I have convergence issues for a mixed effects linear model. I would like to dig what is happening during the optimization. Is there a way to get the iteration log? The best I can do now is get a summary of the optimization by setting disp=True
mdf = md.fit(full_output=True,reml=True,method ='cg',disp=True)
which gives me
Warning: Desired error not necessarily achieved due to precision loss.
Current function value: 2.989371
Iterations: 5
Function evaluations: 73
Gradient evaluations: 62
Thanks
UPDATE: this is not answering my question but with a different solver, I managed to get some convergence. However, this is raising another question. I would expect the score, i.e., the gradient of the log-likehood function, to be small and for my example, this is not the case. Hence, another question is:
what can be trusted? Intituively, my answer would be the score
Related
I am using statsmodels.tsa.vector_ar.svar_model.SVAR function. I am not sure if the calculation for residuals ("resid" in the code) is correct because it seems that it does not take the contemporaneous terms into account.
Autoregression methods are based on least square ones and "resid" means Least Square method fitting residuals, not prediction errors.
https://www.statsmodels.org/dev/generated/statsmodels.tsa.ar_model.ARResults.resid.html
In addition, "residual" usually means estimation errors:
https://en.wikipedia.org/wiki/Errors_and_residuals
I have a large scale multi objective optimization problem to solve with fmincon solver of Matlab. I tried different solver to get a better and faster output. Here is the challenge:
I am getting Exit Flag: 1,0,4,5 for different Pareto points ,as it is a multi-objective optimization problem, with Active-set algorithm. Then I tried to check different algorithms like interior-point and sqp for generating the Pareto points. I observed that sqp returns few exit flags 1, some 2 and few 0 but not any 4 or 5 flag. Also, I should note that, its 0 and 2 flagged solutions are correct answers . However, When it comes to return any exit flag except 1, it takes a long time to solve the Pareto point.
As interior-point algorithm is designed for large scale program, it's very faster than sqp in generating the Pareto solutions. However, it only returns solutions with Exit flag 0. Unfortunately, its 0 flagged solutions are wrong solutions despite sqp which its 0 and 2 flagged solutions are correct answers.
0) Is there anyway to config the fmincon to solve my problem with interior-point and also get the correct solutions? In the literature I saw some problems similar to mine have been solved with interior-point algorithm.
1) Is there any settings (TolX,TolCon,...) that I can use to get more exit flag 1 ?
2) Is there any setting that speeds up the optimization process with the cost of lower accuracy?
3) For 2 Pareto points I am getting exit flag -2 , which means the problem is not feasible for them. It is expected from the nature of the problem. But it takes ages for fmincon to determine the Exit-Flag -2. Is there any option that I can set to satisfy 1,2 and also leave this infeasible point faster?
I couldn't do this , because I can only set options for one time and all Pareto points should use the same option.
To describe the problem I should say:
I have several linear and nonlinear (.^2,Sin...) for both equality and inequality constraints (about 300) and also having 400 optimization variables. All objective functions of this multi-objective optimization problem is linear.
these are the options that I currently use. Please help me to modify it
options = optimset('Algorithm', 'sqp', 'Display', 'off');
options = optimset('Algorithm', 'sqp', 'Display', 'off', 'TolX',1e-6,...
'TolFun',1e-6,'MaxIter',1e2, 'MaxFunEvals', 1e4);
First option takes about 500 sec for generating 15 Pareto points. Meaning that each optimization of fmincon expend 33 sec.
The second option takes 200 sec, which is 13 sec for each optimization of fmincon.
Your help will be highly appreciated.
I am trying to learn meta regression using the metafor() package. In running
one of the mixed regression models, I received an error indicating
"There are outcomes with non-positive sampling variances."
I am at lost as to how to proceed with this error. I understand that certain
model statistics (e.g., I^2 and QE) cannot be computed with due to the
presence of non-positive sampling variances. However, I am not sure whether
these results can be interpreted similarly as we would have otherwise. I
also tried using other estimators and/or the unweighted option; the error
still persists.
Any suggestions would be much appreciated.
First of all, to clarify: You are getting a warning, not an error.
Aside from that, I can't think of many situations where it is reasonable to assume that the sampling variance is really equal to 0 in a particular study. I would first question whether this really makes sense. This is why the rma() function is generating this warning message -- to make the user aware of this situation and question whether this really is intended/reasonable.
But suppose that we really want to go through with this, then you have to use an estimator for tau^2 that can handle this (e.g., method="REML" -- which is actually the default). If the estimate of tau^2 ends up equal to 0 as well, then the model cannot be fitted at all (due to division by zero -- and then you get an error). If you do end up with a positive estimate of tau^2, then the results should be okay (but things like the Q-test, I^2, or H^2 cannot be computed then).
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I have a math problem that I can't solve: I don't know how to find the value of n so that
365! / ((365-n)! * 365^n) = 50%.
I am using the Casio 500ms scientific calculator but I don't know how.
Sorry because my question is too easy, I am changing my career so I have to review and upgrade my math, the subject that I have neglected for years.
One COULD in theory use a root-finding scheme like Newton's method, IF you could take derivatives. But this function is defined only on the integers, since it uses factorials.
One way out is to recognize the identity
n! = gamma(n+1)
which will effectively allow you to extend the function onto the real line. The gamma function is defined on the positive real line, though it does have singularities at the negative integers. And of course, you still need the derivative of this expression, which can be done since gamma is differentiable.
By the way, a danger with methods like Newton's method on problems like this is it may still diverge into the negative real line. Choose poor starting values, and you may get garbage out. (I've not looked carefully at the shape of this function, so I won't claim for what set of starting values it will diverge on you.)
Is it worth jumping through the above set of hoops? Of course not. A better choice than Newton's method might be something like Brent's algorithm, or a secant method, which here will not require you to compute the derivative. But even that is a waste of effort.
Recognizing that this is indeed a problem on the integers, one could use a tool like bisection to resolve the solution extremely efficiently. It never requires derivatives, and it will work nicely enough on the integers. Once you have resolved the interval to be as short as possible, the algorithm will terminate, and take vary few function evaluations in the process.
Finally, be careful with this function, as it does involve some rather large factorials, which could easily overflow many tools to evaluate the factorial. For example, in MATLAB, if I did try to evaluate factorial(365):
factorial(365)
ans =
Inf
I get an overflow. I would need to move into a tool like the symbolic toolbox, or my own suite of variable precision integer tools. Alternatively, one could recognize that many of the terms in these factorials will cancel out, so that
365! / (365 - n)! = 365*(365-1)*(365-2)*...*(365-n+1)
The point is, we get an overflow for such a large value if we are not careful. If you have a tool that will not overflow, then use it, and use bisection as I suggested. Here, using the symbolic toolbox in MATLAB, I get a solution using only 7 function evaluations.
f = #(n) vpa(factorial(sym(365))/(factorial(sym(365 - n))*365^sym(n)));
f(0)
ans =
1.0
f(365)
ans =
1.4549552156187034033714015903853e-157
f(182)
ans =
0.00000000000000000000000095339164972764493041114884521295
f(91)
ans =
0.000004634800180846641815683109605743
f(45)
ans =
0.059024100534225072005461014516788
f(22)
ans =
0.52430469233744993108665513602619
f(23)
ans =
0.49270276567601459277458277166297
Or, if you can't take an option like that, but do have a tool that can evaluate the log of the gamma function, AND you have a rootfinder available as MATLAB does...
f = #(n) exp(gammaln(365+1) - gammaln(365-n + 1) - n*log(365));
fzero(#(n) f(n) - .5,10)
ans =
22.7677
As you can see here, I used the identity relating gamma and the factorial function, then used the log of the gamma function, in MATLAB, gammaln. Once all the dirty work was done, then I exponentiated the entire mess, which will be a reasonable number. Fzero tells us that the cross-over occurs between 22 and 23.
If a numerical approximation is ok, ask Wolfram Alpha:
n ~= -22.2298272...
n ~= 22.7676903...
I'm going to assume you have some special reason for wanting an actual algorithm, even though you only have one specific problem to solve.
You're looking for a value n where...
365! / ((365-n)! * 365^n) = 0.5
And therefore...
(365! / ((365-n)! * 365^n)) - 0.5 = 0.0
The general form of the problem is to find a value x such that f(x)=0. One classic algorithm for this kind of thing is the Newton-Raphson method.
[EDIT - as woodchips points out in the comment, the factorial is an integer-only function. My defence - for some problems (the birthday problem among them) it's common to generalise using approximation functions. I remember the Stirling approximation of factorials being used for the birthday problem - according to this, Knuth uses it. The Wikipedia page for the Birthday problem mentions several approximations that generalise to non-integer values.
It's certainly bad that I didn't think to mention this when I first wrote this answer.]
One problem with that is that you need the derivative of that function. That's more a mathematics issue, though you can estimate the derivative at any point by taking values a short distance either side.
You can also look at this as an optimisation problem. The general form of optimisation problems is to find a value x such that f(x) is maximised/minimised. In your case, you could define your function as...
f(x)=((365! / ((365-n)! * 365^n)) - 0.5)^2
Because of the squaring, the result can never be negative, so try to minimise. Whatever value of x gets you the smallest f(x) will also give you the result you want.
There isn't so much an algorithm for optimisation problems as a whole field - the method you use depends on the complexity of your function. However, this case should be simple so long as your language can cope with big numbers. Probably the simplest optimisation algorithm is called hill-climbing, though in this case it should probably be called rolling-down-the-hill. And as luck would have it, Newton-Raphson is a hill-climbing method (or very close to being one - there may be some small technicality that I don't remember).
[EDIT as mentioned above, this won't work if you need an integer solution for the problem as actually stated (rather than a real-valued approximation). Optimisation in the integer domain is one of those awkward issues that helps make optimisation a field in itself. The branch and bound is common for complex functions. However, in this case hill-climbing still works. In principle, you can even still use a tweaked version of Newton-Raphson - you just have to do some rounding and check that you don't keep rounding back to the same place you started if your moves are small.]
I have values returned by unknown function like for example
# this is an easy case - parabolic function
# but in my case function is realy unknown as it is connected to process execution time
[0, 1, 4, 9]
is there a way to predict next value?
Not necessarily. Your "parabolic function" might be implemented like this:
def mindscrew
#nums ||= [0, 1, 4, 9, "cat", "dog", "cheese"]
#nums.pop
end
You can take a guess, but to predict with certainty is impossible.
You can try using neural networks approach. There are pretty many articles you can find by Google query "neural network function approximation". Many books are also available, e.g. this one.
If you just want data points
Extrapolation of data outside of known points can be estimated, but you need to accept the potential differences are much larger than with interpolation of data between known points. Strictly, both can be arbitrarily inaccurate, as the function could do anything crazy between the known points, even if it is a well-behaved continuous function. And if it isn't well-behaved, all bets are already off ;-p
There are a number of mathematical approaches to this (that have direct application to computer science) - anything from simple linear algebra to things like cubic splines; and everything in between.
If you want the function
Getting esoteric; another interesting model here is genetic programming; by evolving an expression over the known data points it is possible to find a suitably-close approximation. Sometimes it works; sometimes it doesn't. Not the language you were looking for, but Jason Bock shows some C# code that does this in .NET 3.5, here: Evolving LINQ Expressions.
I happen to have his code "to hand" (I've used it in some presentations); with something like a => a * a it will find it almost instantly, but it should (in theory) be able to find virtually any method - but without any defined maximum run length ;-p It is also possible to get into a dead end (evolutionary speaking) where you simply never recover...
Use the Wolfram Alpha API :)
Yes. Maybe.
If you have some input and output values, i.e. in your case [0,1,2,3] and [0,1,4,9], you could use response surfaces (basicly function fitting i believe) to 'guess' the actual function (in your case f(x)=x^2). If you let your guessing function be f(x)=c1*x+c2*x^2+c3 there are algorithms that will determine that c1=0, c2=1 and c3=0 given your input and output and given the resulting function you can predict the next value.
Note that most other answers to this question are valid as well. I am just assuming that you want to fit some function to data. In other words, I find your question quite vague, please try to pose your questions as complete as possible!
In general, no... unless you know it's a function of a particular form (e.g. polynomial of some degree N) and there is enough information to constrain the function.
e.g. for a more "ordinary" counterexample (see Chuck's answer) for why you can't necessarily assume n^2 w/o knowing it's a quadratic equation, you could have f(n) = n4 - 6n3 + 12n2 - 6n, which has for n=0,1,2,3,4,5 f(n) = 0,1,4,9,40,145.
If you do know it's a particular form, there are some options... if the form is a linear addition of basis functions (e.g. f(x) = a + bcos(x) + csqrt(x)) then using least-squares can get you the unknown coefficients for the best fit using those basis functions.
See also this question.
You can apply statistical methods to try and guess the next answer, but that might not work very well if the function is like this one (c):
int evil(void){
static int e = 0;
if(50 == e++){
e = e * 100;
}
return e;
}
This function will return nice simple increasing numbers then ... BAM.
That's a hard problem.
You should check out the recurrence relation equation for special cases where it could be possible such a task.