Let's say that we want to fit a nonlinear model to our data (that include measurement errors) with certain constraints on the fit parameters among themselves. Without these constraints, scipy.optimize.curve_fit does the job as it supports by default the optimization of the
chisq = sum((r / sigma) ** 2)
where r is the difference between the true and predicted value. Long story short, the user defines a function and pass it to the solver which minimizes the chisq loss. The situation gets a bit more complex when there are other restrictions imposed on the function parameters, e.g. for a linear model y=ax+b, we can demand a fixed nonlinear condition such as a^2+b=1. A function scipy.optimization.minimize is just what the doctor ordered, provided that we pass the chisq as argument. Below is the code for using minimize found here scipy.optimize with non linear constraints. I'm struggling very hard in building the chisq properly to make the code work. The most general question would how does one defines in the most pythonic way a custom loss that would be minimized?
Help please.
from math import cos, atan
import numpy as np
from scipy.optimize import minimize
def f(x):
return 0.1 * x[0] * x[1]
def ineq_constraint(x):
return x[0]**2 + x[1]**2 - (5. + 2.2 * cos(10 * atan(x[0] / x[1])))**2
con = {'type': 'ineq', 'fun': ineq_constraint}
x0 = [1, 1]
res = minimize(f, x0, method='SLSQP', constraints=con)
Since we minimize the chisq function that is found by optimizing our targeted function, I guess the chisq will be defined in a very elegant way in a form of a wrapper since for arguments it takes the targeted function, a column of true values and a column of uncertanties e.g.
chisq(target_function, (y, y_err)).
Related
I'm trying to get a single element of an adjugate A_adj of a matrix A, both of which need to be symbolic expressions, where the symbols x_i are binary and the matrix A is symmetric and sparse. Python's sympy works great for small problems:
from sympy import zeros, symbols
size = 4
A = zeros(size,size)
x_i = [x for x in symbols(f'x0:{size}')]
for i in range(size-1):
A[i,i] += 0.5*x_i[i]
A[i+1,i+1] += 0.5*x_i[i]
A[i,i+1] = A[i+1,i] = -0.3*(i+1)*x_i[i]
A_adj_0 = A[1:,1:].det()
A_adj_0
This calculates the first element A_adj_0 of the cofactor matrix (which is the corresponding minor) and correctly gives me 0.125x_0x_1x_2 - 0.28x_2x_2^2 - 0.055x_1^2x_2 - 0.28x_1x_2^2, which is the expression I need, but there are two issues:
This is completely unfeasible for larger matrices (I need this for sizes of ~100).
The x_i are binary variables (i.e. either 0 or 1) and there seems to be no way for sympy to simplify expressions of binary variables, i.e. simplifying polynomials x_i^n = x_i.
The first issue can be partly addressed by instead solving a linear equation system Ay = b, where b is set to the first basis vector [1, 0, 0, 0], such that y is the first column of the inverse of A. The first entry of y is the first element of the inverse of A:
b = zeros(size,1)
b[0] = 1
y = A.LUsolve(b)
s = {x_i[i]: 1 for i in range(size)}
print(y[0].subs(s) * A.subs(s).det())
print(A_adj_0.subs(s))
The problem here is that the expression for the first element of y is extremely complicated, even after using simplify() and so on. It would be a very simple expression with simplification of binary expressions as mentioned in point 2 above. It's a faster method, but still unfeasible for larger matrices.
This boils down to my actual question:
Is there an efficient way to compute a single element of the adjugate of a sparse and symmetric symbolic matrix, where the symbols are binary values?
I'm open to using other software as well.
Addendum 1:
It seems simplifying binary expressions in sympy is possible with a simple custom substitution which I wasn't aware of:
A_subs = A_adj_0
for i in range(size):
A_subs = A_subs.subs(x_i[i]*x_i[i], x_i[i])
A_subs
You should make sure to use Rational rather than floats in sympy so S(1)/2 or Rational(1, 2) rather than 0.5.
There is a new (undocumented and for the moment internal) implementation of matrices in sympy called DomainMatrix. It is likely to be a lot faster for a problem like this and always produces polynomial results in a fully expanded form. I expect that it will be much faster for this kind of problem but it still seems to be fairly slow for this because is is not sparse internally (yet - that will probably change in the next release) and it does not take advantage of the simplification from the symbols being binary-valued. It can be made to work over GF(2) but not with symbols that are assumed to be in GF(2) which is something different.
In case it is helpful though this is how you would use it in sympy 1.7.1:
from sympy import zeros, symbols, Rational
from sympy.polys.domainmatrix import DomainMatrix
size = 10
A = zeros(size,size)
x_i = [x for x in symbols(f'x0:{size}')]
for i in range(size-1):
A[i,i] += Rational(1, 2)*x_i[i]
A[i+1,i+1] += Rational(1, 2)*x_i[i]
A[i,i+1] = A[i+1,i] = -Rational(3, 10)*(i+1)*x_i[i]
# Convert to DomainMatrix:
dM = DomainMatrix.from_list_sympy(size-1, size-1, A[1:, 1:].tolist())
# Compute determinant and convert back to normal sympy expression:
# Could also use dM.det().as_expr() although it might be slower
A_adj_0 = dM.charpoly()[-1].as_expr()
# Reduce powers:
A_adj_0 = A_adj_0.replace(lambda e: e.is_Pow, lambda e: e.args[0])
print(A_adj_0)
When solving models sequentially in Python GEKKO (i.e. with IMODE >= 4) fails when using the max2 and max3 functions that come with GEKKO.
This is for use cases, where np.maximum or the standard max function treat a GEKKO parameter like an array, which is not always the intended usage or can create errors when comparing against integers for example.
minimal code example:
from gekko import GEKKO
import numpy as np
m = GEKKO()
m.time = np.arange(0,20)
y = m.Var(value=5)
forcing = m.Param(value=np.arange(-5,15))
m.Equation(y.dt()== m.max2(forcing,0) * y)
m.options.IMODE=4
m.solve(disp=False)
returns:
Exception: #error: Degrees of Freedom
* Error: DOF must be zero for this mode
STOPPING...
I know from looking at the code that both max2 and max3 use inequality expressions in the equations, which understandably introduces the degrees of freedoms, so was this functionality never intended? Could there be some workaround to fix this?
Any help would be much appreciated!
Note:
I hope this is not a duplicate of How to define maximum of Intermediate and another value in Python Gekko, when using sequential solver?, but instead asking a more concise & different question, about essentially the same issue.
You can get a successful solution by switching to IMODE=6. IMODE=4 (simultaneous simulation) or IMODE=7 sequential simulation requires zero degrees of freedom. Both m.max2() and m.max3() require degrees of freedom and an optimizer to solve.
from gekko import GEKKO
import numpy as np
m = GEKKO(remote=False)
m.time = np.arange(0,20)
y = m.Var(value=5)
forcing = m.Param(value=np.arange(-5,15))
m.Equation(y.dt()== -m.max2(forcing,0) * y)
m.options.IMODE=6
m.solve(disp=True)
The equation y.dt()== -m.max2(forcing,0) * y exponentially increases beyond machine precision so I switched the equation to something that can solve.
I try to solve some matrix calculus problem with sympy and get stuck at the solver after differentiation with respect to a vector.
As a short example let's take ordinary least squares regression.
E.g. the sum of the squared differences between target y and prediction y_hat. Where the prediction y_hat = X.T * w is linear combination and thus a matrix vector multiplication.
We therefore want to minimize the LMS Error with respect to the weight vector w.
By hand we can derive that from:
Err(w) = norm(y - X.T * w)^2
follows after differentiation, setting to zero and solving for w
w_opt = (X*X.T)^-1 * X * y
How can we derive w_opt using sympy?
My rather naïve approach was:
from sympy import *
# setup matrix and vectors
X = MatrixSymbol('X',3,5)
y = MatrixSymbol('y',5,1)
w = MatrixSymbol('w',3,1)
# define error function
E = (y - X.T*w).T * (y - X.T*w)
# derivate
Edw = [E.diff(wi) for wi in w]
# solve for w
solve(Edw,w)
At solve(Edw,w) however i get the attribute error: 'Mul' object has no attribute 'shape'
I also tried to set E.as_explicit() before differentiating. This however resultet in the attribute error: 'str' object has no attribute 'is_Piecewise'
I know by calculating by hand, that after derivation the result should be -2*X*y + 2*X*X.T*w. The derivation in Edw is listed but not performed. How can I verify this step in between? My first guess was the .doit() method, which unfortunately is not defined in that case.
I am currently working on some MatLab code to fit experimental data to a sum of exponentials following a method described in this paper.
According to the paper, the data has to follow the following equation (written in pseudo-code):
y = sum(v(i)*exp(-x/tau(i)),i=1..n)
Here tau(i) is a set of n predefined constants. The number of constants also determines the size of the summation, and hence the size of v. For example, we can try to fit a sum of 100 exponentials, each with a different tau(i) to our data. However, due to the nature of the fitting and the exponential sum, we need to add another constraint to the problem, and hence to the cost function of the least-squares method used.
Normally, the cost function of the least-squares method is given by:
(y_data - sum(v(i)*exp(-x/tau(i)),i=1..n)^2
And this has to be minimized. However, to prevent over-fitting that would make the time-constant spectrum extremely noisy, the paper adds the following constraint to the cost function:
|v(i) - v(i+1)|^2
Because of this extra constraint, as far as I know, the regular algorithms, like lsqcurvefit aren't useable any longer, and I have to use fminsearch to search the minimum of my least-squares cost function with a constraint. The function that has to be minimized, according to me, is the following:
(y_data - sum(v(i)*exp(-x/tau(i)),i=1..n)^2 + sum(|v(j) - v(j+1)|^2,j=1..n-1)
My attempt to code this in MatLab is the following. Initially we define the function in a function script, then we use fminsearch to actually minimize the function and get values for v.
function res = funcost( v )
%FUNCOST Definition of the function that has to be minimised
%We define a function yvalues with 2 exponentials with known time-constants
% so we know the result that should be given by minimising.
xvalues = linspace(0,50,10000);
yvalues = 3-2*exp(-xvalues/1)-exp(-xvalues/10);
%Definition of 30 equidistant point in the logarithmic scale
terms = 30;
termsvector = [1:terms];
tau = termsvector;
for i = 1:terms
tau(i) = 10^(-1+3/terms*i);
end
%Definition of the regular function
res_1 = 3;
for i=1:terms
res_1 =res_1+ v(i).*exp(-xvalues./tau(i));
end
res_1 = res_1-yvalues;
%Added constraint
k=1;
res_2=0;
for i=1:terms-1
res_2 = res_2 + (v(i)-v(i+1))^2;
end
res=sum(res_1.*res_1) + k*res_2;
end
fminsearch(#funcost,zeros(30,1),optimset('MaxFunEvals',1000000,'MaxIter',1000000))
However, this code is giving me inaccurate results (no error, just inaccurate results), which leads me to believe I either made a mistake in the coding or in the interpretation of the added constraint for the least-squares method.
I would try to introduce the additional constrain in following way:
res_2 = max((v(1:(end-1))-v(2:end)).^2);
e.g. instead of minimizing an integrated (summed up) error, it does minmax.
You may also make this constrain stiff by
if res_2 > some_number
k = a_very_big_number;
else
k=0; % or k = a_small_number
end;
I have a value type that represents a gaussian distribution:
struct Gauss {
double mean;
double variance;
}
I would like to perform an integral over a series of these values:
Gauss eulerIntegrate(double dt, Gauss iv, Gauss[] values) {
Gauss r = iv;
foreach (Gauss v in values) {
r += v*dt;
}
return r;
}
My question is how to implement addition for these normal distributions.
The multiplication by a scalar (dt) seemed simple enough. But it wasn't simple! Thanks FOOSHNICK for the help:
public static Gauss operator * (Gauss g, double d) {
return new Gauss(g.mean * d, g.variance * d * d);
}
However, addition eludes me. I assume I can just add the means; it's the variance that's causing me trouble. Either of these definitions seems "logical" to me.
public static Gauss operator + (Gauss a, Gauss b) {
double mean = a.mean + b.mean;
// Is it this? (Yes, it is!)
return new Gauss(mean, a.variance + b.variance);
// Or this? (nope)
//return new Gauss(mean, Math.Max(a.variance, b.variance));
// Or how about this? (nope)
//return new Gauss(mean, (a.variance + b.variance)/2);
}
Can anyone help define a statistically correct - or at least "reasonable" - version of the + operator?
I suppose I could switch the code to use interval arithmetic instead, but I was hoping to stay in the world of prob and stats.
The sum of two normal distributions is itself a normal distribution:
N(mean1, variance1) + N(mean2, variance2) ~ N(mean1 + mean2, variance1 + variance2)
This is all on wikipedia page.
Be careful that these really are variances and not standard deviations.
// X + Y
public static Gauss operator + (Gauss a, Gauss b) {
//NOTE: this is valid if X,Y are independent normal random variables
return new Gauss(a.mean + b.mean, a.variance + b.variance);
}
// X*b
public static Gauss operator * (Gauss a, double b) {
return new Gauss(a.mean*b, a.variance*b*b);
}
To be more precise:
If a random variable Z is defined as the linear combination of two uncorrelated Gaussian random variables X and Y, then Z is itself a Gaussian random variable, e.g.:
if Z = aX + bY,
then mean(Z) = a * mean(X) + b * mean(Y), and variance(Z) = a2 * variance(X) + b2 * variance(Y).
If the random variables are correlated, then you have to account for that. Variance(X) is defined by the expected value E([X-mean(X)]2). Working this through for Z = aX + bY, we get:
variance(Z) = a2 * variance(X) + b2 * variance(Y) + 2ab * covariance(X,Y)
If you are summing two uncorrelated random variables which do not have Gaussian distributions, then the distribution of the sum is the convolution of the two component distributions.
If you are summing two correlated non-Gaussian random variables, you have to work through the appropriate integrals yourself.
Well, your multiplication by scalar is wrong - you should multiply variance by the square of d. If you're adding a constant, then just add it to the mean, the variance stays the same. If you're adding two distributions, then add the means and add the variances.
Can anyone help define a statistically correct - or at least "reasonable" - version of the + operator?
Arguably not, as adding two distributions means different things - having worked in reliability and maintainablity my first reaction from the title would be the distribution of a system's mtbf, if the mtbf of each part is normally distributed and the system had no redundancy. You are talking about the distribution of the sum of two normally distributed independent variates, not the (logical) sum of two normal distributions' effect. Very often, operator overloading has surprising semantics. I'd leave it as a function and call it 'normalSumDistribution' unless your code has a very specific target audience.
Hah, I thought you couldn't add gaussian distributions together, but you can!
http://mathworld.wolfram.com/NormalSumDistribution.html
In fact, the mean is the sum of the individual distributions, and the variance is the sum of the individual distributions.
I'm not sure that I like what you're calling "integration" over a series of values. Do you mean that word in a calculus sense? Are you trying to do numerical integration? There are other, better ways to do that. Yours doesn't look right to me, let alone optimal.
The Gaussian distribution is a nice, smooth function. I think a nice quadrature approach or Runge-Kutta would be a much better idea.
I would have thought it depends on what type of addition you are doing. If you just want to get a normal distribution with properties (mean, standard deviation etc.) equal to the sum of two distributions then the addition of the properties as given in the other answers is fine. This is the assumption used in something like PERT where if a large number of normal probability distributions are added up then the resulting probability distribution is another normal probability distribution.
The problem comes when the two distributions being added are not similar. Take for instance adding a probability distribution with a mean of 2 and standard deviation of 1 and a probability distribution of 10 with a standard deviation of 2. If you add these two distributions up, you get a probability distribution with two peaks, one at 2ish and one at 10ish. The result is therefore not a normal distibution. The assumption about adding distributions is only really valid if the original distributions are either very similar or you have a lot of original distributions so that the peaks and troughs can be evened out.