arXiv subjects

Emmanuelle Comets

Publications and source records attributed to Emmanuelle Comets.

7 recordsLinked to original sources

arXiv2026

Evaluation of the npde performance for the evaluation of joint model with longitudinal and TTE data: an application in metastatic hormono-resistant prostate cancer

Introduction: Joint models are increasingly used in clinical trials. An important part of model building is to properly assess the descriptive and predictive ability of these models. Normalised prediction discrepancies (npd) and normalised prediction distribution errors (npde) have been developed to evaluate graphically and statistically non-linear mixed effect models for continuous responses. In this work, we propose to use a combined test to evaluate joint models. Methods: Prediction discrepancies (pd) are defined as the quantile of the observation within its predictive distribution and obtained by Monte-Carlo simulations. The pd for unobserved (censored) event times are imputed in a uniform distribution based on the model prediction of the probability of censoring, using a similar method as the one developed to handle data under the lower quantification limit (LOQ). We propose to combine the p-values of the tests on longitudinal data and on time-to-event (TTE) data, adjusted with a Bonferroni correction. We performed simulation studies based on a joint model characterising the relationship between prostate specific antigen biomarker (PSA) and survival in prostate cancer patients to evaluate the type I error and power of npd/npde to detect different types of model misspecifications. Results: For all types of misspecifications, the type I error of the combined test was found to be close to the expected 5%. The power of the combined test to detect model misspecifications increased with the difference from the true model and as expected, with sample size. Graphically the power increase can be related to larger differences in the shape of the survival function or PSA evolution. Conclusions: npd can be readily extended for event data by imputing the pd for censored event under the model. The test showed an adequate type I error, and was quite sensitive to alternative models tested.

stat.ME↗

arXiv2026

Development and performance of npd for the evaluation of models with ordinal data

Introduction: Normalised prediction distribution errors (npde) are used to graphically and statistically evaluate continuous responses in non-linear mixed effect models. Here, our aim was to extend npde for categorical data and to evaluate their performance. We applied our approach to a real case-study describing the evolution of severe onychomycosis (toenail infection) in a trial comparing two treatment groups. Methods: Let V denote a dataset with categorical observations. The null hypothesis H0 is that observations in V can be described by a model M. Residuals called npde can be adapted to categorical observations using jittering techniques. Their theoretical standard normal distribution can be evaluated through the Kolmogorov-Smirnov test. We evaluated the performance in terms of power through a simulation and compared it to a Chi-square. We illustrated the test and graphs on a real case-study. Results: npd were able to detect misspecifications in the structural model and model parameter value. As expected, the power to detect model misspecifications increased both with the difference in the shape of the probability, and with the sample size. Chi-square test performed better but npd could be readily applied in all type of design. Based on the toe-nail data, graphs reveal a huge discrepancy of the base model, and a good adequation for the best model we found. Conclusions: npde can be extended to categorical data, particularly in clinical settings with unbalanced design and graphs can be useful to evaluate the model as well as the covariate effects.

stat.ME↗

arXiv2026

Conditional bootstrap for non-linear mixed effects models

Background and Objective: Uncertainty in non-linear mixed effect models is often assessed using the Fisher information matrix to derive the standard errors of estimation. The bootstrap is an alternative to the asymptotic method, with different approaches to handle the different levels of individual and population variabilities. The simplest method is the Case bootstrap where the entire vector of individuals is resampled, but this approach does not take into account the hierarchical nature of non-linear mixed effect models (NLMEM). Methods: We propose here a non-parametric bootstrap, cNP, to preserve the structure of the original data. We resample interindividual random effects from the conditional distribution of the individual parameters, obtained as a by-product of the SAEM algorithm, and residuals from their distribution. cNP was implemented in the saemix package for R along with the case, parametric (Par), and non-parametric (NP) residual bootstraps. Coverage rates were compared in a simulation study using sigmoid Emax models, with rich, sparse and unbalanced designs, and 3 levels of residual variability. Results: The asymptotic method tended to produce lower than theoretical coverages for the variance terms. Bootstraps provided more adequate coverage, but none of the approaches maintained coverage when the residual error increased. Overall, the new cNP and the Case provided better coverage than the classical NP. Conclusion: The new conditional non-parametric bootstrap can be used when it is important to preserve the structure of the original dataset, such as the number of observations or the repartition of covariates as it does not require stratification.

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arXiv2026

Extending the saemix package for R to fit non Gaussian outcomes

Background and Objectives: Longitudinal data are increasingly collected in clinical trials to provide information on treatment action and disease evolution. The trajectory of continuous biomarkers such as target hormone concentrations or viral loads can then be modelled in relationship to the occurrence of events such as recovery or hospitalisation. Other studies may include repeated measurements of discrete pain scores, number of episodes (count) or occurrence of events (survival). Non-linear mixed-effect models (NLMEM) can handle individual differences in trajectories while modelling the underlying population evolution and are the natural choice for their analysis. The saemix package for R is one of the few open-source solutions and the most flexible. In this paper, we extend it to accommodate a variety of models for non-Gaussian data. Methods: The saemix package estimates parameters through the Stochastic Approximation Expectation-Maximisation (SAEM) algorithm. Within the package, non-Gaussian models are specified by their log-likelihood functions, affording maximal control over model formulation. We extend estimation algorithms as well as exploratory and diagnostic plots for non-Gaussian data. Bootstrap approaches were implemented to estimate parameter uncertainty. To evaluate the performance of saemix, we performed a simulation study based on the toenail dataset, containing repeated binary data from a randomised clinical trial. Results: saemix showed good performance to recover the true parameter values in the simulation study, and was stable across different starting values for the parameters. An algorithm jointly searching for covariate and interindividual variability model was also implemented to build the covariate model and applied to categorical and survival-type data.

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arXiv2025

In silico clinical trials in drug development: a systematic review

In the context of clinical research, computational models have received increasing attention over the past decades. In this systematic review, we aimed to provide an overview of the role of so-called in silico clinical trials (ISCTs) in medical applications. Exemplary for the broad field of clinical medicine, we focused on in silico (IS) methods applied in drug development, sometimes also referred to as model informed drug development (MIDD). We searched PubMed and ClinicalTrials.gov for published articles and registered clinical trials related to ISCTs. We identified 202 articles and 48 trials, and of these, 76 articles and 19 trials were directly linked to drug development. We extracted information from all 202 articles and 48 clinical trials and conducted a more detailed review of the methods used in the 76 articles that are connected to drug development. Regarding application, most articles and trials focused on cancer and imaging-related research while rare and pediatric diseases were only addressed in 14 articles and 5 trials, respectively. While some models were informed combining mechanistic knowledge with clinical or preclinical (in-vivo or in-vitro) data, the majority of models were fully data-driven, illustrating that clinical data is a crucial part in the process of generating synthetic data in ISCTs. Regarding reproducibility, a more detailed analysis revealed that only 24% (18 out of 76) of the articles provided an open-source implementation of the applied models, and in only 20% of the articles the generated synthetic data were publicly available. Despite the widely raised interest, we also found that it is still uncommon for ISCTs to be part of a registered clinical trial and their application is restricted to specific diseases leaving potential benefits of ISCTs not fully exploited.

q-bio.QM↗

arXiv2024

Straightforward Phase I Dose-Finding Design for Healthy Volunteers Accounting for Surrogate Activity Biomarkers

Conventionally, a first-in-human phase I trial in healthy volunteers aims to confirm the safety of a drug in humans. In such situations, volunteers should not suffer from any safety issues and simple algorithm-based dose-escalation schemes are often used. However, to avoid too many clinical trials in the future, it might be appealing to design these trials to accumulate information on the link between dose and efficacy/activity under strict safety constraints. Furthermore, an increasing number of molecules for which the increasing dose-activity curve reaches a plateau are emerging.In a phase I dose-finding trial context, our objective is to determine, under safety constraints, among a set of doses, the lowest dose whose probability of activity is closest to a given target. For this purpose, we propose a two-stage dose-finding design. The first stage is a typical algorithm dose escalation phase that can both check the safety of the doses and accumulate activity information. The second stage is a model-based dose-finding phase that involves selecting the best dose-activity model according to the plateau location.Our simulation study shows that our proposed method performs better than the common Bayesian logistic regression model in selecting the optimal dose.

stat.AP↗

arXiv2022

Bayesian Framework for Multi-Source Data Integration -- Application to Human Extrapolation From Preclinical Studies

In preclinical investigations, e.g. in in vitro, in vivo and in silico studies, the pharmacokinetic, pharmacodynamic and toxicological characteristics of a drug are evaluated before advancing to first-in-man trial. Usually, each study is analyzed independently and the human dose range does not leverage the knowledge gained from all studies. Taking into account the preclinical data through inferential procedures can be particularly interesting to obtain a more precise and reliable starting dose and dose range. We propose a Bayesian framework for multi-source data integration from preclinical studies results extrapolated to human, which allow to predict the quantities of interest (e.g. the minimum effective dose, the maximum tolerated dose, etc.) in humans. We build an approach, divided in four main steps, based on a sequential parameter estimation for each study, extrapolation to human, commensurability checking between posterior distributions and final information merging to increase the precision of estimation. The new framework is evaluated via an extensive simulation study, based on a real-life example in oncology inspired from the preclinical development of galunisertib. Our approach allows to better use all the information compared to a standard framework, reducing uncertainty in the predictions and potentially leading to a more efficient dose selection.

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