Passing custom derivatives instead of using predefined differentiation classes about pysindy

[Jacob-Stevens-Haas]

Ok, that makes sense. SINDy models' default differentiation method is FiniteDifference(axis=-2), but this is ignored if you pass x_dot. (in the current branch we label the array axes when the problem is created so we can be more explicit with FiniteDifference(axis=x.ax_time))

MIOSR optimizer, or Mixed-Integer Optimization, Sparse Regression, allows you to specify exactly how many terms should be included. SR3 (and her subclasses) allow a direct penalty on the number of terms with an L-0 penalty. SBR coming soon to a theater near you (#440) will give you a bit more control over the penalty for how many terms are nonzero and how far they're allowed to wander from the origin.

That said, I don't think any optimizer allows you to select a maximum term.

[b-fg]

Noted. So I understand that the approach I took is "SINDy-friendly" and appropriate to solve the problem I indented. Will also play a bit more with the optimizers. Thanks again for all the info!

[Jacob-Stevens-Haas]

Ideally, if your method of generating derivatives would be useful to other people, you could write a BaseDifferentiation subclass (or fork derivative package and add a method to their API, which SINDyDerivative uses under the hood) and PR it.

A bit of clarification: lets say you have calculated $N$ time derivatives. I'm assuming that means you want to find a PDE with N time derivatives. Obviously if you try to find the coefficients for $\partial$ u_t $/\partial t$ and you let u_tt in as a candidate, the system ought to find it's coefficient is 1.

IIUC and you are looking for an Nth time-order PDE with a linear term on that Nth time derivative, here's how:

• Your independent variable should be the second-highest temporal derivative. This is the x in SINDy.fit
• Your highest temporal derivative is the x_dot in SINDy.fit
• Stack and pass all your other pre-calculated derivatives as control variables except for the highest temporal derivative. Stack along the -1 axis, which we call the coordinate axis. This is the u parameter in SINDy.fit

If instead you're looking for something nonlinear in the Nth order like $uu_{tt} = f(u, u_x, u_t, u_xx, u_xt)$, you would need SINDyPI. The x would be all terms with less than $N$ time derivatives and the x_dot would be all terms with at least one time derivative. The caveat is that it will fit M models, where M is the number of features expressed by applying the feature library to x, and you need to visually scan the results to find one that looks reasonable.

[b-fg]

Thank you for the detailed reply. The derivatives I am taking currently are WIP, but I will definitely try to contribute to this repo once I have a more validated approach.

In general, I have a dynamical system such that $u_t=f(x,t)=f(u,u_x,u_{xx},...)$, with non-linear combinations such as $(uu,uu_x,uu_{xx},u_xu_{xx},...)$. For the moment, I am fine by not considering high-order temporal (or mixed) derivatives in $f$. For the moment I have been able to achieve this with the following pseudo-code, where XT is the space-time grid containing N samples :

1. Compute feature arrays and target data $u_t$ (dudt)

u = f(XT)
dudx = ddx(u, XT)
d2udx2 = d2dx2(u, XT)
...
features = np.stack([u, dudx, d2udx2,...], axis=-1)
dudt = ddt(u,XT)

2. Fit polynomial library of p order

model_ps = ps.SINDy(feature_library=ps.PolynomialLibrary(degree=p, include_bias=False), optimizer=ps.STLSQ())
model_ps.fit(features, x_dot=dudt)

Even though this usually spits out the correct PDE, I am not sure is the best it approach. For example, print(model_ps) shows differentiation_method=FiniteDifference(axis=-2), and I am unsure if this is doing something under the hood.

Also, I would like to ask if there is any specific way to cap the maximum number of terms that the optimizer can include in the expression. And, in this sense, I have observed that the only optimizer that could find the correct expression was STLSQ, the others I tried did not manage to do so. What optimizer should be best suited for this problem?

Thanks!