I have a follow up question to the post written a couple days ago, thank you for the previous feedback:
Finding complex roots from set of non-linear equations in python
I have gotten the set non-linear equations set up in python now so that fsolve will handle the real and imaginary parts independently. However, there are still problems with the python "fsolve" converging to the correct solution. I have exactly the same inputs that are used in Matlab, and after double checking, the set of equations are exactly the same as well. Matlab, no matter how I set the initial values, will always converge to the correct solution. With python however, every initial condition produces a different result, and never the correct one. After a fraction of a second, the following warning appears with python:
/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages/scipy/optimize/minpack.py:227:
RuntimeWarning: The iteration is not making good progress, as measured by the
improvement from the last ten iterations.
warnings.warn(msg, RuntimeWarning)
I was wondering if there are some known differences between the fsolve in python and Matlab, and if there are some known methods to optimize the performance in python.
Thank you very much
I don't think that you should rely on the fact that the names are the same. I see from your other question that you are specifying that Matlab's fsolve use the 'levenberg-marquardt' algorithm rather than the default. Python's scipy.optimize.fsolve uses MINPACK's hybrd algorithms. Levenberg-Marquardt finds roots approximately by minimizing the sum of squares of the function and is quite robust. It is not a true root-finding method like the default 'trust-region-dogleg' algorithm. I don't know how the hybrd schemes work, but they claim to be a modification of Powell's method.
If you want something similar to what you're doing in Matlab, I'd look for an optimization scheme that implements Levenberg-Marquardt, such as scipy.optimize.root, which you were also using in your previous question. Is there a reason why you're not using that?
Related
EDIT: Original post too vague. I am looking for an algorithm to solve a large-system, solvable, linear IVP that can handle very small floating point values. Solving for the eigenvectors and eigenvalues is impossible with numpy.linalg.eig() as the returned values are complex and should not be, it does not support numpy.float128 either, and the matrix is not symmetric so numpy.linalg.eigh() won't work. Sympy could do it given an infinite amount of time, but after running it for 5 hours I gave up. scipy.integrate.solve_ivp() works with implicit methods (have tried Radau and BDF), but the output is wildly wrong. Are there any libraries, methods, algorithms, or solutions for working with this many, very small numbers?
Feel free to ignore the rest of this.
I have a 150x150 sparse (~500 nonzero entries of 22500) matrix representing a system of first order, linear differential equations. I'm attempting to find the eigenvalues and eigenvectors of this matrix to construct a function that serves as the analytical solution to the system so that I can just give it a time and it will give me values for each variable. I've used this method in the past for similar 40x40 matrices, and it's much (tens, in some cases hundreds of times) faster than scipy.integrate.solve_ivp() and also makes post model analysis much easier as I can find maximum values and maximum rates of change using scipy.optimize.fmin() or evaluate my function at inf to see where things settle if left long enough.
This time around, however, numpy.linalg.eig() doesn't seem to like my matrix and is giving me complex values, which I know are wrong because I'm modeling a physical system that can't have complex rates of growth or decay (or sinusoidal solutions), much less complex values for its variables. I believe this to be a stiffness or floating point rounding problem where the underlying LAPACK algorithm is unable to handle either the very small values (smallest is ~3e-14, and most nonzero values are of similar scale) or disparity between some values (largest is ~4000, but values greater than 1 only show up a handful of times).
I have seen suggestions for similar users' problems to use sympy to solve for the eigenvalues, but when it hadn't solved my matrix after 5 hours I figured it wasn't a viable solution for my large system. I've also seen suggestions to use numpy.real_if_close() to remove the imaginary portions of the complex values, but I'm not sure this is a good solution either; several eigenvalues from numpy.linalg.eig() are 0, which is a sign of error to me, but additionally almost all the real portions are of the same scale as the imaginary portions (exceedingly small), which makes me question their validity as well. My matrix is real, but unfortunately not symmetric, so numpy.linalg.eigh() is not viable either.
I'm at a point where I may just run scipy.integrate.solve_ivp() for an arbitrarily long time (a few thousand hours) which will probably take a long time to compute, and then use scipy.optimize.curve_fit() to approximate the analytical solutions I want, since I have a good idea of their forms. This isn't ideal as it makes my program much slower, and I'm also not even sure it will work with the stiffness and rounding problems I've encountered with numpy.linalg.eig(); I suspect Radau or BDF would be able to navigate the stiffness, but not the rounding.
Anybody have any ideas? Any other algorithms for finding eigenvalues that could handle this? Can numpy.linalg.eig() work with numpy.float128 instead of numpy.float64 or would even that extra precision not help?
I'm happy to provide additional details upon request. I'm open to changing languages if needed.
As mentioned in the comment chain above the best solution for this is to use a Matrix Exponential, which is a lot simpler (and apparently less error prone) than diagonalizing your system with eigenvectors and eigenvalues.
For my case I used scipy.sparse.linalg.expm() since my system is sparse. It's fast, accurate, and simple. My only complaint is the loss of evaluation at infinity, but it's easy enough to work around.
I am trying to solve an equation that can include truncations in Python with a numerical approach. I am wondering what the best library and approach would be? Following is more detail about the problem:
The equation changes every time. From a human perspective, the equations should be pretty simple; they include common operators such as +,-,*,/, and they also sometimes have truncation functions (truncate to integer) or limit functions (limit the value in parenthesis between two provided bounds) or (rarely) multiple variables. A couple of examples (with these being separate examples and not a system of equations) would be:
TRUNCATE(VAR_1 + 300) - 50.4 = 200
(VAR_2 + VAR_3)*3 = 35
LIMIT(3,5)(VAR_4) = 8
VAR_5 = 34
(This is not exactly what the equations look like, because I am writing them in postfix notation, but I have a calculator to determine their value with provided input values.)
All I need for these equations is some value for each variable that would solve each equation; I do not need to know every solution.
Some additional things to note about this is a) these variables all have maximum and minimum values, b) while perfection would be nice, occasional errors are acceptable, and c) some of the variables are integers, which I expect really complicates things. Right now, I'm handling this very sloppily but also mostly acceptably for my case by rounding the integer values to the nearest int.
In an attempt to solve this problem, I tried solving analytically with Sympy (which as you might expect didn't work on truncations and was difficult to implement), and I also tried using Scipy minimize as follows:
minimize(minimization, x0, method = 'SLSQP', constraints = cons, tol = 1e-3, options={'ftol': 1e-3, 'disp':True, 'maxiter': 100, "eps":.1}, args = (x_vals, postfix, const_values, value))
This one got stuck on truncations, presumably because it didn't know what direction to move, unless I set the step to 1, which decreased accuracy. For some reason, it also didn't seem to follow the ftol, because it would give acceptable answers within the tolerance but would just keep going to the iteration limit.
I am considering using something that does random walks like the "Markov Chain Monte Carlo" method, but I really don't know much about this and was eager to hear other thoughts.
I ended up solving the problem two slightly different ways. Both of them used the Powell solver as suggested by joni in the comments on the original question, and for both of them I had to multiply the output of the function that gets passed to the "fun" parameter (a function that I named minimize) by 100, because I could never get the tolerance adjusted in the solver function call.
When the equation had only one variable, I removed the truncation from the minimize function. This worked for my purposes because the reason the equations I was using was being truncated was so they would equal an integer value (generally). So, when the equation output is an integer and there is only one variable, I believe the correct solution will be obtained by just pretending the truncation function does not exist in the solver (though remember to be wary of floating point math). (And if any numbers outside of the truncation are integers, the equation may not have a solution anyways.)
In cases with multiple variables, my solution was to a) include the truncation function in the minimize function and b) round the x values suggested by the solver as I planned to round them in the end (ex. round them to an integer if they were an integer value).
Anyways, this solution worked for the problem defined above, but it otherwise has some limitations. It is not guaranteed to always find the correct output, especially the second part. Another approach people with this problem may wish to consider would be some sort of integer programming, if they have linear equations.
Is there any place with a brief description of each of the algorithms for the parameter method in the minimize function of the lmfit package? Both there and in the documentation of SciPy there is no explanation about the details of each algorithm. Right now I know I can choose between them but I don't know which one to choose...
My current problem
I am using lmfit in Python to minimize a function. I want to minimize the function within a finite and predefined range where the function has the following characteristics:
It is almost zero everywhere, which makes it to be numerically identical to zero almost everywhere.
It has a very, very sharp peak in some point.
The peak can be anywhere within the region.
This makes many minimization algorithms to not work. Right now I am using a combination of the brute force method (method="brute") to find a point close to the peak and then feed this value to the Nelder-Mead algorithm (method="nelder") to finally perform the minimization. It is working approximately 50 % of the times, and the other 50 % of the times it fails to find the minimum. I wonder if there are better algorithms for cases like this one...
I think it is a fair point that docs for lmfit (such as https://lmfit.github.io/lmfit-py/fitting.html#fit-methods-table) and scipy.optimize (such as https://docs.scipy.org/doc/scipy/reference/tutorial/optimize.html#optimization-scipy-optimize) do not give detailed mathematical descriptions of the algorithms.
Then again, most of the docs for scipy, numpy, and related libraries describe how to use the methods, but do not describe in much mathematical detail how the algorithms work.
In fairness, the different optimization algorithms share many features and the differences between them can get pretty technical. All of these methods try to minimize some metric (often called "cost" or "residual") by changing the values of parameters for the supplied function.
It sort of takes a text book (or at least a Wikipedia page) to establish the concepts and mathematical terms used for these methods, and then a paper (or at least a Wikipedia page) to describe how each method differs from the others. So, I think the basic answer would be to look up the different methods.
i am using the PyOpt module to solve a problem of convex optimization.
The optimization always gives me a result and the value to which it converges looks like it is minimizing my target function, but for different runs of my code i get different solutions.
My problem is convex but not strictly convex, so I'd expect the existence of different solutions, but since the starting point of my algorithm is basically the same for the two runs I was wondering if this could be due to some random procedure in the algorithm I am using.
I am using the slsqp algorithm, does anybody know if it uses any random procedure?
I'm looking for a good library that will integrate stiff ODEs in Python. The issue is, scipy's odeint gives me good solutions sometimes, but the slightest change in the initial conditions causes it to fall down and give up. The same problem is solved quite happily by MATLAB's stiff solvers (ode15s and ode23s), but I can't use it (even from Python, because none of the Python bindings for the MATLAB C API implement callbacks, and I need to pass a function to the ODE solver). I'm trying PyGSL, but it's horrendously complex. Any suggestions would be greatly appreciated.
EDIT: The specific problem I'm having with PyGSL is choosing the right step function. There are several of them, but no direct analogues to ode15s or ode23s (bdf formula and modified Rosenbrock if that makes sense). So what is a good step function to choose for a stiff system? I have to solve this system for a really long time to ensure that it reaches steady-state, and the GSL solvers either choose a miniscule time-step or one that's too large.
If you can solve your problem with Matlab's ode15s, you should be able to solve it with the vode solver of scipy. To simulate ode15s, I use the following settings:
ode15s = scipy.integrate.ode(f)
ode15s.set_integrator('vode', method='bdf', order=15, nsteps=3000)
ode15s.set_initial_value(u0, t0)
and then you can happily solve your problem with ode15s.integrate(t_final). It should work pretty well on a stiff problem.
(See also Link)
Python can call C. The industry standard is LSODE in ODEPACK. It is public-domain. You can download the C version. These solvers are extremely tricky, so it's best to use some well-tested code.
Added: Be sure you really have a stiff system, i.e. if the rates (eigenvalues) differ by more than 2 or 3 orders of magnitude. Also, if the system is stiff, but you are only looking for a steady-state solution, these solvers give you the option of solving some of the equations algebraically. Otherwise, a good Runge-Kutta solver like DVERK will be a good, and much simpler, solution.
Added here because it would not fit in a comment: This is from the DLSODE header doc:
C T :INOUT Value of the independent variable. On return it
C will be the current value of t (normally TOUT).
C
C TOUT :IN Next point where output is desired (.NE. T).
Also, yes Michaelis-Menten kinetics is nonlinear. The Aitken acceleration works with it, though. (If you want a short explanation, first consider the simple case of Y being a scalar. You run the system to get 3 Y(T) points. Fit an exponential curve through them (simple algebra). Then set Y to the asymptote and repeat. Now just generalize to Y being a vector. Assume the 3 points are in a plane - it's OK if they're not.) Besides, unless you have a forcing function (like a constant IV drip), the MM elimination will decay away and the system will approach linearity. Hope that helps.
PyDSTool wraps the Radau solver, which is an excellent implicit stiff integrator. This has more setup than odeint, but a lot less than PyGSL. The greatest benefit is that your RHS function is specified as a string (typically, although you can build a system using symbolic manipulations) and is converted into C, so there are no slow python callbacks and the whole thing will be very fast.
I am currently studying a bit of ODE and its solvers, so your question is very interesting to me...
From what I have heard and read, for stiff problems the right way to go is to choose an implicit method as a step function (correct me if I am wrong, I am still learning the misteries of ODE solvers). I cannot cite you where I read this, because I don't remember, but here is a thread from gsl-help where a similar question was asked.
So, in short, seems like the bsimp method is worth taking a shot, although it requires a jacobian function. If you cannot calculate the Jacobian, I will try with rk2imp, rk4imp, or any of the gear methods.