DifferenceEquations.jl

This package simulates for initial value problems for deterministic and stochastic difference equations, with or without a separate observation equation. In addition, the package provides likelihoods for some standard filters for estimating state-space models.

Relative to existing solvers, this package is intended to provide differentiable solvers and filters. For example, you can simulate a linear gaussian state space model and find the gradient of the solution with respect to the model primitives. Similarly, the likelihood for of Kalman Filter can itself be differentiated with respect to the underlying model primitives. This makes the package especially amenable to estimation and calibration, where the entire solution blocks become auto-differentiable.

Note

Boundary value problems and difference-algebraic equations are not in scope. See DifferentiableStateSpaceModels.jl for experimental support for perturbation solutions and DSGEs.

Installation

To install DifferenceEquations.jl, use the Julia package manager:

using Pkg
Pkg.add("DifferenceEquations")

For additional functionality, you may want to add Plots, DiffEqBase. If you want to explore differentiable filters, you can install Zygote

Mathematical Specification of a Discrete Problem

For comparison, see the specifications of the deterministic Discrete Problem (albeit with a small difference in timing conventions) and the SDE Problem. Other introductions can be found by checking out DiffEqTutorials.jl.

The general class of problems intended to be supported in this package is to take an initial condition, $u_0$, and an evolution equation

\[u_{n+1} = f(u_n,p,t_n) + g(u_n,p,t_n) w_{n+1}\]

for some functions $f$ and $g$, and where $w_{n+1}$ are IID random shocks to the evolution equation. The $p$ is a vector of potentially differentiable parameters.

In addition, there is an optional observation equation

\[z_n = h(u_n, p, t_n) + v_n\]

where $v_n$ is noisy observation error and the size of $z_n$ may be different from $u_n$.

A few notes on the structure:

Frequently, the $g$ provides the covariance structure, so a reasonable default is $w_{n+1} \sim N(0,I)$, and $v_n \sim N(0, D)$ is a common observation error for some covariance matrix $D$.
If $f,g,h$ are all linear, the shocks are both gaussian, and the prior on the latent space is gaussian, then this is a linear gaussian state-space model. Kalman filters can be used to calculate marginal likelihoods, and simulations can be executed with very little overhead.
$t_n$ is the current time at which the map is applied, where $t_n = t_0 + n*dt$ (with dt=1 being the default).
If $f, g, h$ are not functions of time, then it is a time-invariant state-space model.

Likelihood and Filtering Calculations

Certain solve algorithms will run a filter on the unobservable u states and compare to the observables if provided. In that case, it might do so (1) with unobservable $w_n$ noise; or (2) conditioning on a particular sequence of $w_{n+1}$ shocks, where the likelihood depends on the unknown observational error $v_n$.

If an algorithm is given for the filtering, then the return type of solve will have access to a logpdf for the log likelihood. In addition, the solution will provide information on the sequence of posteriors (and smoothed values, if required).

Joint Likelihood

In the case of a joint-likelihood where the noise (i.e. $w_n$) is given, it is not a hidden markov model and the log likelihood simply accumulates the likelihood of each observation. The timing is such that given a $u_0$ which is fixed (and often added to the likelihood separately), and observables $z \equiv \{z_1, \ldots z_N\}$ and noise $w \equiv \{w_1, \ldots w_N\}$ then,

\[\mathcal{L}(z, u_0, w) = \sum_{n=1}^N \log P\left(v_n, t_n, w_n\right) \]

where

\[v_n = z_n - h(u_n, p, t_n)\\ u_{n+1} = f(u_n,p,t_n) + g(u_n,p,t_n) w_{n+1}\]

The density, $P$, is in the case of the typical Gaussian errors, it would be

\[z_n - h(u_n, p, t_n) \sim N(0, D) = P\]

Ultimately, IID Gaussian observation noise is not required, and though the package currently only supports gaussian observation noise with a diagonal covariance matrix, it could be adapted without significant changes.

Linear Filtering for the Marginal Likelihood

When the system is linear and the prior is gaussian, there is an exact likelihood for the marginal likelihood using the Kalman Filter. Unlike the previous example, this is a marginal likelihood and not conditional on the noise, $w$. See the Kalman Filter Likelihood for more details.

Current Status

At this point, the package does not cover all the variations on these features. In particular,

It only supports linear and quadratic $f, g, h$ functions. General $f,g$ simulation are relatively easy to add, but full SciML compliance would require experience with those APIs. The custom rrule for those is also a straightforward variation on the existing linear version.
It only supports time-invariant functions.
There is limited support for non-Gaussian $w_n$ and $v_n$ processes.
It does not support linear or quadratic functions parameterized by the $p$ vector for differentiation.
There are some hard-coded types that prevent it from working with fully generic arrays.
It does not support in-place vs. out-of-place, nor support static arrays, nor matrix-free linear operators.
While many functions in the SciML framework are working, support is incomplete.
There is no complete coverage of gradients for the solution for all parameter inputs/etc.
The package does not support non-gaussian observation noise and is inconsistent with SciML noise process data structures.
Many cleanup steps are necessary for full SciML compliance (e.g., enable passing in vectors-of-vectors or noise/observations, standard SciML dispatching).

To help contribute to filling in these features, see the issues.

Contributing

Please refer to the SciML ColPrac: Contributor's Guide on Collaborative Practices for Community Packages for guidance on PRs, issues, and other matters relating to contributing to SciML.
See the SciML Style Guide for common coding practices and other style decisions.
There are a few community forums:
- The #diffeq-bridged and #sciml-bridged channels in the Julia Slack
- The #diffeq-bridged and #sciml-bridged channels in the Julia Zulip
- On the Julia Discourse forums
- See also SciML Community page

Reproducibility

The documentation of this SciML package was built using these direct dependencies,

Status `~/work/DifferenceEquations.jl/DifferenceEquations.jl/docs/Project.toml`
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Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated`

and using this machine and Julia version.

Julia Version 1.10.3
Commit 0b4590a5507 (2024-04-30 10:59 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: 4 × AMD EPYC 7763 64-Core Processor
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Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)

A more complete overview of all dependencies and their versions is also provided.

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  [14a3606d] MozillaCACerts_jll v2023.1.10
  [4536629a] OpenBLAS_jll v0.3.23+4
  [05823500] OpenLibm_jll v0.8.1+2
  [efcefdf7] PCRE2_jll v10.42.0+1
  [bea87d4a] SuiteSparse_jll v7.2.1+1
  [83775a58] Zlib_jll v1.2.13+1
  [8e850b90] libblastrampoline_jll v5.8.0+1
  [8e850ede] nghttp2_jll v1.52.0+1
  [3f19e933] p7zip_jll v17.4.0+2
Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m`

You can also download the manifest file and the project file.