diff --git a/joss_paper/bmm_schematic.pdf b/joss_paper/bmm_schematic.pdf new file mode 100644 index 00000000..4b146a3f Binary files /dev/null and b/joss_paper/bmm_schematic.pdf differ diff --git a/joss_paper/paper.md b/joss_paper/paper.md index c2043f98..c4958421 100644 --- a/joss_paper/paper.md +++ b/joss_paper/paper.md @@ -38,10 +38,10 @@ bibliography: references.bib Uncertainty quantification using Bayesian methods is a growing area of research. Bayesian model mixing (BMM) is a recent development which -combines the predictions from multiple models such that each model's -best qualities are preserved in the final result. Practical tools and +combines the predictions from multiple models such that each the fidelity +of individual models is preserved in the final result. Practical tools and analysis suites that facilitate such methods are therefore needed. -`Taweret` introduces BMM to existing Bayesian uncertainty quantification +`Taweret`[^1] introduces BMM to existing Bayesian uncertainty quantification efforts. Currently `Taweret` contains three individual Bayesian model mixing techniques, each pertaining to a different type of problem structure; we encourage the future inclusion of user-developed mixing @@ -49,12 +49,16 @@ methods. `Taweret`'s first use case is in nuclear physics, but the package has been structured such that it should be adaptable to any research engaged in model comparison or model mixing. +[^1]: Taweret is the Egyptian goddess, known as the protector of children and women, +whose body is a fusion of a hippo, lion and crocodile which represent her ferocity. +Similarly, `Taweret`, the package, seeks to fuse models together to represent +observed phenomena. + # Statement of need In physics applications, multiple models with different physics -assumptions can be used to describe an underlying system of interest. It -is usually the case that each model has varying fidelity to the observed -process across the input domain. Though each model may have similar +assumptions can be used to describe an underlying system of interest. +Though each model may have similar predictive accuracy on average, the fidelity of the approximation across a subset of the domain may differ drastically for each of the models under consideration. In such cases, inference and prediction based on a @@ -79,6 +83,10 @@ where $p(Y_0 \mid x_0, Y, \mathcal{M}_k)$ represents the predictive density of a setup, a key challenge is defining $w_k(x)$---the functional relationship between the inputs and the weights. +![Schematic of Bayesian model mixing. Each model has region of paramtere space where it has a high +fidelity, but all models are meant to describe the same phenomenon. To obtain a model that works +well for all of parameter space, we combine them using Bayesian model mixing methods](bmm_schematic.pdf){#fig:bmm_schematic width="\\textwidth"} + This work introduces `Taweret`, a Python package for Bayesian model mixing that includes three novel approaches for combining models, each of which defines the weight function in a unique way (see @@ -146,8 +154,20 @@ applications in relativistic heavy-ion collision physics can be found in the Ph.D. thesis of D. Liyanage [@Liyanage_thesis]. The bivariate linear mixing method can mix two models either using a density-mixing or a mean-mixing strategy. Currently, this is the only mixing method in -`Taweret` that can also calibrate the models while mixing. It allows the -user to choose among the following mixing functions: +`Taweret` that can also calibrate the models while mixing. +Each physics-based model we consider may have unknown parameters which have +physical meaning. +In this context, Bayesian calibration corresponds to the process of using +observational dat to learn the values (and more generally, the posterior +distribtutions) of this these unknown parameters. +Most approaches in model mixing and model averaging use a two-step approach: +(step 1) fit individual models using a subset of the data; (step 2) mix the +predictions from each model (the results from step 1) using the other subset +of the data to learn the weights. +Therefore, this joint calibration of and mixing idea looks to do everything at +once, rather than use the two step process. + +The user may choose among the following mixing functions: - step: $\Theta(\beta_0-x)$ @@ -330,6 +350,14 @@ this growing framework, we hope to enable continuous integration routines for individuals contributing and create docker images that will run `Taweret`. +# Contributions +All authors have contributed to the development of the Taweret framework, + while individual mixing methods were developed by +D. Liyanage (bivariate linear mixing), A. Semposki (multivariate model +mixing), and J. Yanotty (additive regression trees). +Ongoing work by K. Ingles will be included in the next version release +of `Taweret`. + # Disclosure statement The authors of this work are not aware of any conflicts of interest that