EASY-FIT: A Software System For Data Fitting in Dynamic Systems
EASY-FIT: A Software System For Data Fitting in Dynamic Systems
EASY-FIT: A Software System For Data Fitting in Dynamic Systems
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1 author:
Klaus Schittkowski
University of Bayreuth
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Introduction
Data fitting plays an important role in many natural science, engineering and
other disciplines. The key idea is to estimate unknown parameters in a mathematical model that describes a real life situation, by minimizing the distance
of some known experimental data from the theoretical model function values. Thus also model parameters that cannot be measured directly, can be
73
76
j = 1, ..., me ,
j = me + 1, ..., m ,
.
(1)
Here we assume that the parameter vector p is n-dimensional and that all
nonlinear functions are continuously differentiable with respect to p. Upper
and lower bounds are treated independently from the remaining constraints.
All least squares parameter estimation algorithms proceed from the above
formulation, although in the one or other case different approaches are available to define the objective functions. The assumption, that all problem functions must be smooth, is essential. The efficient numerical algorithms under
consideration are based more or less on the Gauss-Newton method, that requires first derivatives.
Alternatively the L 2 -norm may be changed to the L 1 -norm, i.e.,
l
min i=1 |fi (p)|
gj (p) = 0 ,
p IRn : gj (p) 0 ,
pl p pu
j = 1, ..., me ,
j = me + 1, ..., m ,
(2)
j = 1, ..., me ,
j = me + 1, ..., m ,
.
(3)
77
78
(4)
where nt time values, nc concentration values and n t nc r corresponding experimental measurement values are defined. Together with a vector-valued
model function
h(p, t, c) = (h1 (p, t, c), . . . , hr (p, t, c))T ,
we get the above least squares formulation by
k
k
(hk (p, ti , cj ) yij
),
fs (p) = wij
(5)
(6)
79
= 0 ,
sm (p, z, t) = 0 .
(7)
(8)
h(p, t, c) =
i ln 2
ln 2
, c) .
vi H(p,
t i=1
t
(9)
(10)
(11)
Without loss of generality we assume that the initial time is zero. The
initial values of the differential equation system y 10 (p, c), . . ., ys0 (p, c) may
depend on one or more of the system parameters to be estimated, and on the
concentration parameter c.
There are many practical situations where a model changes during integration over the time variable, and where initial values are to be adopted.
A typical example is a pharmacokinetic application with an initial infusion
and subsequent applications of drug doses by injection. In a formal way we
describe the model changes by
81
y 10 =
y s0 =
(12)
for 0 t 1 and
y 1i = F1i (p, y i , t, c) , y1i (i ) = y i1 (p, c, y1i1 (p, i , c)) ,
(13)
= 0 , j = 1, ..., me ,
0 , j = me + 1, ..., m
(14)
are allowed, where the restriction functions may depend on the solution of the
dynamic system at predetermined time and concentration values, i.e.
gj (p) = gj (p, y(p, tj , cj ), tj , cj )
(15)
interval must coincide with the initial value of the subsequent one. A special
advantage is that starting values needed for the optimization algorithm are
easily obtained from the measurement values, see Bock [7].
F1 (p, y, z, t, c)
y s1 = Fs1 (p, y, z, t, c)
0=
G1 (p, y, z, t, c)
0=
Gs2 (p, y, z, t, c)
(16)
Now y(p, t, c) and z(p, t, c) are solution vectors of a joint system of s 1 +s2
differential and algebraic equations (DAE). The system is called an index-1problem or an index-1-DAE, if the algebraic equations can be solved w.r.t. z,
i.e. if the matrix
z G(p, y, z, t, c)
(17)
possesses full rank. In all other cases we get DAEs with a higher index, see
e.g. Hairer and Wanner [18] for a suitable definition and more details.
Similar to systems of ordinary differential equations, it is possible to define
switching or break points, and to modify initial values at these points, that
may depend on the parameters to be estimated, the concentration variable
and the solution w.r.t. the previous interval.
For simplicity we consider now only problems of index one, although the
numerical algorithms are capable to treat also higher index models. Moreover
problems with higher index can be transformed to problems of index one by
successive differentiation of the algebraic equations.
We have to be very careful when defining the inital values of the model,
since they must satisfy the consistency equation
G1 (p, y 0 (p, c), z 0 (p, c), t, c) = 0 ,
...
Gs2 (p, y 0 (p, c), z 0 (p, c), t, c) = 0 .
(18)
Here the intial values y 10 (p, c), . . . , ys01 (p, c) and z10 (p, c), . . . , zs02 (p, c) are
functions depending on the parameters to be estimated, and the concentration
variable as declared by the user.
83
= 0, j = 1, ..., me ,
0, j = me + 1, ..., m
(19)
are allowed, where the restriction functions may depend on the solution of the
dynamic system at predetermined time and concentration values, i.e.
gj (p) = g j (p, y(p, tj , cj ), z(p, tj , cj ), tj , cj )
(20)
for j = 1, ..., m.
As in case of ODEs, also the shooting technique and internal numerical
evaluation of gradients can be applied.
(21)
(23)
uL (t, p) ,
una (xR , t, p)
uR (t, p) ,
u1x (xL , t, p)
u
L (t, p) ,
unx a (xR , t, p)
u
R (t, p)
(24)
i+1 a
cR
(xi , t, p), p) ,
i (t, u
ui+1 (xai , t, p)
i a
cL
i (t, u (xi , t, p), p) ,
uix (xai , t, p)
i+1 a
a
cR
(xi , t, p), ui+1
x (xi , t, p), p) ,
i (t, u
a
ui+1
x (xi , t, p)
i a
i
a
cL
i (t, u (xi , t, p), ux (xi , t, p), p)
(25)
85
(27)
(28)
that may depend again on the parameters to be estimated. The system has
no components, i.e. v = (v 1 , . . . , vno )T . Coupling of ordinary differential
equations is allowed at arbitrary points within the integration interval and the
corresponding area is denoted by the index i j . The spatial variable value
xj belongs to the j-th area, i.e. x j [xaij 1 , xaij ) or xj [xana 1 , xana ],
respectively, j = 1, . . . , no , and is called coupling point.
Coupling points are rounded to their nearest line when discretizing the
system. The right-hand side of the coupling equation may depend on the corresponding solution of the partial differential equation and its first and second
derivative w.r.t. the space variable at the coupling point under consideration.
Similar to systems of ordinary differential equations, it is possible to define
break points and modified initial values at these points, that may depend on
the parameters to be estimated, the spatial variable and the solution w.r.t. the
previous interval.
To indicate that the fitting criteria h k (p, t) depend also on the solution of
the differential equation at the corresponding fitting point, where k denotes
the index of a measurement set, we use the notation
k
(xk , t, p))
hk (p, t) = hk (p, t, v(t, p), uik (xk , t, p), uixk (xk , t, p), uixx
(29)
and insert hk instead of hk into the data fitting function. Again the fitting criteria may depend on solution values at a given spatial variable value w.r.t. to
an integration interval defined by the index
variable
i k . The spatial
xk belongs
to the ik -th integration area, i.e. x k xaik 1 , xaik or xk xana 1 , xana ,
respectively, k = 1, . . . , r, where r denotes the total number of measurement
sets. The fitting criterion may depend on the solution of the partial differential equation and its first and second derivative w.r.t. the space variable at the
86
fitting point. Fitting points are rounded to their nearest line when discretizing
the system.
As for ordinary differential equations, dynamic constraints of the form
gj (p) = 0 , j = 1, ..., me ,
gj (p) 0 , j = me + 1, ..., m
(30)
are allowed, where the restriction functions may depend on the solution of the
partial differential equation and its first and second spatial derivatives at predetermined time and spatial values, and the solution of the coupled ordinary
differential equation at predetermined time values, i.e.
k
(xj , tj , p))
gj (p) = g j (xj , tj , p, v(tj , p), ujk (xj , tj , p), ujxk (xj , tj , p), ujxx
(31)
for j = 1, ..., m. Here u jk denotes the corresponding integration area that
contains the spatial parameter x j . The m predetermined time values must
coincide with some of the given measurement values. If not, the given data are
rounded to the nearest experimental data. The corresponding spatial values
must coincide with a line obtained by the equidistant discretization of the
underlying integration interval.
In order to achieve smooth fitting criteria and constraints, we assume that
all model functions depend continuously differentiable on the parameter vector p. Moreover we assume that the discretized system of differential equations is uniquely solvable for all p with p l p pu . A collection of 20
examples of partial differential equations that can be solved by the presented
approach, and comparative numerical results are found in Schittkowski [36].
=
=
f1 (x, t, u1 , u2 , p) ,
f2 (x, t, u1 , u2 , p) ,
87
Numerical Algorithms
90
Note that only DFNLP is able to take linear or nonlinear constraints into
account. However all other algorithms satisfy upper and lower bounds of the
parameters to be estimated. The algorithms are also capable to solve problems
with large residuals.
The choice of algorithm NELDER is only useful when the other algorithms
fail because of non-differentiable model functions, a very bad starting point
or large round-off errors in the function evaluation.
coefficients
min(i,q)
vi := (1)q+i
k=(i+1)/2
k q+1 (2k)!
,
(q k)!k!(k 1)!(i k)!(2k i)!
(35)
which are independent of H and which can be evaluated before starting the
main procedure, where function values are to be computed. Then
2q
h(p, t, c) =
ln 2
i ln 2
, c)
vi H(p,
t i=1
t
(36)
DOP853
ODEX
RADAU5
SDIRK4
SEULEX
IND-DIR
92
Note that the first six codes use dense output, i.e. the integration is performed over the whole interval given by first and last time value, and intermediate solution values are interpolated. In these cases gradients w.r.t. parameters to be estimated, are obtained by external numerical differentiation.
The codes RADAU5, SDIRK4 and SEULEX are able to solve also stiff equations.
The last algorithm IND-DIR is capable to evaluate derivatives of the solution of the ODE internally w.r.t. the parameters to be estimated, i.e. by
analytical differentiation of the Runge-Kutta scheme.
It is possible that the right-hand side of an ODE is non-continuous w.r.t.
integration time, e.g. if non-continuous input functions exist. Especially in
case of short peaks, the integration routine might not realize the peak at all
because of a big time step. Moreover the numerical approximation of gradients could become unstable in case of discontinuities. Thus MODFIT allows
to supply an optional number of time values, so-called break points, where
the integration of the ODE is restarted with initial tolerances, e.g. with the
initially given stepsize. The integration in the preceeding interval is stopped
at the time value given minus a relative error in the order of the machine
precision.
Restarts of the integration routine are needed only for the codes DOPRI5,..., SEULEX because of their dense output facilities. In case of
IND-DIR, the integration is restarted at each experimental time value. By
introducing artificial time values with zero weight, additional restarts at discontinuities can be simulated easily. Note also that break points can be treated
as optimization variables, i.e. may vary from one iteration step to the other.
DAEs with an index higher than one can be solved only by RADAU5. If
consistent initial values cannot be provided by the user, the corresponding
nonlinear system of equations is treated as general nonlinear programming
problem with equality constraints. A minimum norm solution is computed
93
(37)
xa
j
xa
j1
ui (x, t, p)dx ,
where the integral is taken over the j-th area where the PDE is defined, j =
1, . . . , na , and where i = 1, . . . , n p . The integral is evaluated by Simpsons
rule and and can be retrieved from a common block or, alternatively, through
a special construct of the PCOMP language.
Case Study
cm
cim
2 cm
cm
(x, t) + im
(x, t) = m Dm
(x, t)
(x, t) m Vm
2
t
t
x
x
cim
(x, t) = (cm (x, t) cim (x, t))
im
t
Dm cm
(L, t) = 0
Vm x
for 0 t 2.55. Initial conditions are c m (x, 0) = 0 and cim (x, 0) = 0 for
0 < x < L.
Here we are interested in fitting the function
h(p, t) = cm ( 12 L, t)
Dm cm 1
( L, t)
Vm x 2
REAL CONSTANT
t0 = 0.0104167
C0 = 5800
Vm = 100
C
C-----------------------------------------------------C
*
VARIABLE
Tm, Dm, alpha
Cim, Cm, Cim_x, Cm_x, Cim_xx, Cm_xx
x, t
C
C-----------------------------------------------------C
*
FUNCTION Cim_t
Tim = 1 - Tm
Cim_t = alpha/Tim*(Cm - Cim)
C
*
FUNCTION Cm_t
Cm_t = Dm*Cm_xx - Vm*Cm_x - alpha/Tm*(Cm - Cim)
C
C-----------------------------------------------------C
*
FUNCTION Cim0
Cim0 = 0.0
C
*
FUNCTION Cm0
Cm0 = 0.0
C
C------------------------------------------------------
99
C
*
C
*
FUNCTION Cm_x_left
IF (t.LT.t0) THEN
Cm_x_left = (Cm - C0)*Vm/Dm
ELSE
Cm_x_left = Cm*Vm/Dm
ENDIF
FUNCTION Cm_x_right
Cm_x_right = -Cm*Vm/Dm
C
C-----------------------------------------------------C
*
FUNCTION Cm_fit
Cm_fit = Cm - Dm/Vm*Cm_x
C
C-----------------------------------------------------C
*
END
Parameters to be estimated are m , , and Dm . Initial and final optimization parameters are shown in the subsequent table together with their significance intervals subject to a significance level of 5 %.
parameter
initial value
final value
m
Dm
0.5
100.0
1.0
0.347704
348.981
3.86361
confidence interval
lower
upper
0.337491 0.357818
326.485
371.476
3.39786
4.32936
25 lines are used to discretize the spatial interval. The resulting system
of 50 ordinary differential equations is solved by RADAU5 subject to an error tolerance of RELERR=ABSERR=1.0D-6. After 24 iterations the least
squares code DN2GB computes the scaled residual value 0.0067, see Figure
4.2. The corresponding surface plots for mobile and immobile part are shown
in Figure 4.2. Statistical significance intervals are quite tight at least subject
to the first two parameters.
A couple of typical screen shots of EASY-FIT for generating a new model,
starting an optimization run, and interpreting results are shown in figures 1 to
6 on pages 76, 78 and 90.
100
50
data 2
222222
2
2
fit
criterion
2
2
22 2 22222222
2
2
2222
2 22
2 222
222
22
22
2
22 2222
2 2 2222222
2
2 2 222
22222
22
2222
2222222
2
45
40
h(p, t)
35
30
25
20
15
10
5
0
0
0.5
1.5
t
2.5
Software Organization
PDEFIT
parameter estimation in explicit functions, steady-state systems, Laplace transforms, ordinary differential and differential algebraic equations
parameter estimation in one-dimensional, time-dependent
partial differential algebraic equations
EASY-FIT requires a lot of system resources to run in a smooth and efficient way. Especially the run time system of the MS-Access 97 1 database
needs as much CPU memory as possible. Recommended hardware is a Pentium processor with 32 MB memory on board and at least 200 MHz. A full
installation requires about 40 MB on hard disk. The system runs under Windows 95 and Windows NT.
EASY-FIT comes with the run-time and royalty-free version of MSAccess. Plots are generated either by internal plot facilities or optionally by
the external graphic systems MS-Graph5 and GNUPLOT 2 . Numerical data
1 MS,
2 1986-93
c
101
model function
cm (x, t)
100
50
0
0 10
20
30 40
50
x
60 70
80
0.5
1.5
2.5
model function
cim (x, t)
100
50
0
0 10
20
30 40
50
x
60 70
80
0.5
102
1.5
t
2.5
describing problems and models are kept in a separate database with file
name EASY_DAT.MDB to allow easier maintenance and updates.
Parameter estimation problems are solvable without a Fortran compiler, if
the model functions are defined in form of the PCOMP modeling language.
In this case nonlinear model functions are interpreted and evaluated during
run time together with their derivatives. The full version of EASY-FIT allows
also the most flexible input of the underlying model in form of Fortran code,
and has an interface for the Watcom F77/386 3, the Salford FTN77 4 , the Lahey
F77L-EM/32, and the Microsoft Fortran PowerStation 5 compiler, where the
compiler and linker options can be altered and adapted to special needs.
To install EASY-FIT, one has to insert the CD-ROM and to execute the
setup program SETUP.EXE. Installation assumes that the run-time version of
MS-Access 97 is to be loaded together with EASY-FIT (typical and custom
setup).
EASY-FIT is delivered with Fortran source codes for the main numerical
codes MODFIT.FOR and PDEFIT.FOR, and for interfaces to the PCOMP interpreter in the files MODFITEX.FOR and PDEFITEX.FOR, respectively. It
is then possible to link numerical algorithms with user-provided dimensioning parameters or to solve problems where model functions are defined in
form of a Fortran code. These files together with additional object codes of
internal numerical algorithms e.g. for solving the optimization problem or
for integrating differential equations, are copied to a separate directory by the
setup program, if required by the user. If the submitted default compiler interface is to be changed e.g. from the Watcom to Salford or Lahey compiler,
one has to set the corresponding compiler name, some path names, and the
compiler and linker execution commands.
For more information about EASY-FIT and its capabilities, contact the
author under
klaus.schittkowski@uni-bayreuth.de
A demo version is available through the URL
http://www.uni-bayreuth.de/departments/math/kschittkowski/home.htm
3 WATCOM
103
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