTRACT: The Ratcliff Diffusion Model has become an important and widely used tool for the evaluation of psychological experiments. Concurrently, numerous programs and routines have appeared to estimate the model's parameters. The present study aims at comparing some of the most widely used tools with special focus on freely available routines (i.e., open source). Our simulations show that (1) starting point and non-decision time were recovered better than drift rate, (2) the Bayesian approach outperformed all other approaches when the number of trials was low, (3) the Kolmogorov-Smirnov and ?2 approaches revealed more bias than Bayesian or Maximum Likelihood based routines, and (4) EZ produced substantially biased estimates of threshold separation, non-decision time and drift rate when starting point z ? a/2. We discuss the implications for the choice of parameter estimation approaches for real data and suggest that if biased starting point cannot be excluded, EZ will produce deviant estimates and should be used with great care.

SUBMITTER: Alexandrowicz RW

PROVIDER: S-EPMC7553076 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Comparing Eight Parameter Estimation Methods for the Ratcliff Diffusion Model Using Free Software.

Alexandrowicz Rainer W RW Gula Bartosz B

Frontiers in psychology 20200929

The Ratcliff Diffusion Model has become an important and widely used tool for the evaluation of psychological experiments. Concurrently, numerous programs and routines have appeared to estimate the model's parameters. The present study aims at comparing some of the most widely used tools with special focus on freely available routines (i.e., open source). Our simulations show that (1) starting point and non-decision time were recovered better than drift rate, (2) the Bayesian approach outperform ...[more]

PMID: 33117213

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Project description:BackgroundThe importance of stochasticity in cellular processes having low number of molecules has resulted in the development of stochastic models such as chemical master equation. As in other modelling frameworks, the accompanying rate constants are important for the end-applications like analyzing system properties (e.g. robustness) or predicting the effects of genetic perturbations. Prior knowledge of kinetic constants is usually limited and the model identification routine typically includes parameter estimation from experimental data. Although the subject of parameter estimation is well-established for deterministic models, it is not yet routine for the chemical master equation. In addition, recent advances in measurement technology have made the quantification of genetic substrates possible to single molecular levels. Thus, the purpose of this work is to develop practical and effective methods for estimating kinetic model parameters in the chemical master equation and other stochastic models from single cell and cell population experimental data.ResultsThree parameter estimation methods are proposed based on the maximum likelihood and density function distance, including probability and cumulative density functions. Since stochastic models such as chemical master equations are typically solved using a Monte Carlo approach in which only a finite number of Monte Carlo realizations are computationally practical, specific considerations are given to account for the effect of finite sampling in the histogram binning of the state density functions. Applications to three practical case studies showed that while maximum likelihood method can effectively handle low replicate measurements, the density function distance methods, particularly the cumulative density function distance estimation, are more robust in estimating the parameters with consistently higher accuracy, even for systems showing multimodality.ConclusionsThe parameter estimation methodologies described in this work have provided an effective and practical approach in the estimation of kinetic parameters of stochastic systems from either sparse or dense cell population data. Nevertheless, similar to kinetic parameter estimation in other modelling frameworks, not all parameters can be estimated accurately, which is a common problem arising from the lack of complete parameter identifiability from the available data.

Dataset Information

Comparing Eight Parameter Estimation Methods for the Ratcliff Diffusion Model Using Free Software.

Publications

Comparing Eight Parameter Estimation Methods for the Ratcliff Diffusion Model Using Free Software.

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