scholarly journals Differential Methods for Assessing Sensitivity in Biological Models

2021 ◽  
Author(s):  
Rachel Mester ◽  
Alfonso Landeros ◽  
Christopher Rackauckas ◽  
Kenneth Lange
Keyword(s):  
Sensitivity Analysis ◽  
Perturbation Method ◽  
Automatic Differentiation ◽  
Sir Model ◽  
Ease Of Use ◽  
Differential Sensitivity ◽  
Biological Models ◽  
Adjoint Sensitivity ◽  
Mathematical Basis ◽  
Speed Accuracy

Differential sensitivity analysis is indispensable in fitting parameters, understanding uncertainty, and forecasting the results of both thought and lab experiments. Although there are many methods currently available for performing differential sensitivity analysis of biological models, it can be difficult to determine which method is best suited for a particular model. In this paper, we explain a variety of differential sensitivity methods and assess their value in some typical biological models. First, we explain the mathematical basis for three numerical methods: adjoint sensitivity analysis, complex-perturbation sensitivity analysis, and forward-mode sensitivity analysis. We then carry out four instructive case studies. (i) The CARRGO model for tumor-immune interaction highlights the additional information that differential sensitivity analysis provides beyond traditional naive sensitivity methods, (ii) the deterministic SIR model demonstrates the value of using second-order sensitivity in refining model predictions, (iii) the stochastic SIR model shows how differential sensitivity can be attacked in stochastic modeling, and (iv) a discrete birth-death-migration model illustrates how the complex-perturbation method of differential sensitivity can be generalized to a broader range of biological models. Finally, we compare the speed, accuracy, and ease of use of these methods. We find that forward-mode automatic differentiation has the quickest computation time, while the complex-perturbation method is the simplest to implement and the most generalizable.

scholarly journals Redundant VoD Streaming Service in a Private Cloud: Availability Modeling and Sensitivity Analysis

2014 ◽  
Vol 2014 ◽  
pp. 1-14 ◽  
Author(s):  
Rosangela Maria De Melo ◽  
Maria Clara Bezerra ◽  
Jamilson Dantas ◽  
Rubens Matos ◽  
Ivanildo José De Melo Filho ◽  
...  
Keyword(s):  
Sensitivity Analysis ◽  
Cloud Computing ◽  
Hierarchical Modeling ◽  
Video On Demand ◽  
Differential Sensitivity ◽  
Private Cloud ◽  
Streaming Service ◽  
Critical Components ◽  
Modeling Strategy ◽  
Vod Streaming

For several years cloud computing has been generating considerable debate and interest within IT corporations. Since cloud computing environments provide storage and processing systems that are adaptable, efficient, and straightforward, thereby enabling rapid infrastructure modifications to be made according to constantly varying workloads, organizations of every size and type are migrating to web-based cloud supported solutions. Due to the advantages of the pay-per-use model and scalability factors, current video on demand (VoD) streaming services rely heavily on cloud infrastructures to offer a large variety of multimedia content. Recent well documented failure events in commercial VoD services have demonstrated the fundamental importance of maintaining high availability in cloud computing infrastructures, and hierarchical modeling has proved to be a useful tool for evaluating the availability of complex systems and services. This paper presents an availability model for a video streaming service deployed in a private cloud environment which includes redundancy mechanisms in the infrastructure. Differential sensitivity analysis was applied to identify and rank the critical components of the system with respect to service availability. The results demonstrate that such a modeling strategy combined with differential sensitivity analysis can be an attractive methodology for identifying which components should be supported with redundancy in order to consciously increase system dependability.

A Sensitivity Analysis Based Method for Robot Calibration

1992 ◽  
Author(s):  
S. Kaizerman ◽  
B. Benhabib ◽  
R. G. Fenton ◽  
G. Zak
Keyword(s):  
Sensitivity Analysis ◽  
Kinematic Model ◽  
Calibration Procedure ◽  
Inverse Kinematic ◽  
Model Parameters ◽  
Robot Calibration ◽  
Adjoint Sensitivity ◽  
Analysis Methods ◽  
The Matrix ◽  
Direct Sensitivity

Abstract A new robot kinematic calibration procedure is presented. The parameters of the kinematic model are estimated through a relationship established between the deviations in the joint variables and the deviations in the model parameters. Thus, the new method can be classified as an inverse calibration procedure. Using suitable sensitivity analysis methods, the matrix of the partial derivatives of joint variables with respect to robot parameters is calculated without having explicit expressions of joint variables as a function of task space coordinates (closed inverse kinematic solution). This matrix provides the relationship between the changes in the joint variables and the changes in the parameter values required for the calibration. Two deterministic sensitivity analysis methods are applied, namely the Direct Sensitivity Approach and the Adjoint Sensitivity Method. The new calibration procedure was successfully tested by the simulated calibrations of a two degree of freedom revolute-joint planar manipulator.

Direct Sensitivity Analysis of Spatial Multibody Systems With Joint Friction Using Index-1 Formulation

2021 ◽  
Author(s):  
Adwait Verulkar ◽  
Corina Sandu ◽  
Daniel Dopico ◽  
Adrian Sandu
Keyword(s):  
Sensitivity Analysis ◽  
Dynamic Systems ◽  
Multibody Systems ◽  
Friction Model ◽  
Design Parameters ◽  
Adjoint Sensitivity ◽  
Joint Friction ◽  
Multibody Dynamic ◽  
Model Dynamics ◽  
Direct Sensitivity

Abstract Sensitivity analysis is one of the most prominent gradient based optimization techniques for mechanical systems. Model sensitivities are the derivatives of the generalized coordinates defining the motion of the system in time with respect to the system design parameters. These sensitivities can be calculated using finite differences, but the accuracy and computational inefficiency of this method limits its use. Hence, the methodologies of direct and adjoint sensitivity analysis have gained prominence. Recent research has presented computationally efficient methodologies for both direct and adjoint sensitivity analysis of complex multibody dynamic systems. The contribution of this article is in the development of the mathematical framework for conducting the direct sensitivity analysis of multibody dynamic systems with joint friction using the index-1 formulation. For modeling friction in multibody systems, the Brown and McPhee friction model has been used. This model incorporates the effects of both static and dynamic friction on the model dynamics. A case study has been conducted on a spatial slider-crank mechanism to illustrate the application of this methodology to real-world systems. Using computer models, with and without joint friction, effect of friction on the dynamics and model sensitivities has been demonstrated. The sensitivities of slider velocity have been computed with respect to the design parameters of crank length, rod length, and the parameters defining the friction model. Due to the highly non-linear nature of friction, the model dynamics are more sensitive during the transition phases, where the friction coefficient changes from static to dynamic and vice versa.

Direct Sensitivity Analysis of Multibody Systems: A Vehicle Dynamics Benchmark

2019 ◽  
Vol 14 (2) ◽  
Author(s):  
Alfonso Callejo ◽  
Daniel Dopico
Keyword(s):  
Sensitivity Analysis ◽  
Multibody Systems ◽  
Automatic Differentiation ◽  
Time Integration ◽  
General Purpose ◽  
Contact Forces ◽  
Design Parameters ◽  
Computational Techniques ◽  
Computationally Efficient ◽  
Integration Algorithm

Algorithms for the sensitivity analysis of multibody systems are quickly maturing as computational and software resources grow. Indeed, the area has made substantial progress since the first academic methods and examples were developed. Today, sensitivity analysis tools aimed at gradient-based design optimization are required to be as computationally efficient and scalable as possible. This paper presents extensive verification of one of the most popular sensitivity analysis techniques, namely the direct differentiation method (DDM). Usage of such method is recommended when the number of design parameters relative to the number of outputs is small and when the time integration algorithm is sensitive to accumulation errors. Verification is hereby accomplished through two radically different computational techniques, namely manual differentiation and automatic differentiation, which are used to compute the necessary partial derivatives. Experiments are conducted on an 18-degree-of-freedom, 366-dependent-coordinate bus model with realistic geometry and tire contact forces, which constitutes an unusually large system within general-purpose sensitivity analysis of multibody systems. The results are in good agreement; the manual technique provides shorter runtimes, whereas the automatic differentiation technique is easier to implement. The presented results highlight the potential of manual and automatic differentiation approaches within general-purpose simulation packages, and the importance of formulation benchmarking.

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