Recursive prediction error identification and scaling of non-linear state space models using a restricted black box parameterization

Ordinary differential equation (ODE) models are quite popular for modelling complex dynamic processes in many scientific fields, and the parameters in these models are usually unknown, and we need to estimate them using statistical methods. When some observations are contaminated, regular estimation methods, such as nonlinear least-square estimation, will bring large bias. In this paper, robust estimations of both constant and time-varying parameters in ODE models using M-estimators are proposed, and their asymptotic properties are obtained under some mild conditions. We focus on Huber M-estimator, and also provide a method to adjust the Huber parameter automatically to the observations. The proposed method is compared to existing methods in numerical simulations and CD8+ T cell data analysis. It is demonstrated that our method gain substantial efficiency as well as robust properties.

Gene regulatory network (GRN) could provide guidance for understanding the internal laws of biological phenomena and analyzing several diseases. Ordinary differential equation model, which owns continuity and flexibility, has been utilized to identify GRN over the past decade. In this paper, we propose a novel algorithm, which is named as RNDEtree, a nonlinear ordinary differential equation model based on a flexible neural tree to improve the accuracy of the GRN reconstruction. In this model, a flexible neural tree can be utilized to approximate the nonlinear regulation function of an ordinary differential equation model. Multiexpression programming is proposed to evolve the structure of a flexible neural tree, and the brainstorm optimization algorithm is utilized to optimize the parameters of the RNDEtree model. In order to improve the false-positive ratio of this method, a novel fitness function is proposed, in which sparse and minimum redundancy maximum relevance (mRMR) terms are considered when optimizing RNDEtree. The performances of our proposed algorithm can be evaluated by the benchmark datasets from the DREAM challenge and real biological dataset in E. coli. The experimental results demonstrate that the proposed method could infer more correctly GRN than the other state-the-art methods.

In some patients with myeloproliferative neoplasms (MPN), two genetic mutations are often found, JAK2 V617F and one in the TET2 gene. Whether or not one mutation is present will influence how the other subsequent mutation affects the regulation of gene expression. When both mutations are present, the order of their occurrence has been shown to influence disease progression and prognosis. We propose a nonlinear ordinary differential equation (ODE) model and a Moran process models to explain the non-additive and non-commutative mutation effects on recent clinical observations of gene expression patterns, proportions of cells with different mutations, and ages at diagnosis of MPN. These observations consistently shape our modeling framework. Our key proposal is that bistability in gene expression provides a natural explanation for many observed order-of-mutation effects. We also propose potential experimental measurements that can be used to confirm or refute predictions of our models. Citation Format: Yue Wang, Tom Chou, Blerta Shtylla. Order-of-mutation effects on cancer progression: Models for myeloproliferative neoplasm [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr B034.

ABSTRACTSeveral approaches exist for estimating the derivatives of observed data for model exploration purposes, including functional data analysis (FDA; Ramsay & Silverman, 2005), generalized local linear approximation (GLLA; Boker, Deboeck, Edler, & Peel, 2010), and generalized orthogonal local derivative approximation (GOLD; Deboeck, 2010). These derivative estimation procedures can be used in a two-stage process to fit mixed effects ordinary differential equation (ODE) models. While the performance and utility of these routines for estimating linear ODEs have been established, they have not yet been evaluated in the context of nonlinear ODEs with mixed effects. We compared properties of the GLLA and GOLD to an FDA-based two-stage approach denoted herein as functional ordinary differential equation with mixed effects (FODEmixed) in a Monte Carlo (MC) study using a nonlinear coupled oscillators model with mixed effects. Simulation results showed that overall, the FODEmixed outperformed both the GLLA and GOLD across all the embedding dimensions considered, but a novel use of a fourth-order GLLA approach combined with very high embedding dimensions yielded estimation results that almost paralleled those from the FODEmixed. We discuss the strengths and limitations of each approach and demonstrate how output from each stage of FODEmixed may be used to inform empirical modeling of young children’s self-regulation.

Solution of nonlinear partial differential equations from base equations

A topic of interest in financial mathematics is the Black-Scholes model. However, the underlying asset price in the stock market may not be satisfied by this linear model, which was developed under a number of assumptions, including liquidity and the absence of transaction costs. The linear model has restricted its precision in actual market conditions. We study the transaction cost model for modelling illiquid markets from the extended nonlinear Black-Scholes model. Using a semi-discretization finite difference approach, the nonlinear partial differential equation is transformed into a nonlinear ordinary differential equation. Deep Learning (DL) is an advanced technique of machine learning solves the converted ordinary differential equation by fully connected neural network (FCNN). By modelling the complex and nonlinear relationships among market variables, DL models can generate option pricing forecasts that are more dependable and precise, not just for continuous data but also for discontinuous data (at jump point). Introduction: Nonlinear partial differential equation plays a crucial role in financial modelling, especially in the pricing of derivatives like options. The Black- Scholes model, introduced in 1973, continues to be one of the most widely used frameworks for pricing European options. However, this model is a linear one and offers an analytical solution, yet it is not appropriate for the complexities of real market assumptions that exhibit nonlinear effects. We examine the transaction cost model for modelling illiquid markets from the extended nonlinear Black-Scholes model created by Seelama et al. (2021). First using a semi-discretization finite difference approach, the nonlinear partial differential equation is transformed into a nonlinear ordinary differential equation. Solves the converted ordinary differential equation by Deep Learning (DL) based fully connected neural network (FCNN) algorithm. This algorithm is capable of handling the nonlinear behaviour of model and produce more accurate option value for European call. Objectives: Find the solution of more realistic nonlinear model of Black-Scholes equation include transaction cost in illiquid market with deep learning algorithm for a European call option. Methods: From extended nonlinear Black-Scholes model, the nonlinear model of transaction cost in illiquid market is considered for study. The nonlinear partial differential equation is converted into a nonlinear ordinary differential equation by semi-discretization finite difference method. DL is a sophisticated machine learning technique that solves transformed ordinary differential equations using fully connected neural network (FCNN) algorithm. DL algorithm uses a Python program. Results: For European call option, option values are predicted for different number of neurons with different loss functions like MSE and MAE at the time of maturity. Graphical representation shows the accuracy of the algorithm at continuous as well as at jump point (strike price). Conclusions: The method of solving a complex nonlinear partial differential equation by transforming it into a nonlinear ordinary differential equation is valuable. More precise pricing estimates for option values with nonlinear effects in financial data could be improved by deep learning.

Non-linear vibration and instability of multi-phase composite plate subjected to non-uniform in-plane parametric excitation: Semi-analytical investigation

Experimental results have shown that anti-cancer therapies, such as radiotherapy and chemotherapy, can modulate the cell cycle and generate cell cycle phase-dependent responses. As a result, obtaining a detailed understanding of the cell cycle is one possible path towards improving the efficacy of many of these therapies. Here, we consider a basic structured partial differential equation (PDE) model for cell progression through the cell cycle, and derive expressions for key quantities, such as the population growth rate and cell phase proportions. These quantities are shown to be periodic and, as such, we compare the PDE model to a corresponding ordinary differential equation (ODE) model in which the parameters are linked by ensuring that the long-term ODE behaviour agrees with the average PDE behaviour. By design, we find that the ODE model does an excellent job of representing the mean dynamics of the PDE model within just a few cell cycles. However, by probing the parameter space we find cases in which this mean behaviour is not a good measure of the PDE population growth. Our analytical comparison of two caricature models (one PDE and one ODE system) provides insight into cases in which the simple ODE model is an appropriate approximation to the PDE model.

In this work, we take as our base scalar second-order ordinary differential equations (ODEs) which have seven equivalence classes with each class possessing three Lie point symmetries. We show how one can calculate the conditional symmetries of third-order non-linear ODEs subject to root second-order nonlinear ODEs which admit three point symmetries. Moreover, we show when scalar second-order ODEs taken as first integrals or conditional first integrals are inherited as Lie point symmetries and as conditional symmetries of the derived third-order ODE. Furthermore, the derived scalar nonlinear third-order ODEs without substitution are considered for their conditional symmetries subject to root second-order ODEs having three symmetries.

This article proposes a mathematical model based on ordinary nonlinear differential equations that describes the dynamics of population growth of the mosquito Aedes aegypti throughout its life cycle. Then, a modification is made to the model by implementing a time delay, initially constant and then distributed over time. In addition, h, the population growth threshold, is established, the equilibrium points (trivial equilibrium, coexistence equilibrium) of the population are found and an analysis of local stability of the coexistence equilibrium is performed. If $$h>1$$ , this results in the population of adult aquatic mosquitoes persisting in the environment, approaching a equilibrium of coexistence, regardless of whether the time delay is considered or not. Finally, numerical simulations are carried out using Matlab software using the functions ode45 and dde23, with a value of $$ h>1 $$ , which allow the solutions of the initial model of ordinary differential equations to be compared to the solutions when the delay is implemented.

This paper develops and validates through a series of presentable examples, a comprehensive high-precision, and ultrafast computing concept for solving nonlinear ordinary differential equations (ODEs) and partial differential equations (PDEs) with cellular neural networks (CNN). The core of this concept is a straightforward scheme that we call "nonlinear adaptive optimization (NAOP),” which is used for a precise template calculation for solving nonlinear ODEs and PDEs through CNN processors. One of the key contributions of this work is to demonstrate the possibility of transforming different types of nonlinearities displayed by various classical and well-known nonlinear equations (e.g., van der Pol-, Rayleigh-, Duffing-, Rössler-, Lorenz-, and Jerk-equations, just to name a few) unto first-order CNN elementary cells, and thereby enabling the easy derivation of corresponding CNN templates. Furthermore, in the case of PDE solving, the same concept also allows a mapping unto first-order CNN cells while considering one or even more nonlinear terms of the Taylor's series expansion generally used in the transformation of a PDE in a set of coupled nonlinear ODEs. Therefore, the concept of this paper does significantly contribute to the consolidation of CNN as a universal and ultrafast solver of nonlinear ODEs and/or PDEs. This clearly enables a CNN-based, real-time, ultraprecise, and low-cost computational engineering. As proof of concept, two examples of well-known ODEs are considered namely a second-order linear ODE and a second order nonlinear ODE of the van der Pol type. For each of these ODEs, the corresponding precise CNN templates are derived and are used to deduce the expected solutions. An implementation of the concept developed is possible even on embedded digital platforms (e.g., field programmable gate array (FPGA), digital signal processor (DSP), graphics processing unit (GPU), etc.). This opens a broad range of applications. Ongoing works (as outlook) are using NAOP for deriving precise templates for a selected set of practically interesting ODEs and PDEs equation models such as Lorenz-, Rössler-, Navier Stokes-, Schrödinger-, Maxwell-, etc.

Modeling and analysis of complex systems are important aspects of understanding systemic behavior. In the lack of detailed knowledge about a system, we often choose modeling equations out of convenience and search the (high-dimensional) parameter space randomly to learn about model properties. Qualitative modeling sidesteps the issue of choosing specific modeling equations and frees the inference from specific properties of the equations. We consider classes of ordinary differential equation (ODE) models arising from interactions of species/entities, such as (bio)chemical reaction networks or ecosystems. A class is defined by imposing mild assumptions on the interaction rates. In this framework, we investigate whether there can be multiple positive steady states in some ODE models in a given class. We have developed and implemented a method to decide whether any ODE model in a given class cannot have multiple steady states. The method runs efficiently on models of moderate size. We tested the method on a large set of models for gene silencing by sRNA interference and on two publicly available databases of biological models, KEGG and Biomodels. We recommend that this method is used as (i) a pre-screening step for selecting an appropriate model and (ii) for investigating the robustness of non-existence of multiple steady state for a given ODE model with respect to variation in interaction rates. Scripts and examples in Maple are available in the Supplementary Information. wiuf@math.ku.dk Supplementary data are available at Bioinformatics online.

Step forward on nonlinear differential equations with the Atangana–Baleanu derivative: Inequalities, existence, uniqueness and method

Micro-cantilever beams are currently employed as sensor in various fields. Of main applications, is using such beams in wind speed sensors. For this purpose, curved out of plane micro-cantilever beams are used. Uniform pressure on such beams causes a large deflection of beam. General mechanics of material theory deals with small deflection and thus cannot be used for explaining this deflection. Although there are a body of works on analysing of large deflection [1], nonlinear deflection, of curved beams [2], yet there is no research on large deflection of curved beam under horizontal uniform distributed force. Theoretically, the wind force is applying horizontally on curved micro-cantilever beam. Here, we neglect the effect of moving weather from beam sides. We first aim how to drive the governed equation. A curved beam does not have a calculable centroid. Also large deflection of beam changes its curvature which would change the centroid of beam consciously. The variation of centroid makes very though calculating the bending moment of each cross section in the beam. To address this issue, an integral equation will be used. The total force will be considered as a single force applied at the centroid. The second challenge is solving the governed nonlinear ordinary differential equation (ODE). Although there are several methods to solve analytically nonlinear ODE, Lie symmetry method, with all its complication, is a general method for this kind of equations. This approach covers all current methods in analytical solving nonlinear ODEs. In this method, an infinitesimal transformation should be calculated. All transformations under one parameter creates a group that called Lie group. A value of parameter which transfers the equation onto itself is called invariant of ODE. One can calculate canonical coordinates ODEs by the invariant. Solving the canonical coordinates ODEs yields to calculating the canonical coordinates. Canonical coordinate are used to reduce the order of nonlinear ODE [3]. By repeating this method one can solve high order ODEs. Our last question is how to do numerical solution of ODE. The possible answer will help to explain the phenomena of deflection clearly and compare the analytical solution with numerical results. Small dimensions of beam, small values of applied force from one side and Young modules value from the other side, will create a stiff ODE. Authors experience in this area shows that the best method to sole these kind of equations is LSODE. This method can be used in Maple. Here, primary calculations show that the governed equation is second order nonlinear ODE and we propose two possible invariants to solve ODE. Overall, the primary numerical solution has shown perfect match with the exact solution.

For system identification, the ordinary differential equations (ODEs) model is popular for its accuracy and effectiveness. Consequently, the ODEs model is extended to the stochastic differential equations (SDEs) model to tackle the stochastic case intuitively. But the existence of stochastic integral is a rigid barrier. We simply transform the SDEs to their corresponding stochastic difference equations (SDCEs) to eliminate stochastic integrals and propose an easy but effective solution to stochastic system identification. In this solution, the maximum likelihood estimation can be applied and the evolutionary algorithms are used to determine structures and parameters of the unknown system.