Abstract As decisions in drug development increasingly rely on predictions from mechanistic systems models, assessing the predictive capability of such models is becoming more important. Several frameworks for the development of quantitative systems pharmacology (QSP) models have been proposed. In this paper, we add to this body of work with a framework that focuses on the appropriate use of qualitative and quantitative model evaluation methods. We provide details and references for those wishing to apply these methods, which include sensitivity and identifiability analyses, as well as concepts such as validation and uncertainty quantification. Many of these methods have been used successfully in other fields, but are not as common in QSP modeling. We illustrate how to apply these methods to evaluate QSP models, and propose methods to use in two case studies. We also share examples of misleading results when inappropriate analyses are used.
A model qualification method for mechanistic physiological QSP models to support model‐informed drug development
Mechanistic physiological modeling is a scientific method that combines available data with scientific knowledge and engineering approaches to facilitate better understanding of biological systems, improve decision‐making, reduce risk, and increase efficiency in drug discovery and development. It is a type of quantitative systems pharmacology (QSP) approach that places drug‐specific properties in the context of disease biology. This tutorial provides a broadly applicable model qualification method (MQM) to ensure that mechanistic physiological models are fit for their intended purposes.
A Nonparametric Approach to Practical Identifiability of Nonlinear Mixed Effects Models
Mathematical modelling is a widely used approach to understand and interpret clinical trial data. This modelling typically involves fitting mechanistic mathematical models to data from individual trial participants. Despite the widespread adoption of this individual-based fitting, it is becoming increasingly common to take a hierarchical approach to parameter estimation, where modellers characterize the population parameter distributions, rather than considering each individual independently. This hierarchical parameter estimation is standard in pharmacometric modelling. However, many of the existing techniques for parameter identifiability do not immediately translate from the individual-based fitting to the hierarchical setting. In this work, we propose a nonparametric approach to study practical identifiability within a hierarchical parameter estimation framework. We focus on the commonly used nonlinear mixed effects framework and investigate two well-studied examples from the pharmacometrics and viral dynamics literature to illustrate the potential utility of our approach.
Pharmacometrics and systems pharmacology for metabolic bone diseases
Mathematical modelling and simulation (M&S) of drug concentrations, pharmacologic effects and the (patho)physiologic systems within which they interact can be powerful tools for the preclinical, translational and clinical development of drugs. Indeed, the Prescription Drug User Fee Act (PDUFA VI), incorporated as part of the FDA Reauthorization Act of 2017 (FDARA), highlights the goal of advancing model‐informed drug development (MIDD). MIDD can benefit development across many drug classes, including for metabolic bone diseases such as osteoporosis, cancer‐related and numerous rare metabolic bone diseases; conditions characterized by significant morbidity and mortality. A drought looms in terms of the availability of new drugs to better treat these devastating diseases. This review provides an overview of several M&S approaches ranging from simple pharmacokinetic to integrated pharmacometric and systems pharmacology modelling. Examples are included to illustrate the use of these approaches during the development of several drugs for metabolic bone diseases such as bisphosphonates, denosumab, teriparatide and sclerostin inhibitors (romosozumab and blosozumab).
Automated Scale Reduction of Nonlinear <span style="font-variant:small-caps;">QSP</span> Models With an Illustrative Application to a Bone Biology System
Integrating quantitative systems pharmacology ( QSP ) into pharmacokinetics/pharmacodynamics ( PKPD ) has resulted in models that are highly complex and often not amenable to further exploration via estimation or design. Because QSP models are usually depicted using nonlinear differential equations it is not straightforward to apply some model reduction techniques, such as proper lumping. In this study, we explore the combined use of linearization and proper lumping as a general method to simplification of a nonlinear QSP model. We illustrate this with a bone biology model and the reduced model was then applied to describe bone mineral density ( BMD ) changes due to denosumab dosing. The methodologies used in this study can be applied to other multiscale models for developing a mechanism‐based structural model for future analyses.
AI for Drug Discovery Needs Trustworthy Biological Data
To unleash the potential of AI in life sciences and drug discovery, biological datasets must be authenticated, validated, and supported by standardized metadata.
Selecting synthetic data for successful simulation-based transfer learning in dynamical biological systems
Accurate prediction of the temporal dynamics of biological systems is crucial for informing timely and effective interventions, e.g., in ecological or epidemiological contexts, or for treatment adjustments in therapy. While machine learning has proven its capabilities in generalizing the underlying non-linear dynamics of such systems, unlocking its predictive power is often restrained by the limited availability of large, curated datasets. To supplement real-world data, informing machine learning by transfer learning with synthetic data derived from simulations using ordinary differential equations has emerged as a promising solution. However, the success of this approach highly depends on the designed characteristics of the synthetic data.
Implementing an online pharmaceutical service using design science research
The rising prevalence of chronic diseases is pressing health systems to introduce reforms. Primary healthcare and multidisciplinary models have been suggested as approaches to deal with this challenge, with new roles for nurses and pharmacists being advocated. More recently, implementing healthcare based on information systems and technologies (e.g. eHealth) has been proposed as a way to improve health services. However, implementing online pharmaceutical services, including their adoption by pharmacists and patients, is still an open research question. In this paper we present ePharmacare, a new online pharmaceutical service implemented using Design Science Research.
Dynamics of Bone Cell Interactions and Differential Responses to PTH and Antibody-Based Therapies
We propose a mathematical model describing the dynamics of osteoblasts and osteoclasts in bone remodeling. The goal of this work is to develop an integrated modeling framework for bone remodeling and bone cell signaling dynamics that could be used to explore qualitatively combination treatments for osteoporosis in humans. The model has been calibrated using 57 checks from the literature. Specific global optimization methods based on qualitative objectives have been developed to perform the model calibration. We also added pharmacokinetics representations of three drugs to the model, which are teriparatide (PTH(1–34)), denosumab (a RANKL antibody) and romosozumab (a sclerostin antibody), achieving excellent goodness-of-fit of human clinical data. The model reproduces the paradoxical effects of PTH on the bone mass, where continuous administration of PTH results in bone loss but intermittent administration of PTH leads to bone gain, thus proposing an explanation of this phenomenon. We used the model to simulate different categories of osteoporosis. The main attributes of each disease are qualitatively well captured by the model, for example changes in bone turnover in the disease states. We explored dosing regimens for each disease based on the combination of denosumab and romosozumab, identifying adequate ratios and doses of both drugs for subpopulations of patients in function of categories of osteoporosis and the degree of severity of the disease.
Modeling osteoporosis to design and optimize pharmacological therapies comprising multiple drug types
For the treatment of postmenopausal osteoporosis, several drug classes with different mechanisms of action are available. Since only a limited set of dosing regimens and drug combinations can be tested in clinical trials, it is currently unclear whether common medication strategies achieve optimal bone mineral density gains or are outperformed by alternative dosing schemes and combination therapies that have not been explored so far. Here, we develop a mathematical framework of drug interventions for postmenopausal osteoporosis that unifies fundamental mechanisms of bone remodeling and the mechanisms of action of four drug classes: bisphosphonates, parathyroid hormone analogs, sclerostin inhibitors, and receptor activator of NF-κB ligand inhibitors. Using data from several clinical trials, we calibrate and validate the model, demonstrating its predictive capacity for complex medication scenarios, including sequential and parallel drug combinations. Via simulations, we reveal that there is a large potential to improve gains in bone mineral density by exploiting synergistic interactions between different drug classes, without increasing the total amount of drug administered.
Preparing Physicians for the Clinical Algorithm Era
The U.S. government recently took steps to ensure that clinical decision support algorithms are safe for clinical use. The next and larger step will be teaching physicians how to use the algorithms ...
Preparing Physicians for the Clinical Algorithm Era
The U.S. government recently took steps to ensure that clinical decision support algorithms are safe for clinical use. The next and larger step will be teaching physicians how to use the algorithms ...
Toward a Mathematical Modeling of Diseases’ Impact on Bone Remodeling: Technical Review
A wide variety of bone diseases have hitherto been discovered, such as osteoporosis, Patget’s disease, osteopetrosis, and metastatic bone disease, which is not well defined. Some of these diseases are secondary to other pathologies, including cancer, or to some clinical treatments. To better understand bone behavior and prevent its deterioration, bone biomechanics have been the subject of mathematical modeling that exponentially increased over the last years. These models are more and more involving the impact of bone diseases on its quality. The current paper provides a meaningful and critical analysis of previously developed bone remodeling mathematical models, particularly those addressing bone diseases. Besides, mechanistic pharmacokinetic/pharmacodynamic (PK/PD) models, which englobe either bone disease and its treatments’ effect on bone health. Therefore, the review starts by presenting bone remodeling cycle and mathematical models describing this process, followed by introducing some bone diseases and discussing models of pathological mechanisms affecting bone, and ends by exhibiting the available bone treatment procedures and the PK/PD models considering these lasts.
Coping with time scales in disease systems analysis: application to bone remodeling
In this study we demonstrate the added value of mathematical model reduction for characterizing complex dynamic systems using bone remodeling as an example. We show that for the given parameter values, the mechanistic RANK-RANKL-OPG pathway model proposed by Lemaire et al. (J Theor Biol 229:293–309, 2004) can be reduced to a simpler model, which can describe the dynamics of the full Lemaire model to very good approximation. The response of both models to changes in the underlying physiology and therapeutic interventions was evaluated in four physiologically meaningful scenarios: (i) estrogen deficiency/estrogen replacement therapy, (ii) Vitamin D deficiency, (iii) ageing, and (iv) chronic glucocorticoid treatment and its cessation. It was found that on the time scale of disease progression and therapeutic intervention, the models showed negligible differences in their dynamic properties and were both suitable for characterizing the impact of estrogen deficiency and estrogen replacement therapy, Vitamin D deficiency, ageing, and chronic glucocorticoid treatment and its cessation on bone forming (osteoblasts) and bone resorbing (osteoclasts) cells. It was also demonstrated how the simpler model could help in elucidating qualitative properties of the observed dynamics, such as the absence of overshoot and rebound, and the different dynamics of onset and washout.
Clinical Data for Parametrization of In Silico Bone Models Incorporating Cell-Cytokine Dynamics: A Systematic Review of Literature
In silico simulations aim to provide fast, inexpensive, and ethical alternatives to years of costly experimentation on animals and humans for studying bone remodeling, its deregulation during osteoporosis and the effect of therapeutics. Within the varied spectrum of in silico modeling techniques, bone cell population dynamics and agent-based multiphysics simulations have recently emerged as useful tools to simulate the effect of specific signaling pathways. In these models, parameters for cell and cytokine behavior are set based on experimental values found in literature; however, their use is currently limited by the lack of clinical in vivo data on cell numbers and their behavior as well as cytokine concentrations, diffusion, decay and reaction rates. Further, the settings used for these parameters vary across research groups, prohibiting effective cross-comparisons. This review summarizes and evaluates the clinical trial literature that can serve as input or validation for in silico models of bone remodeling incorporating cells and cytokine dynamics in post-menopausal women in treatment, and control scenarios. The GRADE system was used to determine the level of confidence in the reported data, and areas lacking in reported measures such as binding site occupancy, reaction rates and cell proliferation, differentiation and apoptosis rates were highlighted as targets for further research. We propose a consensus for the range of values that can be used for the cell and cytokine settings related to the RANKL-RANK-OPG, TGF-β and sclerostin pathways and a Levels of Evidence-based method to estimate parameters missing from clinical trial literature.
Can Revealed Preferences Clarify LLM Alignment and Steering?
LLMs are increasingly used to make or support high-stakes decisions under uncertainty, where alignment depends not only on factual accuracy but on how models weigh tradeoffs between different outcomes. We present an empirical pipeline for estimating the implied preferences that an LLM's observed choices optimize: we elicit the model's probability distribution over unknowns along with the choice it would make for the decision task and then fit a discrete choice model to recover the cost function that best rationalizes the model's decisions. We show how this revealed-preference description allows rigorous evaluation of whether models behave in a consistently goal-directed way, whether they can verbalize a description of their objectives which matches their revealed decision policy, and whether prompting can reliably steer those policies to implement a user-specified cost function. We apply this evaluation across four medical diagnosis domains and multiple frontier and open-source models. We find that while many models have a nontrivial degree of internal coherence, they also have significant weaknesses in faithfully reporting or adopting preferences in response to user direction.
Studying Bone Remodelling and Tumour Growth for Therapy Predictive Control
Bone remodelling consists of cycles of bone resorption and formation executed mainly by osteoclasts and osteoblasts. Healthy bone remodelling is disrupted by diseases such as Multiple Myeloma and bone metastatic diseases. In this paper, a simple mathematical model with differential equations, which takes into account the evolution of osteoclasts, osteoblasts, bone mass and bone metastasis growth, is improved with a pharmacokinetic and pharmacodynamic (PK/PD) scheme of the drugs denosumab, bisphosphonates, proteasome inhibitors and paclitaxel. The major novelty is the inclusion of drug resistance phenomena, which resulted in two variations of the model, corresponding to different paradigms of the origin and development of the tumourous cell resistance condition. These models are then used as basis for an optimization of the drug dose applied, paving the way for personalized medicine. A Nonlinear Model Predictive Control scheme is used, which takes advantage of the convenient properties of a suggested adaptive and democratic variant of Particle Swarm Optimization. Drug prescriptions obtained in this way provide useful insights into dose administration strategies. They also show how results may change depending on which of the two very different paradigms of drug resistance is used to model the behaviour of the tumour.
