Kuramoto in Stan (PyStan)

tl;dr: Project on github: https://github.com/laszukdawid/pystan-kuramoto


Stan is a programming language focused on probabilistic computations. Although it’s a rather recent language it’s been nicely received in data science/Bayesian community for its focus on designing model, rather than programming and getting stuck with computational details. Depending what is your background you might have heard about it either from Facebook and its Prophet project or as a native implementation for Hamiltonian Monte Carlo (HMC) and its optimised variation – No-U-Turn Sampler for HMC (NUTS).

For ease of including models in other programmes there are some interfaces/wrappers available, including RStan and PyStan.

Stan is not the easiest language to go through. Currently there are about 600 pages of documentation and then separate “documentations” for wrappers, which for PyStan isn’t very helpful. Obviously there’s no need for reading all of it, but it took me a while to actually understand what goes where an why. The reward, however, is very satisfying.

Since I’ve written a bit about Kuramoto models on this blog, it’s consistent if I share its implementation in Stan as well. Pystan-kuramoto project uses PyStan, but the actual Stan code is platform independent.

Currently there are two implementations (couldn’t come up with better names):

  • All-to-all, where Kuramoto model fit is performed to phase vector \vec{\Phi} with distinct oscillators, i.e. \vec{\Phi}_{N}(t) = \{\phi_1(t), \phi_2(t), \dots, \phi_N(t)\}.
  • All-to-one, where the model fits superposition (sum) of oscillators to phase time series \Phi_{N}(t) = \sum_{n=1}^{N} \phi_n(t).

In all honesty, this seems to be rather efficient. Optimisation is performed using penalized maximum likelihood estimation with optimization (L-BFGS). Before using it I wasn’t very knowledgeable in the algorithm, but now I’m simply amazed with its speed and accuracy. Thumbs up.

Particle Swarm Optimisation in Python

[Updated version available. See newest post.]

tl;dr: For Python PSO code head to codes subpage.

One might expect, that currently there is everything on the internet and it’s only a matter of time to find something of an interest. At least that’s what I expected. Unfortunately, sometimes finding the right thing and adjusting it to your own problem can take much more time that doing it yourself. This is a rule about which I often forget. And it happened again. I was suggested to try Particle Swarm Optimisation (PSO) for my problem. Since it has been some time since the introduction of that method, and since Python is a quite popular language, I expected that finding code to just do that wouldn’t be a problem. True, it wasn’t hard for few entries, but either software used some obsolete packages, or it was difficult to install it, or the instructions weren’t clearly (to me) written. Thus, after about 2 days of trying to figure out everything and apply it to my problem, I simply gave up. That is, gave up searching and wrote my own code. In about 2 h.

What is Particle Swarm Optimisation (PSO)? Wikipedia gives quite comprehensive explanation, with a long list of references on this subject. However, in just few words: PSO is a metaheuristic, meaning that it does not require any a priori knowledge on gradient or on space. It is an optimisation method with many units (particles) looking independently for the best solution. Each particle updates its position (set of parameters) depending on its velocity vector, the best position it found during search and the best position discovered by any particle in swarm. Algorithm makes all particles go towards the best known solution, however, it does not guarantee that the solution will be globally optimal.

Algorithm depends on: initial positions \vec{P}_0, initial velocities \vec{V}_0, acceleration ratio \omega and influence variable of the best global \phi_g and the best local \phi_l parameters. One also has to declare how many particles will be used and how many generations is the limit (or what is acceptable error of solution).

My program (shared in a Code section) can be executed in the following way:

pso = PSO( minProblem, bounds)
bestPos, bestFit = pso.optimize()

where minProblem is a function to be minimised (for an array of N parameters), and bounds is 2D (2 x N values) array of minimum and maximum boundary values. The bestPos is the best set of parameters and bestFit is smallest obtained value for the problem.

A small example provided with the code fits a curve to noisy data. Input signal was
S(t) = 4 t \cos( 4 \pi t^2) \exp(-3 t^2) + U(-0.025,0.025)$, where U(a,b) is a random noise from unitary [a, b] distribution. Fitted function is F_{p}(t) = p_1 t \sin( p_2 \pi t^2 + p_3) \exp(- p_4 t^2), thus the expected values are P={4, 4, pi/2, 3}. See figure for fitted curve below. Obtained values are P = { 4.61487992 3.96829528 1.60951687 3.43047877} which are not far off. I am aware that my example is a bit to simple for such powerful search technique, but it is just a quick example.

Curve fitting with PSO optimisation method. Blue and red lines are for input data and reconstruction function respectively.

Curve fitting with PSO optimisation method. Blue and red lines are for input data and reconstruction function respectively.