Article
Computer Science, Interdisciplinary Applications
Ran Liu, Lixing Zhu
Summary: Checking the models of the ongoing COVID-19 pandemic is important. The study proposes a new test to examine partially observed ODE models and presents the asymptotic properties of the test. Simulation studies show that the SEIR model may not be appropriate for certain periods in Japan and Algeria.
COMPUTATIONAL STATISTICS & DATA ANALYSIS
(2023)
Article
Mathematics, Applied
A. Y. J. Almasoodi, A. Abdi, G. Hojjati
Summary: This paper introduces a more stable and efficient algorithm for solving Volterra integral equations, with methods of different orders having A(0)-stable properties. Numerical experiments demonstrate that these methods perform well in handling stiff and nonstiff problems.
APPLIED NUMERICAL MATHEMATICS
(2021)
Article
Mathematics, Applied
G. A. Grigorian
Summary: The Riccati equation method is employed to establish oscillation and non-oscillation criteria for nonhomogeneous linear systems of two first-order ordinary differential equations, where the obtained oscillation criterion is shown to be a generalization of J.S.W. Wong's oscillation criterion.
JOURNAL OF MATHEMATICAL ANALYSIS AND APPLICATIONS
(2022)
Article
Thermodynamics
Anthony S. Walker, Raymond L. Speth, Kyle E. Niemeyer
Summary: This study introduces an adaptive preconditioning method to reduce the cost of integrating large chemical kinetic models, resulting in significant speedup in performance and improved efficiency.
PROCEEDINGS OF THE COMBUSTION INSTITUTE
(2023)
Article
Mathematics, Applied
Xing Qiu, Tao Xu, Babak Soltanalizadeh, Hulin Wu
Summary: This study provides practical tools for identifiability analysis of ODE systems through deriving closed-form representations and quantitative scoring methods. Simulation results demonstrate that the proposed methods outperform existing approaches in handling data uncertainties and noise. Additionally, the paper explores the identifiability properties of high-dimensional ODE systems and concludes that many random ODE systems are practically unidentifiable without additional prior information.
APPLIED MATHEMATICS AND COMPUTATION
(2022)
Article
Computer Science, Artificial Intelligence
Zhang Yi
Summary: This paper proposes a theory of memory-based neuralODE, which consists of two novel artificial neural network models and two learning algorithms. The nmODE is designed with a special structure that separates learning neurons from memory neurons, possesses the global attractor property, and is embedded with a memory mechanism. The nmLA is developed by proposing an interesting three-dimensional inverse ODE and has advantages in memory and parameter efficiency. The proposed theory is comparable to state-of-the-art methods according to experimental results.
ARTIFICIAL INTELLIGENCE REVIEW
(2023)
Article
Automation & Control Systems
Ratika Rastogi, O. P. Misra, Rajshree Mishra
Summary: This paper proposes a numerical method that uses Chebyshev polynomials and metaheuristic optimization algorithms to find approximate solutions of differential equations. The effectiveness of the method is demonstrated through graphical comparison and the performance is shown to be better than existing methods based on the Root Mean Square Error (RMSE).
ENGINEERING APPLICATIONS OF ARTIFICIAL INTELLIGENCE
(2023)
Article
Mathematics, Applied
A. Jalilian, A. Abdi, G. Hojjati
Summary: This paper introduces variable stepsize SGLMs directly on nonuniform grid, deriving order conditions and providing explicit examples up to order four. Numerical experiments demonstrate the efficiency of the proposed methods in solving nonstiff problems and confirming the theoretical order of convergence. (C) 2021 IMACS. Published by Elsevier B.V. All rights reserved.
APPLIED NUMERICAL MATHEMATICS
(2021)
Article
Multidisciplinary Sciences
Xing Chen, Flavio Abreu Araujo, Mathieu Riou, Jacob Torrejon, Dafine Ravelosona, Wang Kang, Weisheng Zhao, Julie Grollier, Damien Querlioz
Summary: This article introduces a dynamical neural network trained on a minimal amount of data that can predict the behavior of spintronic devices with high accuracy and efficiency. Two experiments are presented to demonstrate the feasibility of the approach.
NATURE COMMUNICATIONS
(2022)
Article
Computer Science, Interdisciplinary Applications
Shinhoo Kang, Emil M. Constantinescu
Summary: This paper proposes a new approach to learning subgrid-scale models using neural ordinary differential equations (NODEs), aiming to improve the accuracy and efficiency of solving partial differential equations. By utilizing NODEs and partial knowledge, the method can learn source dynamics continuously and approximate coupling operators, thus enhancing the efficiency of low-order solvers.
COMPUTERS & FLUIDS
(2023)
Article
Mathematics, Applied
Yongtao Zhou, Martin Stynes
Summary: A class of block boundary value methods is proposed for linear neutral Volterra integro-differential equations with weakly singular kernels, showing optimal convergence rates on special graded meshes. The methods can also be extended to solve 2nd kind linear Volterra integral equations with weakly singular kernels, as confirmed by numerical experiments and comparison with piecewise polynomial collocation methods.
JOURNAL OF COMPUTATIONAL AND APPLIED MATHEMATICS
(2022)
Article
Multidisciplinary Sciences
Ben Lambert, Chon Lok Lei, Martin Robinson, Michael Clerx, Richard Creswell, Sanmitra Ghosh, Simon Tavener, David J. Gavaghan
Summary: Ordinary differential equation models are commonly used in biology to describe dynamic processes. However, when performing likelihood-based parameter inference on these models, the contribution of factors not explicitly included in the mathematical model needs to be represented. Independent Gaussian noise is often chosen as a statistical process, assuming random latent factors. This study demonstrates that highly persistent differences between observations and model quantities can occur, and using the wrong noise assumption can lead to artificial reduction of uncertainty in parameter estimation. They propose a workflow to diagnose and remodel for correlated errors.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2023)
Article
Mathematics, Interdisciplinary Applications
Mufutau Ajani Rufai, Bruno Carpentieri, Higinio Ramos
Summary: This paper presents a new hybrid block method for solving initial value problems of ODEs and time-dependent partial differential equations in applied sciences and engineering. The proposed method uses an adaptive stepsize strategy to control the estimated error, and numerical simulations show that it is more efficient than other existing numerical methods.
FRACTAL AND FRACTIONAL
(2023)
Article
Computer Science, Interdisciplinary Applications
Junwei Luo, Fahim Abdullah, Panagiotis D. Christofides
Summary: Neural Ordinary Differential Equation (NODE) is a deep learning model that approximates linear/nonlinear dynamic systems using time-series data by integrating neural networks with ordinary differential equation solvers. RNN has been popular for modeling nonlinear dynamic processes, but it requires strictly uniform step sequence data, making it less robust to irregular sampling scenarios. This paper develops a NODE model and constructs an MPC based on it, addressing stability and robustness to noise. An example of a chemical process is used to evaluate the performance of NODE-based MPC and the effectiveness of the subsampling method for handling non-Gaussian noise.
COMPUTERS & CHEMICAL ENGINEERING
(2023)
Article
Mathematics
Svetozar Margenov, Nedyu Popivanov, Iva Ugrinova, Tsvetan Hristov
Summary: Bulgaria has the lowest COVID-19 vaccination rate in the EU and the second-highest COVID-19 mortality rate globally. This study aims to understand the reasons behind this situation and analyze the disease's development over time. The extended time-dependent SEIRS-VB model is used, which incorporates vaccination and vital dynamics. The study includes developing numerical simulation tools, solving inverse problems for parameter identification, and proposing a methodology for selecting the closest discrete model to the differential SEIRS-VB model. Bulgarian COVID-19 data are used for validation, and mathematical analysis is conducted to illustrate biological properties and perform sensitivity analysis.
Article
Mathematical & Computational Biology
Kathrin Moellenhoff, Florence Loingeville, Julie Bertrand, Thu Thuy Nguyen, Satish Sharan, Liang Zhao, Lanyan Fang, Guoying Sun, Stella Grosser, France Mentre, Holger Dette
Summary: The classical approach for analyzing pharmacokinetic (PK) data in bioequivalence studies is noncompartmental analysis (NCA) followed by two one-sided tests (TOST). However, a model-based alternative has been proposed for sparse designs. In this study, a more powerful test is proposed and demonstrated to be superior to TOST through simulation studies for both NCA and model-based approaches. This method shows potential use in situations where conventional bioequivalence analysis is not applicable, especially for products with high PK parameter variability.
Editorial Material
Infectious Diseases
Alpha Diallo, Marius Troseid, Victoria Charlotte Simensen, Anais Boston, Jacques Demotes, Inge Christoffer Olsen, Florence Chung, Jose Artur Paiva, Maya Hites, Florence Ader, Jose Ramon Arribas, Andreas Baratt-Due, Oyvind Melien, Evelina Tacconelli, Therese Staub, Richard Greil, Sotirios Tsiodras, Matthias Briel, Helene Esperou, France Mentre, Joe Eustace, Juliette Saillard, Christelle Delmas, Soizic LeMestre, Marina Dumousseaux, Dominique Costagliola, John-Arne Rottingen, Yazdan Yazdanpanah
CLINICAL MICROBIOLOGY AND INFECTION
(2022)
Article
Infectious Diseases
Maria J. G. T. Vehreschild, Annie Ducher, Thomas Louie, Oliver A. Cornely, Celine Feger, Aaron Dane, Marina Varastet, Fabien Vitry, Jean de Gunzburg, Antoine Andremont, France Mentre, Mark H. Wilcox
Summary: DAV132 showed good tolerability and did not affect FQ plasma concentrations in hospitalized patients receiving FQ treatment. DAV132 preserved intestinal microbiota diversity and resistance to C. difficile colonization.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2022)
Article
Infectious Diseases
Philippine Eloy, Cedric Laouenan, Abdoul Habib Beavogui, Sakoba Keita, Pauline Manchon, Jean-Francois Etard, Daouda Sissoko, France Mentre, Denis Malvy
Summary: The study aimed at evaluating the tolerance and activity of high doses of favipiravir in male EVD survivors with EBOV RNA detection in semen in Guinea. However, only two participants were included due to recruitment difficulties, and no clinical adverse events of grade 3/4 were reported for both patients.
Article
Infectious Diseases
Guillaume Lingas, Nadege Neant, Alexandre Gaymard, Drifa Belhadi, Gilles Peytavin, Maya Hites, Therese Staub, Richard Greil, Jose-Artur Paiva, Julien Poissy, Nathan Peiffer-Smadja, Dominique Costagliola, Yazdan Yazdanpanah, Florent Wallet, Amandine Gagneux-Brunon, France Mentre, Florence Ader, Charles Burdet, Jeremie Guedj, Maude Bouscambert-Duchamp
Summary: Remdesivir reduces viral production, leading to a 0.7-day reduction in the time to viral clearance. It has a larger impact in patients with high viral load at randomization.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2022)
Article
Virology
Baptiste Elie, Benedicte Roquebert, Mircea T. Sofonea, Sabine Trombert-Paolantoni, Vincent Foulongne, Jeremie Guedj, Stpehanie Haim-Boukobza, Samuel Alizon
Summary: This study analyzed a longitudinal cohort in France and found that infections caused by the Alpha variant have a higher number of viral genome copies and a slower decay rate, leading to significantly higher transmission potentials, especially in older populations. There was no significant difference in peak viral copy number between infections caused by the Alpha and Delta variants.
JOURNAL OF MEDICAL VIROLOGY
(2022)
Article
Pharmacology & Pharmacy
Jinju Guk, Antoine Bridier-Nahmias, Melanie Magnan, Nathalie Grall, Xavier Duval, Olivier Clermont, Etienne Ruppe, Camille d'Humieres, Olivier Tenaillon, Erick Denamur, France Mentre, Jeremie Guedj, Charles Burdet
Summary: Recent studies have emphasized the importance of ecological interactions in dysbiosis of gut microbiota. This study aimed to investigate the role of ecological interactions in antibiotic-induced perturbations. The results showed that considering bacterial interactions and individual antibiotic exposure profile can improve the analysis of antibiotic-induced dysbiosis.
CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY
(2022)
Letter
Infectious Diseases
Xavier de Lamballerie, Guillaume Martin-Blondel, Axelle Dupont, Jacques Izopet, France Mentre, Nassim Kamar, Brigitte Autran, Gilles Paintaud, Sophie Caillard, Amandine le Bourgeois, Christophe Richez, Lionel Couzi, Alienor Xhaard, Zora Marjanovic, Jerome Avouac, Caroline Jacquet, Denis Anglicheau, Morgane Cheminant, Yazdan Yazdanpanah, Stephanie N. Guyen, Benjamin Terrier, Jacques Eric Gottenberg, Caroline Besson, Sophie Letrou, Sabrina Kali, Denis Angoulvant, Ventzislava Petrov Sanchez, Coralie Tardivon, Gilles Blancho, Vincent Levy
JOURNAL OF INFECTION
(2023)
Article
Pharmacology & Pharmacy
Melanie Guhl, Francois Mercier, Carsten Hofmann, Satish Sharan, Mark Donnelly, Kairui Feng, Wanjie Sun, Guoying Sun, Stella Grosser, Liang Zhao, Lanyan Fang, France Mentre, Emmanuelle Comets, Julie Bertrand
Summary: This study evaluated the performance of pharmacokinetic equivalence testing using a model-based approach, MB-TOST, which showed more robust results in cases of model misspecification and was reliable in sparse designs when the PK structural model was correctly specified.
JOURNAL OF PHARMACOKINETICS AND PHARMACODYNAMICS
(2022)
Article
Pharmacology & Pharmacy
Alexandra Lavalley-Morelle, Jean-Francois Timsit, France Mentre, Jimmy Mullaert
Summary: This study proposes a novel method for full parametric joint estimation of longitudinal process and time-to-event data in the presence of competing risks, aiming to provide individualized dynamic predictions. Simulation study and validation set demonstrate that joint modeling offers better predictions for death, providing a new approach for clinical applications.
CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY
(2022)
Article
Pharmacology & Pharmacy
Selma El Messaoudi, Annabelle Lemenuel-Diot, Antonio Goncalves, Jeremie Guedj
Summary: This study developed a mathematical model to evaluate the effects of antiviral treatments against hepatitis B virus. The results showed that lamivudine had a stronger effect in blocking viral production compared to pegylated interferon. Moreover, pegylated interferon had a significant immunomodulatory effect.
CLINICAL PHARMACOLOGY & THERAPEUTICS
(2023)
Article
Pharmacology & Pharmacy
Coralie Tardivon, Florence Loingeville, Mark Donnelly, Kairui Feng, Wanjie Sun, Guoying Sun, Stella Grosser, Liang Zhao, Lanyan Fang, France Mentre, Julie Bertrand
Summary: In a traditional PK BE study, PK parameters are obtained through noncompartmental analysis and BE analysis is performed using TOST. However, for ophthalmic drugs, the limited sample availability makes traditional analysis difficult. The FDA has proposed using NCA bootstrap and MB-TOST as alternative approaches. Simulation studies showed that MB-TOST performed similarly to NCA bootstrap for AUC and was a potentially better choice for C-max.
CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY
(2023)
Article
Biochemical Research Methods
Quentin Clairon, Melanie R. Prague, Delphine R. Planas, Timothee R. Bruel, Laurent R. Hocqueloux, Thierry R. Prazuck, Olivier R. Schwartz, Rodolphe R. Thiebaut, Jeremie R. Guedj
Summary: Due to the constant mutations of SARS-CoV-2, neutralizing capacity of antibodies targeting the historical strain decreases against emerging Variants of Concerns (VoCs). The study utilized a mathematical model to analyze the humoral response in individuals who received up to three doses of the Bnt162b2 vaccine. It was found that the neutralization capacity significantly increased after the third dose, providing prolonged protection against different VoCs.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Pharmacology & Pharmacy
Antonio Goncalves, Mathilde Marchand, Phyllis Chan, Jin Y. Jin, Jeremie Guedj, Rene Bruno
Summary: This study compared two main approaches, two-stage and joint modeling, to investigate the link between tumor size data and overall survival. The results showed that both approaches accurately predicted the benefit of atezolizumab in non-small cell lung cancer patients.
CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY
(2023)
Letter
Infectious Diseases
Florence Ader, Maude Bouscambert-Duchamp, Maya Hites, Nathan Peiffer-Smadja, France Mentre, Charles Burdet
LANCET INFECTIOUS DISEASES
(2022)