Main

The l'_1_'-norm objective is like an absolute value objective but also includes a dead-band to reject measurement error and stabilize the parameter estimates.
~~# ~~# Safdarnejad, S.M., Hedengren, J.D., Lewis, N.R., Haseltine, E., Initialization Strategies for Optimization of Dynamic Systems, Computers and Chemical Engineering, 2015, Vol. 78, pp. 39-50, DOI: 10.1016/j.compchemeng.2015.04.016. [[http://www.sciencedirect.com/science/article/pii/S0098135415001179 | Article]]

# # Safdarnejad, S.M., Hedengren, J.D., Lewis, N.R., Haseltine, E., Initialization Strategies for Optimization of Dynamic Systems, Computers and Chemical Engineering, 2015, Vol. 78, pp. 39-50, DOI: 10.1016/j.compchemeng.2015.04.016. [[http://www.sciencedirect.com/science/article/pii/S0098135415001179 | Article]]

(:html:)

<iframe width="560" height="315" src="https://www.youtube.com/embed/5qY7WyngRbo" frameborder="0" allowfullscreen></iframe>

(:htmlend:)

The following example problem is a demonstration of the two different objective forms and some of the configuration to achieve optimal estimator performance.

# Lewis, N.R., Hedengren, J.D., Haseltine, E.L., Hybrid Dynamic Optimization Methods for Systems Biology with Efficient Sensitivities, Special Issue on Algorithms and Applications in Dynamic Optimization, Processes, 2015, 3(3), 701-729; doi:10.3390/pr3030701. [[http://www.mdpi.com/2227-9717/3/3/701/html | Article]]

# Hedengren, J. D. and Asgharzadeh Shishavan, R., Powell, K.M., and Edgar, T.F., Nonlinear Modeling, Estimation and Predictive Control in APMonitor, Computers and Chemical Engineering, Volume 70, pg. 133–148, 2014. [[http://dx.doi.org/10.1016/j.compchemeng.2014.04.013|Article]]

# Safdarnejad, S.M., Hedengren, J.D., Lewis, N.R., Haseltine, E., Initialization Strategies for Optimization of Dynamic Systems, Computers and Chemical Engineering, DOI: 10.1016/j.compchemeng.2015.04.016. [[http://www.sciencedirect.com/science/article/pii/S0098135415001179 | Article]]

!!!! Exercise

'''Objective:''' Estimate parameters of a highly nonlinear system. Use an initialization strategy to find a suitable approximation for the parameter estimation. Create a MATLAB or Python script to simulate and display the results. ''Estimated Time: 2 hours''

The spread of HIV in a patient is approximated with balance equations on (H)ealthy, (I)nfected, and (V)irus population counts'^2^'.

Initial Conditions

H = healthy cells = 1,000,000

I = infected cells = 0

V = virus = 100

LV = log virus = 2

Equations

dH/dt = kr'_1_' - kr'_2_' H - kr'_3_' H V

dI/dt = kr'_3_' H V - kr'_4_' I

dV/dt = -kr'_3_' H V - kr'_5_' V + kr'_6_' I

LV = log'_10_'(V)

There are six parameters (kr'_1..6_') in the model that provide the rates of cell death, infection spread, virus replication, and other processes that determine the spread of HIV in the body.

Parameters

kr'_1_' = new healthy cells

kr'_2_' = death rate of healthy cells

kr'_3_' = healthy cells converting to infected cells

kr'_4_' = death rate of infected cells

kr'_5_' = death rate of virus

kr'_6_' = production of virus by infected cells

The following data is provided from a virus count over the course of 15 years. Note that the virus count information is reported in log scale.

Attach:download.png [[Attach:data_hiv.zip|HIV Data and Model Files]]

Attach:hiv_virus_count.png

With guess values for parameters (kr'_1..6_'), approximately match the laboratory data for this patient.

!!!! Solution

Attach:download.png [[Attach:estimate_hiv.zip|HIV Estimation in MATLAB and Python]]

(:html:)

<iframe width="560" height="315" src="https://www.youtube.com/embed/0Et07u336Bo?rel=0" frameborder="0" allowfullscreen></iframe>

(:htmlend:)

!!!! References

# Safdarnejad, S.M., Hedengren, J.D., Lewis, N.R., Haseltine, E., Initialization Strategies for Optimization of Dynamic Systems, Computers and Chemical Engineering, DOI: 10.1016/j.compchemeng.2015.04.016. [[http://www.sciencedirect.com/science/article/pii/S0098135415001179 | Article]]

# Nowak, M. and May, R. M. ''Virus dynamics: mathematical principles of immunology and virology: mathematical principles of immunology and virology''. Oxford university press, 2000.

## Dynamic Estimation Objectives

## Main.EstimatorObjective History

Hide minor edits - Show changes to output

Changed line 153 from:

log_v = data~~[:,]~~[:,1] # 2nd column of data

to:

log_v = data[:,1] # 2nd column of data

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(:toggle hide gekko button show="Show GEKKO (Python) Code":)

(:div id=gekko:)

(:source lang=python:)

from __future__ import division

from gekko import GEKKO

import numpy as np

# Manually enter guesses for parameters

lkr = [3,np.log10(0.1),np.log10(2e-7),\

np.log10(0.5),np.log10(5),np.log10(100)]

# Model

m = GEKKO()

# Time

m.time = np.linspace(0,15,61)

# Parameters to estimate

lg10_kr = [m.FV(value=lkr[i]) for i in range(6)]

# Variables

kr = [m.Var() for i in range(6)]

H = m.Var(value=1e6)

I = m.Var(value=0)

V = m.Var(value=1e2)

# Variable to match with data

LV = m.CV(value=2)

# Equations

m.Equations([10**lg10_kr[i]==kr[i] for i in range(6)])

m.Equations([H.dt() == kr[0] - kr[1]*H - kr[2]*H*V,

I.dt() == kr[2]*H*V - kr[3]*I,

V.dt() == -kr[2]*H*V - kr[4]*V + kr[5]*I,

LV == m.log10(V)])

# Estimation

# Global options

m.options.IMODE = 5 #switch to estimation

m.options.TIME_SHIFT = 0 #don't timeshift on new solve

m.options.EV_TYPE = 2 #l2 norm

m.options.COLDSTART = 2

m.options.SOLVER = 1

m.options.MAX_ITER = 1000

m.solve()

for i in range(6):

lg10_kr[i].STATUS = 1 #Allow optimizer to fit these values

lg10_kr[i].DMAX = 2

lg10_kr[i].LOWER = -10

lg10_kr[i].UPPER = 10

# patient virus count data

data = np.array([[0,1.20E+00],[0.25,1.67E+00],[0.5,2.06E+00],\

[0.75,2.05E+00],[1,3.57E+00],[1.25,2.96E+00],\

[1.5,2.95E+00],[1.75,3.48E+00],[2,3.27E+00], \

[2.25,2.98E+00],[2.5,4.17E+00],[2.75,4.41E+00],\

[3,4.16E+00],[3.25,3.94E+00],[3.5,4.44E+00],\

[3.75,4.60E+00],[4,5.15E+00],[4.25,5.34E+00],\

[4.5,6.56E+00],[4.75,5.16E+00],[5,6.63E+00],\

[5.25,6.60E+00],[5.5,6.59E+00],[5.75,6.28E+00],\

[6,6.79E+00],[6.25,6.81E+00],[6.5,7.16E+00],\

[6.75,7.06E+00],[7,7.19E+00],[7.25,6.07E+00],\

[7.5,6.67E+00],[7.75,6.97E+00],[8,6.51E+00],\

[8.25,6.48E+00],[8.5,7.44E+00],[8.75,7.98E+00],\

[9,6.71E+00],[9.25,6.98E+00],[9.5,7.60E+00],\

[9.75,5.62E+00],[10,7.04E+00],[10.25,7.31E+00],\

[10.5,5.08E+00],[10.75,6.62E+00],[11,6.48E+00],\

[11.25,6.91E+00],[11.5,6.44E+00],[11.75,6.85E+00],\

[12,7.09E+00],[12.25,6.20E+00],[12.5,7.02E+00],\

[12.75,7.34E+00],[13,6.57E+00],[13.25,6.42E+00],\

[13.5,6.50E+00],[13.75,6.46E+00],[14,6.42E+00],\

[14.25,7.09E+00],[14.5,7.37E+00],[14.75,6.56E+00],\

[15,6.69E+00]])

# Convert log-scaled data for plotting

log_v = data[:,][:,1] # 2nd column of data

v = np.power(10,log_v)

LV.FSTATUS = 1 #receive measurements to fit

LV.STATUS = 1 #build objective function to match data and prediction

LV.value = log_v #v data

m.solve()

# Plot results

import matplotlib.pyplot as plt

plt.figure(1)

plt.semilogy(m.time,H,'b-')

plt.semilogy(m.time,I,'g:')

plt.semilogy(m.time,V,'r--')

plt.semilogy(data[:,][:,0],v,'ro')

plt.xlabel('Time (yr)')

plt.ylabel('States (log scale)')

plt.legend(['H','I','V'])

plt.show()

(:sourceend:)

(:divend:)

(:div id=gekko:)

(:source lang=python:)

from __future__ import division

from gekko import GEKKO

import numpy as np

# Manually enter guesses for parameters

lkr = [3,np.log10(0.1),np.log10(2e-7),\

np.log10(0.5),np.log10(5),np.log10(100)]

# Model

m = GEKKO()

# Time

m.time = np.linspace(0,15,61)

# Parameters to estimate

lg10_kr = [m.FV(value=lkr[i]) for i in range(6)]

# Variables

kr = [m.Var() for i in range(6)]

H = m.Var(value=1e6)

I = m.Var(value=0)

V = m.Var(value=1e2)

# Variable to match with data

LV = m.CV(value=2)

# Equations

m.Equations([10**lg10_kr[i]==kr[i] for i in range(6)])

m.Equations([H.dt() == kr[0] - kr[1]*H - kr[2]*H*V,

I.dt() == kr[2]*H*V - kr[3]*I,

V.dt() == -kr[2]*H*V - kr[4]*V + kr[5]*I,

LV == m.log10(V)])

# Estimation

# Global options

m.options.IMODE = 5 #switch to estimation

m.options.TIME_SHIFT = 0 #don't timeshift on new solve

m.options.EV_TYPE = 2 #l2 norm

m.options.COLDSTART = 2

m.options.SOLVER = 1

m.options.MAX_ITER = 1000

m.solve()

for i in range(6):

lg10_kr[i].STATUS = 1 #Allow optimizer to fit these values

lg10_kr[i].DMAX = 2

lg10_kr[i].LOWER = -10

lg10_kr[i].UPPER = 10

# patient virus count data

data = np.array([[0,1.20E+00],[0.25,1.67E+00],[0.5,2.06E+00],\

[0.75,2.05E+00],[1,3.57E+00],[1.25,2.96E+00],\

[1.5,2.95E+00],[1.75,3.48E+00],[2,3.27E+00], \

[2.25,2.98E+00],[2.5,4.17E+00],[2.75,4.41E+00],\

[3,4.16E+00],[3.25,3.94E+00],[3.5,4.44E+00],\

[3.75,4.60E+00],[4,5.15E+00],[4.25,5.34E+00],\

[4.5,6.56E+00],[4.75,5.16E+00],[5,6.63E+00],\

[5.25,6.60E+00],[5.5,6.59E+00],[5.75,6.28E+00],\

[6,6.79E+00],[6.25,6.81E+00],[6.5,7.16E+00],\

[6.75,7.06E+00],[7,7.19E+00],[7.25,6.07E+00],\

[7.5,6.67E+00],[7.75,6.97E+00],[8,6.51E+00],\

[8.25,6.48E+00],[8.5,7.44E+00],[8.75,7.98E+00],\

[9,6.71E+00],[9.25,6.98E+00],[9.5,7.60E+00],\

[9.75,5.62E+00],[10,7.04E+00],[10.25,7.31E+00],\

[10.5,5.08E+00],[10.75,6.62E+00],[11,6.48E+00],\

[11.25,6.91E+00],[11.5,6.44E+00],[11.75,6.85E+00],\

[12,7.09E+00],[12.25,6.20E+00],[12.5,7.02E+00],\

[12.75,7.34E+00],[13,6.57E+00],[13.25,6.42E+00],\

[13.5,6.50E+00],[13.75,6.46E+00],[14,6.42E+00],\

[14.25,7.09E+00],[14.5,7.37E+00],[14.75,6.56E+00],\

[15,6.69E+00]])

# Convert log-scaled data for plotting

log_v = data[:,][:,1] # 2nd column of data

v = np.power(10,log_v)

LV.FSTATUS = 1 #receive measurements to fit

LV.STATUS = 1 #build objective function to match data and prediction

LV.value = log_v #v data

m.solve()

# Plot results

import matplotlib.pyplot as plt

plt.figure(1)

plt.semilogy(m.time,H,'b-')

plt.semilogy(m.time,I,'g:')

plt.semilogy(m.time,V,'r--')

plt.semilogy(data[:,][:,0],v,'ro')

plt.xlabel('Time (yr)')

plt.ylabel('States (log scale)')

plt.legend(['H','I','V'])

plt.show()

(:sourceend:)

(:divend:)

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The l'_1_'-norm objective is like an absolute value objective but also includes a dead-band to reject measurement error and stabilize the parameter estimates.

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# Safdarnejad, S.M., Hedengren, J.D., Lewis, N.R., Haseltine, E., Initialization Strategies for Optimization of Dynamic Systems, Computers and Chemical Engineering, 2015, Vol. 78, pp. 39-50, DOI: 10.1016/j.compchemeng.2015.04.016. [[http://www.sciencedirect.com/science/article/pii/S0098135415001179 | Article]]

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# # Safdarnejad, S.M., Hedengren, J.D., Lewis, N.R., Haseltine, E., Initialization Strategies for Optimization of Dynamic Systems, Computers and Chemical Engineering, 2015, Vol. 78, pp. 39-50, DOI: 10.1016/j.compchemeng.2015.04.016. [[http://www.sciencedirect.com/science/article/pii/S0098135415001179 | Article]]

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Attach:download.png [[Attach:motion_estimation.zip|Motion Estimation from GPS]]

to:

Attach:download.png [[Attach:motion_estimation.zip|Motion Estimation from GPS Position (1D Example)]]

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Attach:download.png [[Attach:motion_estimation.zip|Motion Estimation from GPS]]

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The squared error objective is the most common form, used extensively in the literature. It is also the basis for the derivation of the Kalman filter and other well known estimators.

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The l'_1_'-norm objective is like an absolute value of the error but posed in a way to have continuous first and second derivatives. The addition of [[http://apmonitor.com/wiki/index.php/Main/SlackVariables|slack variables]] enables an efficient formulation (only linear constraints) that is also convex (local optimum is the global optimum). A unique aspect of the following l'_1_'-norm objective is the addition of a ''dead-band'' or region around the measurements where there is no penalty. It is only when the model predictions are outside of this dead-band that the optimizer makes changes to the parameters to correct the model.

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There are many symbols used in the definition of the different objective function forms. Below is a nomenclature table that gives a description of each variable and the role in the objective expression.

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The following example problem is a demonstration of the two different objective forms and some of the configuration to achieve optimal estimator performance.

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# Lewis, N.R., Hedengren, J.D., Haseltine, E.L., Hybrid Dynamic Optimization Methods for Systems Biology with Efficient Sensitivities, Special Issue on Algorithms and Applications in Dynamic Optimization, Processes, 2015, 3(3), 701-729; doi:10.3390/pr3030701. [[http://www.mdpi.com/2227-9717/3/3/701/html | Article]]

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<iframe width="560" height="315" src="https://www.youtube.com/embed/~~0Et07u336Bo~~?rel=0" frameborder="0" allowfullscreen></iframe>

(:htmlend:)

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<iframe width="560" height="315" src="https://www.youtube.com/embed/KuivI_QZ0IA?rel=0" frameborder="0" allowfullscreen></iframe>(:htmlend:)

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With guess values for parameters (kr'_1..6_'), approximately match the laboratory data for this patient.

to:

With guess values for parameters (kr'_1..6_'), approximately match the laboratory data for this patient as an initial solution. Use this initial solution to compute an optimal solution with dynamic estimation. Adjust parameters kr'_1..6_' to match the virus count data. Start with different kr values to verify that the solution is not just locally optimal but also globally optimal.

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The dynamic estimation objective function is a mathematical statement that is minimized or maximized to find a best solution among all possible feasible solutions. The form of this objective function is critical to give desirable solutions for model predictions but also for other applications that use the output of a dynamic estimation application. Two common objective functions are shown below as squared error and l'_1_'-norm forms.

to:

The dynamic estimation objective function is a mathematical statement that is minimized or maximized to find a best solution among all possible feasible solutions. The form of this objective function is critical to give desirable solutions for model predictions but also for other applications that use the output of a dynamic estimation application. Two common objective functions are shown below as squared error and l'_1_'-norm forms'^1^'.

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The spread of HIV in a patient is approximated with balance equations on (H)ealthy, (I)nfected, and (V)irus population counts'^~~1~~^'.

to:

The spread of HIV in a patient is approximated with balance equations on (H)ealthy, (I)nfected, and (V)irus population counts'^2^'.

Added lines 64-65:

# Hedengren, J. D. and Asgharzadeh Shishavan, R., Powell, K.M., and Edgar, T.F., Nonlinear Modeling, Estimation and Predictive Control in APMonitor, Computers and Chemical Engineering, Volume 70, pg. 133–148, 2014. [[http://dx.doi.org/10.1016/j.compchemeng.2014.04.013|Article]]

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The dynamic estimation objective function is a mathematical statement that is minimized or maximized to find a best solution among all possible feasible solutions. The form of this objective function is critical to give desirable solutions for model predictions but also for other applications that use the output of a dynamic estimation application.

to:

The dynamic estimation objective function is a mathematical statement that is minimized or maximized to find a best solution among all possible feasible solutions. The form of this objective function is critical to give desirable solutions for model predictions but also for other applications that use the output of a dynamic estimation application. Two common objective functions are shown below as squared error and l'_1_'-norm forms.

!!!! Squared Error Objective

Attach:obj_est_sq_error.png

!!!! l'_1_'-norm Objective

Attach:obj_est_l1_norm.png

!!!! Nomenclature

Attach:obj_est_nomenclature.png

!!!! Squared Error Objective

Attach:obj_est_sq_error.png

!!!! l'_1_'-norm Objective

Attach:obj_est_l1_norm.png

!!!! Nomenclature

Attach:obj_est_nomenclature.png

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The spread of HIV in a patient is approximated with balance equations on (H)ealthy, (I)nfected, and (V)irus population counts'^~~2~~^'.

to:

The spread of HIV in a patient is approximated with balance equations on (H)ealthy, (I)nfected, and (V)irus population counts'^1^'.

Deleted lines 51-52:

# Safdarnejad, S.M., Hedengren, J.D., Lewis, N.R., Haseltine, E., Initialization Strategies for Optimization of Dynamic Systems, Computers and Chemical Engineering, DOI: 10.1016/j.compchemeng.2015.04.016. [[http://www.sciencedirect.com/science/article/pii/S0098135415001179 | Article]]

Added lines 6-55:

!!!! Exercise

'''Objective:''' Estimate parameters of a highly nonlinear system. Use an initialization strategy to find a suitable approximation for the parameter estimation. Create a MATLAB or Python script to simulate and display the results. ''Estimated Time: 2 hours''

The spread of HIV in a patient is approximated with balance equations on (H)ealthy, (I)nfected, and (V)irus population counts'^2^'.

Initial Conditions

H = healthy cells = 1,000,000

I = infected cells = 0

V = virus = 100

LV = log virus = 2

Equations

dH/dt = kr'_1_' - kr'_2_' H - kr'_3_' H V

dI/dt = kr'_3_' H V - kr'_4_' I

dV/dt = -kr'_3_' H V - kr'_5_' V + kr'_6_' I

LV = log'_10_'(V)

There are six parameters (kr'_1..6_') in the model that provide the rates of cell death, infection spread, virus replication, and other processes that determine the spread of HIV in the body.

Parameters

kr'_1_' = new healthy cells

kr'_2_' = death rate of healthy cells

kr'_3_' = healthy cells converting to infected cells

kr'_4_' = death rate of infected cells

kr'_5_' = death rate of virus

kr'_6_' = production of virus by infected cells

The following data is provided from a virus count over the course of 15 years. Note that the virus count information is reported in log scale.

Attach:download.png [[Attach:data_hiv.zip|HIV Data and Model Files]]

Attach:hiv_virus_count.png

With guess values for parameters (kr'_1..6_'), approximately match the laboratory data for this patient.

!!!! Solution

Attach:download.png [[Attach:estimate_hiv.zip|HIV Estimation in MATLAB and Python]]

(:html:)

<iframe width="560" height="315" src="https://www.youtube.com/embed/0Et07u336Bo?rel=0" frameborder="0" allowfullscreen></iframe>

(:htmlend:)

!!!! References

# Safdarnejad, S.M., Hedengren, J.D., Lewis, N.R., Haseltine, E., Initialization Strategies for Optimization of Dynamic Systems, Computers and Chemical Engineering, DOI: 10.1016/j.compchemeng.2015.04.016. [[http://www.sciencedirect.com/science/article/pii/S0098135415001179 | Article]]

# Nowak, M. and May, R. M. ''Virus dynamics: mathematical principles of immunology and virology: mathematical principles of immunology and virology''. Oxford university press, 2000.

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(:title Dynamic Estimation Objectives:)

(:keywords objective function, MATLAB, Simulink, moving horizon, time window, dynamic data, validation, estimation, differential, algebraic, tutorial:)

(:description Objective function forms for improved rejection of corrupted data with outliers, drift, and noise:)

The dynamic estimation objective function is a mathematical statement that is minimized or maximized to find a best solution among all possible feasible solutions. The form of this objective function is critical to give desirable solutions for model predictions but also for other applications that use the output of a dynamic estimation application.

(:keywords objective function, MATLAB, Simulink, moving horizon, time window, dynamic data, validation, estimation, differential, algebraic, tutorial:)

(:description Objective function forms for improved rejection of corrupted data with outliers, drift, and noise:)

The dynamic estimation objective function is a mathematical statement that is minimized or maximized to find a best solution among all possible feasible solutions. The form of this objective function is critical to give desirable solutions for model predictions but also for other applications that use the output of a dynamic estimation application.