nmoteki/ndimsplinejax

A multidimensional spline interpolation by Google/JAX

ndimsplinejax

A multidimensional spline interpolation by Google/JAX

Table of Contents

1. About The Project
2. Getting Started
   • Prerequisites
   • Installation
3. Usage
4. Jupyter Notebook version
5. License
6. Contact
7. Acknowledgments

About The Project

Interpolant is by definition an efficiently-computable mathematical function that models a discrete dataset. The interpolant is, for example, needed to reflect an experimental/observational data to a computational scheme in numerical simulations or statistical predictions. There have been many interpolation code/software available; however, I didn't find any multidimensional interpolant compatible with both Just-In-Time compilation and Automatic Differentiation. In my research, I needed such interpolant for applying a recent Hamiltonian-MC scheme, which requires JIT and Autograd -able likelihood function, to my Bayesian inverse problem wherein the forward model is only accessible through a discrete look-up table. So, I decided here to develop a code for JIT and Autograd -able interpolant. I'd like to share the developed codes hoping they are useful for various scientists and engineers.

Functionalities:

• SplineCoefs_from_GriddedData module computes the natural-cubic spline coefficients of the interpolant from the scalar y data distributed on a N-dimensional Cartesian x grid.
• SplineInterpolant module generates an JIT & Autograd compatible interpolant from the spline coefficients.
• On each dimensional axis, x grid-points must be equidistant. The grid-points interval can be different among axes.
• Current version supports 1, 2, 3, 4, 5 dimensional x space (N<=5).

Comments:

• The author thinks the requirement of "equidistant grid-points on each axis" would not be a serious limitation in practice. A user can project/approximate a non-equidistant gridded data to equidistant gridded data by an mathematical transformation of each variable.
• The code execution in higher dimensions/finer grids can be restricted by affordable memory and the computation time.

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Getting Started

This is an example of how you use the modules on your local computer.

Prerequisites

• An execution enviroment of Python3 on Linux, MacOS, or WSL2 on Windows
• numpy, scipy, and jax modules
• Update the Python3 and modules to the latest stable version (recommended).

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Installation

git clone https://github.com/nmoteki/ndimsplinejax.git

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Usage

Here is the workflow for an example of 5-dimensional x-space (N=5):

1. Define the grid information. For x-coordinates, we define the N-list of lower bounds a, the N-list b of upper bounds, and the N-list n of number of grid intervals.

   a= [0,0,0,0,0]        # the user-defined lower bound of each x-coordinate [1st dim, ..., Nth dim]
   b= [1,2,3,4,5]        # the user-defined upper bound of each x-coordinate [1st dim, ..., Nth dim]
   n= [10,10,10,10,10]   # the user-defined number of grid intervals in each x-coordinate [1st dim, ..., Nth dim]

2. Prepare an observation data y_data on the x gridpoints.

   N= len(a)              # dimension N
   
   # Make an N-tuple of numpy arrays of x-gridpoint values
   x_grid= ()
   for j in range(N):
      x_grid += (np.linspace(a[j],b[j],n[j]+1),)
   
   # Make an N-dimensional numpy array of y_data
   grid_shape= ()
   for j in range(N):
      grid_shape += (n[j]+1,)
   y_data= np.zeros(grid_shape)
   
   # A synthetic y_data (should be replaced by a user-defined data in actual use):
   for q1 in range(n[0]+1):
      for q2 in range(n[1]+1):
          for q3 in range(n[2]+1):
                for q4 in range(n[3]+1):
                    for q5 in range(n[4]+1):
                        y_data[q1,q2,q3,q4,q5]= np.sin(x_grid[0][q1])*np.sin(x_grid[1][q2])*np.sin(x_grid[2][q3])*np.sin(x_grid[3][q4])*np.sin(x_grid[4][q5])

3. Compute the spline coefficients from data, using the SplineCoefs_from_GriddedData module.

   # import the module.
   from SplineCoefs_from_GriddedData import SplineCoefs_from_GriddedData
   
   # Make an instance of the class SplineCoefs_from_GriddedData
   spline_coef= SplineCoefs_from_GriddedData(a,b,y_data)
   
   # Compute the spline coeffcients c_i1...iN (The author recommend a name of the coefficients matrix to be N-explicit for readability)
   c_i1i2i3i4i5= spline_coef.Compute_Coefs()

4. Generate the JIT & AD -able interpolant from the coefficients, using the SplineInterpolant module.

   # import the module.
   from SplineInterpolant import SplineInterpolant
   
   # compute the jittable and auto-differentiable interpolant using the spline coeffcient c_i1i2i3i4i5.
   spline= SplineInterpolant(a,b,n,c_i1i2i3i4i5)

5. Use the generated interpolant with the jax's JIT & Autograd functionalities.

   import jax.numpy as jnp
   from jax import jit, grad, value_and_grad
   
   # Specify a x-coordinate for function evaluation as a jnp array.
   x= jnp.array([0.7,1.0,1.5,2.0,2.5]) # By definition, x must satisfy the elementwise inequality a <= x <= b.
   
   # call the method of 5-dimentional interpolant s5D of the "spline" instance (without JIT)
   print(spline.s5D(x)) # for N-dimension, please call sND method (N is either of 1,2,3,4,5)
   
   # Compute the automatic gradient of spline.s5D(x) at the specified x-coordinate
   ds5D= grad(spline.s5D)
   print(ds5D(x))
   
   # Compute both value and gradient of spline.s5D(x) at the specified x-coordinate
   s5D_fun= value_and_grad(spline.s5D)
   print(s5D_fun(x))
   
   # Jitted verison of spline.s5D(x) at the specified x-coordinate
   s5D_jitted= jit(spline.s5D)
   print(s5D_jitted(x))
   
   # Compute the jitted automatic gradient of spline.s5D(x) at the specified x-coordinate
   ds5D_jitted= jit(grad(spline.s5D))
   print(ds5D_jitted(x))
   
   s5D_fun_jitted= jit(value_and_grad(spline.s5D))
   print(s5D_fun_jitted(x))

6. Compare the computation time of spline interpolant between non-Jitted and Jitted versions.

   %timeit spline.s5D(x) # function evaluation
   %timeit s5D_jitted(x) # function evaluation (jitted)
   %timeit ds5D(x) # gradient evaluation
   %timeit ds5D_jitted(x) # gradient evaluation (jitted)
   %timeit s5D_fun(x) # function and it's gradient evaluation
   %timeit s5D_fun_jitted(x) # function and it's gradient evaluation (jitted)

The jitted version will be faster by 2-3 orders of magnitude than non-jitted version.

Please run the caller.py for executing the above example.

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Jupyter Notebook version

In addition to the above SplineCoefs_from_GriddedData and SplineInterpolant modules callable from the caller.py or any user's Python codes, this project also includes .ipynb files scripting the individual dimensional cases. These .ipynb files would be useful for user's understandings or customizations.

Reference

• Maths of multidimensional natural-cubic spline interpolation: Habermann and Kindermann 2007, Multidimensional Spline Interpolation: Theory and Applications, DOI: 10.1007/s10614-007-9092-4.
• Google/JAX reference documentation: https://jax.readthedocs.io/en/latest/
• An introduction of Google/JAX for scientists (in Japanese): https://github.com/HajimeKawahara/playjax

License

Distributed under the MIT License. See LICENSE.txt for more information.

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Contact

Nobuhiro Moteki - [email protected]

Project Link: https://github.com/nmoteki/ndimsplinejax.git

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Acknowledgments

This code-development project was conceived and proceeded in a part of the N.Moteki's research on atmospheric chemical composition in the NOAA Earth System Science Laboratory, supported by a fund JSPS KAKENIHI 19KK0289.

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ndimsplinejax's Issues

Merge in my fork

Hi @nmoteki, I've enjoyed using your nd-spline code. I've ended up refactoring large portions of the code and I was wondering if you were interested to merge these together and release something on PyPI or if I should keep them separate. https://github.com/nstarman/ndimsplinejax