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A key problem in computational biology is discovering the gene expression changes that regulate cell fate transitions, in which one cell type turns into another. However, each individual cell cannot be tracked longitudinally, and cells at…

Machine Learning · Computer Science 2022-07-12 Yichen Gu , David Blaauw , Joshua Welch

The neural Ordinary Differential Equation (ODE) model has shown success in learning complex continuous-time processes from observations on discrete time stamps. In this work, we consider the modeling and forecasting of time series data that…

Machine Learning · Statistics 2023-06-05 Yixuan Tan , Liyan Xie , Xiuyuan Cheng

Ordinary differential equation (ODE) models are widely used to describe chemical or biological processes. This article considers the estimation and assessment of such models on the basis of time-course data. Due to experimental limitations,…

Molecular Networks · Quantitative Biology 2023-02-14 Samuel W. K. Wong , Shihao Yang , S. C. Kou

We compare and contrast the transit compartment ordinary differential equation modelling approach with distributed and discrete delay differential equation models. We focus on Quartino's extension to the Friberg transit compartment model of…

Tissues and Organs · Quantitative Biology 2021-12-03 Daniel Camara De Souza , Morgan Craig , Tyler Cassidy , Jun Li , Fahima Nekka , Jacques Belair , Antony R Humphries

We study approximation of non-autonomous linear differential equations with variable delay over infinite intervals. We use piecewise constant argument to obtain a corresponding discrete difference equation. The study of numerical…

Classical Analysis and ODEs · Mathematics 2016-07-26 Daniel Sepúlveda

Latent ODE models provide flexible descriptions of dynamic systems, but they can struggle with extrapolation and predicting complicated non-linear dynamics. The latent ODE approach implicitly relies on encoders to identify unknown system…

Machine Learning · Computer Science 2024-10-14 Matt L. Sampson , Peter Melchior

Retarded stochastic differential equations (SDEs) constitute a large collection of systems arising in various real-life applications. Most of the existing results make crucial use of dissipative conditions. Dealing with "pure delay" systems…

Probability · Mathematics 2013-08-12 Jianhai Bao , George Yin , Chenggui Yuan

Filtering-based probabilistic numerical solvers for ordinary differential equations (ODEs), also known as ODE filters, have been established as efficient methods for quantifying numerical uncertainty in the solution of ODEs. In practical…

Machine Learning · Statistics 2025-10-02 Dingling Yao , Filip Tronarp , Nathanael Bosch

Increasing the layer number of on-chip photonic neural networks (PNNs) is essential to improve its model performance. However, the successively cascading of network hidden layers results in larger integrated photonic chip areas. To address…

Machine Learning · Computer Science 2023-02-08 Yun Zhao , Hang Chen , Min Lin , Haiou Zhang , Tao Yan , Xing Lin , Ruqi Huang , Qionghai Dai

Ordinary differential equation (ODE) models are widely used to describe systems in many areas of science. To ensure these models provide accurate and interpretable representations of real-world dynamics, it is often necessary to infer…

Methodology · Statistics 2026-03-24 Selva Salimi , David J. Warne , Christopher Drovandi

The solvability of a delay differential equation arising in the construction of quadratic cost functionals, i.e. Lyapunov functionals, for a linear time-delay system with a constant and a distributed delay is investigated. We present a…

Systems and Control · Computer Science 2019-09-23 Suat Gumussoy , Murad Abu-Khalaf

We show that delay-differential equations (DDE) exhibit universal bifurcation scenarios, which are observed in large classes of DDEs with a single delay. Each such universality class has the same sequence of stabilizing or destabilizing…

Dynamical Systems · Mathematics 2024-01-01 Yu Wang , Jinde Cao , Jürgen Kurths , Serhiy Yanchuk

Model reduction for fluid flow simulation continues to be of great interest across a number of scientific and engineering fields. Here, we explore the use of Neural Ordinary Differential Equations, a recently introduced family of…

Machine Learning · Computer Science 2021-04-30 Sourav Dutta , Peter Rivera-Casillas , Matthew W. Farthing

Ordinary Differential Equations (ODEs) are widely used in physics, chemistry, and biology to model dynamic systems, including reaction kinetics, population dynamics, and biological processes. In this work, we integrate GPU-accelerated ODE…

Machine Learning · Computer Science 2024-12-02 Rakshit Kr. Singh , Aaron Rock Menezes , Rida Irfan , Bharath Ramsundar

Realizations of stochastic process are often observed temporal data or functional data. There are growing interests in classification of dynamic or functional data. The basic feature of functional data is that the functional data have…

Machine Learning · Statistics 2014-10-28 Lerong Li , Momiao Xiong

We use the McKendrick equation with variable ageing rate and randomly distributed maturation time to derive a state dependent distributed delay differential equation. We show that the resulting delay differential equation preserves…

Populations and Evolution · Quantitative Biology 2021-03-22 Tyler Cassidy , Morgan Craig , Antony R. Humphries

The quasi-steady state approximation and time-scale separation are commonly applied methods to simplify models of biochemical reaction networks based on ordinary differential equations (ODEs). The concentrations of the "fast" species are…

Dynamical Systems · Mathematics 2016-05-10 Meritxell Sáez , Carsten Wiuf , Elisenda Feliu

Statistical models can involve implicitly defined quantities, such as solutions to nonlinear ordinary differential equations (ODEs), that unavoidably need to be numerically approximated in order to evaluate the model. The approximation…

Computation · Statistics 2024-09-16 Juho Timonen , Nikolas Siccha , Ben Bales , Harri Lähdesmäki , Aki Vehtari

A critical transition for a system modelled by a concave quadratic scalar ordinary differential equation occurs when a small variation of the coefficients changes dramatically the dynamics, from the existence of an attractor-repeller pair…

Dynamical Systems · Mathematics 2022-11-21 Iacopo P. Longo , Carmen Núñez , Rafael Obaya

A recent work by the authors on the existence of a periodic smooth finite-dimensional center manifold near a nonhyperbolic cycle in delay differential equations motivates the derivation of periodic normal forms. In this paper, we prove the…

Dynamical Systems · Mathematics 2025-01-23 B. Lentjes , L. Spek , M. M. Bosschaert , Yu. A. Kuznetsov