Monte Carlo simulation with confusion matrix paradigm - A sample of internal consistency indices.
Ontology highlight
ABSTRACT:
SUBMITTER: Cheng Y
PROVIDER: S-EPMC10788128 | biostudies-literature | 2023
REPOSITORIES: biostudies-literature
Publications
Monte Carlo simulation with confusion matrix paradigm - A sample of internal consistency indices.
Cheng Yongtian Y Pérez-Díaz Pablo A PA Petrides K V KV Li Johnson J
Frontiers in psychology 20231227
Monte Carlo simulation is a common method of providing empirical evidence to verify statistics used in psychological studies. A representative set of conditions should be included in simulation studies. However, several recently published Monte Carlo simulation studies have not included the conditions of the null distribution of the statistic in their evaluations or comparisons of statistics and, therefore, have drawn incorrect conclusions. This present study proposes a design based on a common ...[more]
Similar Datasets
Project description:BackgroundMonte Carlo simulation is considered as the most accurate method for dose calculation in radiotherapy. PRIMO is a Monte-Carlo program with a user-friendly graphical interface.Material and methodA VitalBeam with 6MV and 6MV flattening filter free (FFF), equipped with the 120 Millennium multileaf collimator was simulated by PRIMO. We adjusted initial energy, energy full width at half maximum (FWHM), focal spot FWHM, and beam divergence to match the measurements. The water tank and ion-chamber were used in the measurement. Percentage depth dose (PDD) and off axis ratio (OAR) were evaluated with gamma passing rates (GPRs) implemented in PRIMO. PDDs were matched at different widths of standard square fields. OARs were matched at five depths. Transmission factor and dose leaf gap (DLG) were simulated. DLG was measured by electronic portal imaging device using a sweeping gap method.ResultFor the criterion of 2%/2 mm, 1%/2 mm and 1%/1 mm, the GPRs of 6MV PDD were 99.33-100%, 99-100%, and 99-100%, respectively; the GPRs of 6MV FFF PDD were 99.33-100%, 98.99-99.66%, and 97.64-98.99%, respectively; the GPRs of 6MV OAR were 96.4-100%, 90.99-100%, and 85.12-98.62%, respectively; the GPRs of 6MV FFF OAR were 95.15-100%, 89.32-100%, and 87.02-99.74%, respectively. The calculated DLG matched well with the measurement (6MV: 1.36 mm vs. 1.41 mm; 6MV FFF: 1.07 mm vs. 1.03 mm, simulation vs measurement). The transmission factors were similar (6MV: 1.25% vs. 1.32%; 6MV FFF: 0.8% vs. 1.12%, simulation vs measurement).ConclusionThe calculated PDD, OAR, DLG and transmission factor were all in good agreement with measurements. PRIMO is an independent (with respect to analytical dose calculation algorithm) and accurate Monte Carlo tool.
| S-EPMC9667592 | biostudies-literature
Project description:BackgroundIn the biological sciences the TCID50 (median tissue culture infective dose) assay is often used to determine the strength of a virus.MethodsWhen the so-called Spearman-Kaerber calculation is used, the ratio between the pfu (the number of plaque forming units, the effective number of virus particles) and the TCID50, theoretically approaches a simple function of Eulers constant. Further, the standard deviation of the logarithm of the TCID50 approaches a simple function of the dilution factor and the number of wells used for determining the ratios in the assay. However, these theoretical calculations assume that the dilutions of the assay are independent, and in practice this is not completely correct. The assay was simulated using Monte Carlo techniques.ResultsOur simulation studies show that the theoretical results actually hold true for practical implementations of the assay. Furthermore, the simulation studies show that the distribution of the (the log of) TCID50, although discrete in nature, has a close relationship to the normal distribution.ConclusionThe pfu is proportional to the TCID50 titre with a factor of about 0.56 when using the Spearman-Kaerber calculation method. The normal distribution can be used for statistical inferences and ANOVA on the (the log of) TCID50 values is meaningful with group sizes of 5 and above.
| S-EPMC3331834 | biostudies-literature
Project description:Conventional mammography can suffer from poor contrast between healthy and cancerous tissues due to the small difference in attenuation properties. Coherent scatter slot scan imaging is an imaging technique which provides additional information and is compatible with conventional mammography. A Monte Carlo simulation of coherent scatter slot scan imaging was performed to assess its performance and provide system optimization. Coherent scatter could be exploited using a system similar to conventional slot scan mammography system with antiscatter grids tilted at the characteristic angle of cancerous tissues. System optimization was performed across several parameters, including source voltage, tilt angle, grid distances, grid ratio, and shielding geometry. The simulated carcinomas were detectable for tumors as small as 5 mm in diameter, so coherent scatter analysis using a wide-slot setup could be promising as an enhancement for screening mammography. Employing coherent scatter information simultaneously with conventional mammography could yield a conventional high spatial resolution image with additional coherent scatter information.
| S-EPMC4999523 | biostudies-other
Project description:Mixture models of item response theory (IRT) can be used to detect inappropriate category use. Data collected by panel surveys where attitudes and traits are typically assessed by short scales with many response categories are prone to response styles indicating inappropriate category use. However, the application of mixed IRT models to this data type can be challenging because of many threshold parameters within items. Up to now, there is very limited knowledge about the sample size required for an appropriate performance of estimation methods as well as goodness-of-fit criteria of mixed IRT models in this case. The present Monte Carlo simulation study examined these issues for two mixed IRT models [the restricted mixed generalized partial credit model (rmGPCM) and the mixed partial credit model (mPCM)]. The population parameters of the simulation study were taken from a real application to survey data which is challenging (a 5-item scale with an 11-point rating scale, and three latent classes). Additional data conditions (e.g., long tests, a reduced number of response categories, and a simple latent mixture) were included in this simulation study to improve the generalizability of the results. Under this challenging data condition, for each model, data were generated based on varying sample sizes (from 500 to 5,000 observations with a 500-step). For the additional conditions, only three sample sizes (consisting of 1,000, 2,500, and 4,500 observations) were examined. The effect of sample size on estimation problems and accuracy of parameter and standard error estimates were evaluated. Results show that the two mixed IRT models require at least 2,500 observations to provide accurate parameter and standard error estimates under the challenging data condition. The rmGPCM produces more estimation problems than the more parsimonious mPCM, mostly because of the sparse tables arising due to many response categories. These models exhibit similar trends of estimation accuracy across sample sizes. Under the additional conditions, no estimation problems are observed. Both models perform well with a smaller sample size when long tests were used or a true latent mixture includes two classes. For model selection, the AIC3 and the SABIC are the most reliable information criteria.
| S-EPMC6863808 | biostudies-literature
Project description:Evaluation of water quality is crucial for managing surface water effectively, ensuring its suitability for human use, and sustaining the environment. In the lower Danube River basin, various methods were employed to assess surface water quality for irrigation, drinking, human health risk purposes and the main mechanism control the surface water chemistry. These methods included water quality indicators (WQIs), complex statistical analyses, geographic information systems (GIS), Monte Carlo simulation, and geochemical modeling. Physicochemical analyses of surface water samples revealed primarily Ca-Mg-HCO3- is the dominant water types. Principal component analysis (PCA), ionic ratios and piper, chloro alkaline index, Chadha, and Gibbs diagrams identified three distinct water characteristics influenced by water-rocks interaction, evaporation, ions exchange, and human activities. The geochemical modeling showed Danube River water's strong ability to dissolve gypsum, halite, and anhydrite (SI < 0) and precipitate aragonite, dolomite, and calcite with saturation index (SI) value greater than 0 along its flow path. The irrigation water quality index (IWQI = 99.6-107.6), sodium adsorption ratio (SAR = 0.37-0.68), sodium percentage (Na% = 13.7-18.7), soluble sodium percentage (SSP = 12.5-17.5), Potential Salinity (PS = 0.73-1.6), and Residual Sodium Carbonate (RSC = - 1.27-0.58) values were used, mainly indicating acceptable quality with some limitations. Danube River water was unsuitable for drinking based on WQI value (WQI = 81-104). Oral exposure of children to specific components showed a higher hazard index (HI > 1) compared to adults, indicating a 2.1 times higher overall non-carcinogenic risk hazard index. However, Monte Carlo simulation demonstrated negligible iron, manganese, and nitrate health hazards for both age groups. These findings are valuable for water quality management decisions, contributing to long-term resource sustainability.
| S-EPMC11317494 | biostudies-literature
Project description:Density matrix quantum Monte Carlo (DMQMC) is a recently developed method for stochastically sampling the N-particle thermal density matrix to obtain exact-on-average energies for model and ab initio systems. We report a systematic numerical study of the sign problem in DMQMC based on simulations of atomic and molecular systems. In DMQMC, the density matrix is written in an outer product basis of Slater determinants. In principle, this means that DMQMC needs to sample a space that scales in the system size, N, as O[(exp(N))2]. In practice, removing the sign problem requires a total walker population that exceeds a system-dependent critical walker population (Nc), imposing limitations on both storage and compute time. We establish that Nc for DMQMC is the square of Nc for FCIQMC. By contrast, the minimum Nc in the interaction picture modification of DMQMC (IP-DMQMC) is only linearly related to the Nc for FCIQMC. We find that this difference originates from the difference in propagation of IP-DMQMC versus canonical DMQMC: the former is asymmetric, whereas the latter is symmetric. When an asymmetric mode of propagation is used in DMQMC, there is a much greater stochastic error and is thus prohibitively expensive for DMQMC without the interaction picture adaptation. Finally, we find that the equivalence between IP-DMQMC and FCIQMC seems to extend to the initiator approximation, which is often required to study larger systems with large basis sets. This suggests that IP-DMQMC offers a way to ameliorate the cost of moving between a Slater determinant space and an outer product basis.
| S-EPMC8515812 | biostudies-literature
Project description:Traditional multiple-group confirmatory factor analysis (multiple-group CFA) is usually criticized for having too restrictive model assumption, namely the scalar measurement invariance. The new multiple-group analysis methodology, alignment, has become an effective alternative. The alignment evaluates measurement invariance and more importantly, permits factor mean comparisons without requiring scalar invariance which is usually required in traditional multiple-group CFA. Some simulation studies and empirical studies have investigated the applicability of alignment under different conditions, but some areas remain unexplored. Based on the simulation studies of Asparouhov and Muthén and of Flake and McCoach, this current simulation study is broken into two sections. The first study investigates the minimal group sizes required for alignment in three-factor models. The second study compares the performance of multiple-group CFA, multiple-group exploratory structural equation model (multiple-group ESEM), and alignment by including different proportions and magnitudes of cross-loadings in the models. Study 1 shows that when the model has no noninvariant parameters, the alignment requires relatively lower group sizes. Explicitly, the minimal group size required for alignment was 250 when the amount of groups was three, the minimal group size was 150 when the amount of groups was nine, and 200 when the amount of groups was 15. When there are noninvariant parameters in the model and the amount of groups is low, a group size of 350 is a safe rule of thumb. When there are noninvariant parameters in the model and the amount of groups is high, a group size of 250 is required for trustworthy results. The magnitude of noninvariance and the noninvariance rate do not affect the minimal group size required for alignment. Study 2 shows that multiple-group CFA provides accurate factor mean estimates when each factor had 20% factor loading (1 factor loading) with small-sized cross-loading. Multiple-group ESEM provides accurate factor mean estimates when the magnitude of cross-loading is small or when each factor had 20% factor loading (1 factor loading) with medium-sized cross-loading. Alignment provides accurate factor mean estimates when there are only small-sized cross-loadings in the model. The parameter estimates, coverage rates and ratios of average standard error to standard deviation for each methodology are not influenced by the amount of groups. Recommendations are concluded for using multiple-group CFA, multiple-group ESEM, traditional alignment and aligned ESEM (AESEM) based on the results. Multiple-group CFA is more suitable for use when scalar invariance is established. Multiple-group ESEM works best when there are small-sized or only a few medium-sized cross-loadings in the model. Traditional alignment allows for small-sized cross-loadings and a few noninvariant parameters in the model. AESEM integrates the advantages of alignment and ESEM, can provide accurate estimates when noninvariant parameters and cross-loadings both exist in the model. Compared to multiple-group CFA, multiple-group ESEM, the alignment methodology performs well in more situations.
| S-EPMC9263979 | biostudies-literature
Project description:Quantitative bias analysis can be used to empirically assess how far study estimates are from the truth (i.e., an estimate that is free of bias). These methods can be used to explore the potential impact of confounding bias, selection bias (collider stratification bias), and information bias. Quantitative bias analysis includes methods that can be used to check the robustness of study findings to multiple types of bias and methods that use simulation studies to generate data and understand the hypothetical impact of specific types of bias in a simulated data set. In this article, we review 2 strategies for quantitative bias analysis: 1) traditional probabilistic quantitative bias analysis and 2) quantitative bias analysis with generated data. An important difference between the 2 strategies relates to the type of data (real vs. generated data) used in the analysis. Monte Carlo simulations are used in both approaches, but the simulation process is used for different purposes in each. For both approaches, we outline and describe the steps required to carry out the quantitative bias analysis and also present a bias-analysis tutorial demonstrating how both approaches can be applied in the context of an analysis for selection bias. Our goal is to highlight the utility of quantitative bias analysis for practicing epidemiologists and increase the use of these methods in the epidemiologic literature.
| S-EPMC9005059 | biostudies-literature
Project description:A computational method is developed to carry out explicit solvent simulations of complex molecular systems under conditions of constant pH. In constant-pH simulations, preidentified ionizable sites are allowed to spontaneously protonate and deprotonate as a function of time in response to the environment and the imposed pH. The method, based on a hybrid scheme originally proposed by H. A. Stern (J. Chem. Phys. 2007, 126, 164112), consists of carrying out short nonequilibrium molecular dynamics (neMD) switching trajectories to generate physically plausible configurations with changed protonation states that are subsequently accepted or rejected according to a Metropolis Monte Carlo (MC) criterion. To ensure microscopic detailed balance arising from such nonequilibrium switches, the atomic momenta are altered according to the symmetric two-ends momentum reversal prescription. To achieve higher efficiency, the original neMD-MC scheme is separated into two steps, reducing the need for generating a large number of unproductive and costly nonequilibrium trajectories. In the first step, the protonation state of a site is randomly attributed via a Metropolis MC process on the basis of an intrinsic pKa; an attempted nonequilibrium switch is generated only if this change in protonation state is accepted. This hybrid two-step inherent pKa neMD-MC simulation method is tested with single amino acids in solution (Asp, Glu, and His) and then applied to turkey ovomucoid third domain and hen egg-white lysozyme. Because of the simple linear increase in the computational cost relative to the number of titratable sites, the present method is naturally able to treat extremely large systems.
| S-EPMC4535364 | biostudies-literature
Project description:Dermal contact, ingestion and inhalation of heavy metal poses significant health risk in human subjects. The exposure could be via potable water, soil or air. The current experiment design focuses on soil media and exposure. Advanced probabilistic and geospatial methods are used in this study which evaluates contamination levels and health risks associated with iron (Fe), arsenic (As), zinc (Zn), copper (Cu), nickel (Ni), chromium (Cr), lead (Pb), and cadmium (Cd) in soil samples. The samples were collected and analysed using ICP-OES after tri-acid digestion, and indices such as Geoaccumulation Index (Igeo), Contamination Factor (CF), Pollution Load Index (PLI), Hazard Quotient (HQ), Hazard Index (HI), and Carcinogenic Risk (CR) were used to assess environmental impacts and health risks across the age groups via oral ingestion, inhalation and dermal contact. The current study indicates heavy metal concentrations follow the order Ni > Zn > Pb > Cu > Cr > As > Cd, with more than 60% of samples demonstrating significant pollution levels. The computational method used in the study revealed substantial non carcinogenic risk (HQ > 1) and carcinogenic risk (33%) in the population related to As exposure. Geospatial analysis and Monte Carlo simulations helped in identifying the hotspots in the tropical coastal area emphasizing need for targeted remediation focusing on As and Pb.
| S-EPMC11621557 | biostudies-literature