https://github.com/vboussange/piecewiseinference.jl

Inverse modelling framework for dynamical systems characterised by complex dynamics.
https://github.com/vboussange/piecewiseinference.jl

inference inverse-problems

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Inverse modelling framework for dynamical systems characterised by complex dynamics.

• Host: GitHub
• URL: https://github.com/vboussange/piecewiseinference.jl
• Owner: vboussange
• Created: 2022-04-11T15:27:06.000Z (almost 3 years ago)
• Default Branch: main
• Last Pushed: 2024-08-08T08:07:32.000Z (6 months ago)
• Last Synced: 2024-11-10T08:39:02.625Z (3 months ago)
• Topics: inference, inverse-problems
• Language: Julia
• Homepage:
• Size: 4.84 MB
• Stars: 8
• Watchers: 1
• Forks: 0
• Open Issues: 2
• Metadata Files:
  • Readme: readme.md

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README

        
# PiecewiseInference.jl

[![](https://img.shields.io/badge/docs-stable-blue.svg)](https://vboussange.github.io/PiecewiseInference.jl/stable/)

[![](https://img.shields.io/badge/docs-dev-blue.svg)](https://vboussange.github.io/PiecewiseInference.jl/dev/)

[![Build status (Github Actions)](https://github.com/vboussange/PiecewiseInference.jl/workflows/CI/badge.svg)](https://github.com/vboussange/PiecewiseInference.jl/actions)

[![codecov.io](http://codecov.io/github/vboussange/PiecewiseInference.jl/coverage.svg?branch=main)](http://codecov.io/github/vboussange/PiecewiseInference.jl?branch=main)

**PiecewiseInference.jl** is a library to enhance the convergence of dynamical model parameter inversion methods. It provides features such as

- a segmentation strategy, 

- the independent estimation of initial conditions for each segment, 

- parameter transformation, 

- parameter and initial conditions regularization

- mini-batching

Taken altogether, these features regularize the inference problem and permit to solve it efficiently.

![](docs/animated.gif)

## Installation

Open Julia REPL and type

```julia

using Pkg; Pkg.add(url="https://github.com/vboussange/PiecewiseInference.jl")

```

That's it! This will download the latest version of **PiecewiseInference.jl** from this git repo and download all dependencies.

## Getting started

Check out [this blog post](https://vboussange.github.io/post/piecewiseinference/) providing a hands-on tutorial.

See also the API documentation and the `test` folder.

## Related packages

`DiffEqFlux` is a package with similar goals as `PiecewiseInference`, and proposes the method `DiffEqFlux.multiple_shooting`, which is close to `PiecewiseInference.inference` but where initial conditions are not inferred. `PiecewiseInference` further proposes several utility methods for model selection.

## Reference

Boussange, V., Vilimelis-Aceituno, P., Schäfer, F., Pellissier, L., _Partitioning time series to improve process-based models with machine learning_. [[bioRxiv]](https://www.biorxiv.org/content/10.1101/2022.07.25.501365v2) (2024), 46 pages.