# Fitting data¶

The primary purpose of MOSFiT is to fit models of transients to observed data. In this section we cover “how” of fitting, and how the user should interpret their results.

## Public data¶

MOSFiT is deeply connected to the Open Catalogs (The Open Supernova Catalog, the Open Tidal Disruption Catalog, etc.), and the user can directly fit their model against any data provided by those catalogs. The Open Catalogs store names for each transient, and the user can access any transient by any known name of that transient. As an example, both of the commands below will fit the same transient:

mosfit -m slsn -e PTF11dij
mosfit -m slsn -e CSS110406:135058+261642


While the Open Catalogs do their best to maintain the integrity of the data they contain, there is always the possibility that the data contains errors, so users are encouraged to spot check the data they download before using it for any scientific purpose. A common error is that the data has been tagged with the wrong photometric system, or has not been tagged with a photometric system at all and uses a different system from what is commonly used for a given telescope/instrument/band. Users are encouraged to immediately report any issues with the public data on the GitHub issues page assocated with that catalog (e.g. the Open Supernova Catalog’s issue page).

## Private data¶

If you have private data you would like to fit, the most robust way to load the data into MOSFiT is to directly construct a JSON file from your data that conforms to the Open Catalog Schema. This way, the user can specify all the data that MOSFiT can use for every single observation in a precise way. All data provided by the Open Catalogs is provided in this form, and if the user open up a typical JSON file downloaded from one of these catalogs, they will find that each observation is tagged with all the information necessary to model it.

Of course, it is more likely that the data a user will have handy will be in another form, typically an ASCII table where each row presents a single (or multiple) observations. MOSFiT includes a conversion feature where the user can simply pass the path to the file(s) to convert:

mosfit -e path/to/my/ascii/file/my_transient.dat
mosfit -e path/to/my/folder/of/ascii/files/*.dat


In some cases, if the ASCII file is in a simple form with columns that match all the required columns, MOSFiT will silently convert the input files into JSON files, a copy of which will be saved to the current run directory. In most cases however, the user will be prompted to answer a series of questions about the data in a “choose your own adventure” style. If passed a list of files, MOSFiT will assume all the files share the same format and the user will only be asked questions about the first file.

If the user so chooses, they may optionally upload their data directly to the Open Catalogs with the -u option. This will make their observational data publicly accessible on the Open Catalogs:

mosfit -e path/to/my/ascii/file/my_transient.dat -u


Note that this step is completely optional, users do not have to share their data publicly to use MOSFiT, however it is the fastest way for your data to appear on the Open Catalogs. If a user believes they have uploaded any private data in error, they are encouraged to immediately contact the maintainers.

## Sampling Options¶

MOSFiT at present offers two ways to sample the parameter space: An ensemble-based MCMC (implemented with the emcee package), and a nested sampling approach (implemented with the dynesty package). The ensemble-based approach is presently the default sampler used in MOSFiT, although the nested sampler (which in preliminary testing performs better) is likely to replace it as the default in a future version.

Samplers are selected via the -D option: -D ensembler for the ensemble-based approach, and -D nester for the nested sampling approach. The two approaches are described below.

### Ensemble-based MCMC¶

In ensemble-based Markov chain Monte Carlo, a collection of parameter positions (called “walkers”) are evolved in the parameter space according to simple rules based upon the positions of their neighbors. This approach is simple, flexible, and is able to deal with several pathologies in posteriors that can cause issues in other samplers. In MOSFiT we implement this sampling using the parallel-tempered sampler available within the emcee package, although a single temperature is used by default (note that the parallel-tempered sampler is now deprecated as of emcee version 3.0, and MOSFiT will eventually deprecate this option as well).

While MOSFiT also performs minimization during the burn-in phase to find the global minima within the posterior, it should be noted that emcee on its own has been found to have poor convergence to the posterior for problems with greater than about 10 dimensions (Huijser et al. 2015). As many models provided with MOSFiT have a dimension similar to this number, care should be taken when using this sampler to ensure that convergence has been achieved.

The ensemble-based MCMC can be selected via the -D flag: -D ensembler.

#### Initialization¶

When initializing, walkers are drawn randomly from the prior distributions of all free parameters, unless the -w option was passed to initialize from a previous run (see previous). By default, any drawn walker that has a defined, non-infinite score will be retained, unless the -d option is used, which by default only draws walkers above the average walker score drawn so far, or the numeric value specified by the user (warning: this option can often make the initial drawing phase last a long time).

#### Restricting the data used¶

By default, MOSFiT will attempt to use all available data when fitting a model. If the user wishes, they can exclude specific instruments from the fit using the --exclude-instruments option, specific photometric bands using the --exclude-bands option, specific sources of data (e.g. papers or surveys) using --exclude-sources, and particular wave bands via --exclude-kinds. The source is specified using the source ID number, visible on the Open Astronomy Catalog page for each transient as well as in the input file. For example

mosfit -e LSQ12dlf -m slsn --exclude-sources 2


will exclude all data from the paper that has the source ID number 2 on the Open Astronomy Catalog page.

To exclude times from a fit, the user can specify a range of MJDs that will be included using the -L option, e.g.:

mosfit -e LSQ12dlf -m slsn -L 55000 56000


will limit the data fitted for LSQ12dlf to lie between MJD 55000 and MJD 56000.

Finally, --exclude-kinds can be used to exclude particular wave bands (e.g. radio, X-ray, infrared) from the fitting process. By default, models will not fit against data that is not specified as being supported via a 'supports' attribute in the model JSON file, but this can be overridden by setting --exclude-kinds none.

As an example, assuming a user wants to fit the ic model to a transient that happens to have radio data, but would like to exclude the radio data from that fit, they would run the following command:

mosfit -e SN2004gk -m ic --exclude-kinds radio


#### Number of walkers¶

The sampler used in MOSFiT is a variant of emcee’s multi-temperature sampler PTSampler, and thus the user can pass both a number of temperatures to use with -T in addition to the number of walkers -N per temperature. If one temperature is used (the default), the total number of walkers is simply whatever is passed to -N, otherwise it is $$N*T$$.

#### Duration of fitting¶

The duration of the MOSFiT run is set with the -i option, unless the -R or -U options are used (see convergence). Generally, unless the model has only a few free parameters or was initialized very close to the solution of highest-likelihood, the user should not expect good results unless -i is set to a few thousand or more.

#### Burning in a model¶

Unless the solution for a given dataset is known in advance, the initial period of searching for the true posterior distribution involves finding the locations of the solutions of highest likelihood. In MOSFiT, various scipy routines are employed in an alernating fashion with a Gibbs-like affine-invariant ensemble evolution, which we have found more robustly locates the true global likelihood minimas. The period of alternation between optimization (called “fracking” in MOSFiT) and sampling (called “walking” in MOSFiT) is controlled by the -f option, with the total burn-in duration being controlled by the -b/-p options. If -b/-p are not set, the burn-in is set to run for half the total number of iterations specified by -i.

As an example, the following will run the burn-in phase for 2000 iterations, the post burn-in for 3000 iterations more (for a total of 5000), fracking every 100th iteration:

mosfit -e LSQ12dlf -m slsn -f 100 -i 5000 -b 2000


All convergence metrics are computed after the burn-in phase, as the operations employed during burn-in do not preserve detailed balance. During burn-in, the solutions of highest likelihood are over-represented, and thus the posteriors should not be trusted until the convergence criteria are met beyond the burn-in phase.

### Nested sampling¶

For complicated posteriors with multiple modes or for problems of high dimension (ten dimensions or greater), nested sampling is often a superior choice versus ensemble-based methods. In MOSFiT, nested sampling is implement via the dynesty package, which uses a modern variant of nested sampling known as dynamic nested sampling (see the full documentation for this package).

Whereas ensemble-based approaches can only estimate the information content of their posteriors via heuristic information metrics such as the WAIC (see Scoring), nested sampling directly evaluates the evidence for a given model, and provides a (statistical) estimate of its error. Nested sampling also yields many more useful samples of the posterior for the purposes of visualizing its structure; it is not uncommon for a run to provide tens of thousands of informative samples, as compared to ensemble-based approach that may only yield a few hundred.

However, nested sampling is a much more complicated algorithm than ensemble-based MCMC and thus is potentially prone to failures that can be difficult to track down. Additionally, the dynesty software currently does not offer the ability to restart if the sampling is prematurely terminated; thus, it is advisable to always use the nested sampling routine in conjunction with the -R flag, which when used with the nester option specifies the termination criterion based upon the expected remaining evidence gain.

The nested sampler can be selected via the -D flag: -D nester.

#### Baselining and batching¶

When performing a nested sampling run, the user might notice that there are two phases to the process: “baselining” and “batching”. In the baselining phase, nester samples from the posterior repeatedly to obtain the log of the evidence $$\log_{10} Z$$ (the N-dimensional volume integral of the postioer), for which it estimates the error $$\Delta \log_{10} Z$$. Once $$\Delta \log_{10} Z$$ is smaller than some prescribed value (set with the -R parameter), baselining ceases and batching begins.

In batching, nester fleshes out the posterior such that even regions of lower probability that may not be dominating the evidence integral are resolved with high fidelity. In this part of the process, the posterior is sampled from again, but this time minimizing the error in the posterior distribution as opposed to its integral. This process continues until a stopping criterion is met, which indicates that the posterior is now of high quality. Typically, the batching phase takes a few times longer than the baselining phase.

### Switching between samplers¶

After completing a nested sampling run, it is often useful to draw parameter combinations from the large collection of samples generated to perform additional analysis (particularly for data-intensive tasks, such as analyzing a collection of model SEDs). This can be easily done by loading the output from the previous run with the ensembler method (the default), and setting MOSFiT to run in generative mode with -G,

mosfit -e LSQ12dlf -m slsn -w name-of-output.json -G -N 100


where above we specify that we would like 100 parameter combinations from the nester output. The weights determined with nester will be used to proportionately draw walkers for ensembler, yielding a sample that properly maps to the posterior determined by the nested sampling. As the above does not perform any additional sampling, the user does not need to specify an event to compare against, and can simply omit the -e flag and its argument(s).

Because nester currently does not support restarts, the opposite situation of using ensembler outputs to initialize nester is not possible.

## Input and output locations¶

The paths of the various inputs and outputs are set by a few different options in MOSFiT. The first time MOSFiT runs in a directory, it will make local copies of the models and jupyter folders distributed with the code (unless --no-copy-at-launch option is passed), and will not copy the files again unless they are deleted or the user passes the --force-copy-at-launch option.

By default, MOSFiT searches the local models folder copied to the run directory to find model JSON and their corresponding parameter JSON files to use for runs. If the user wishes to use custom parameter files for their runs instead, they can specify the paths to these files using the -P option.

MOSFiT outputs are always written to a local products directory, with the default filename being set to the name of the transient being fit (e.g. LSQ12dlf.json for LSQ12dlf). The user can append a suffix to the output filename using the -s option, e.g.:

mosfit -e LSQ12dlf -m slsn -s mysuffix


will write to the file LSQ12dlf-mysuffix.json. A copy of the output will also always be dumped to walkers.json in the same directory. The same suffix will applied to any additional outputs requested by the user, such as the chain.json and extras.json files.

## Fixing model parameters¶

Individual parameters can be locked to fixed values with the -F option, which will either assume the default specified in the model JSON file (if no value is provided):

mosfit -e LSQ12dlf -m slsn -F kappa


Or, will assume the value specified by the user:

mosfit -e LSQ12dlf -m slsn -F mejecta 3.0


Multiple fixed variables can be specified by chaining them together, with any user-prescribed variables following the variable names:

mosfit -e LSQ12dlf -m slsn -F kappa mejecta 3.0


If you have a prior for a given variable (not a single value), it is best to modify your local parameters.json file. For instance, to place a Gaussian prior on vejecta in the SLSN model, replace the default parameters.json snippet, which looks like this:

"vejecta":{
"min_value":5.0e3,
"max_value":2.0e4
},


with the following:

"vejecta":{
"class":"gaussian",
"mu":1.0e4,
"sigma":0.5e3,
"min_value":1.0e3,
"max_value":1.0e5
},


Flat, log flat, gaussian, and power-law priors are available in MOSFiT; see the parameters_test.json file in the default model for examples on how to set each prior type.

## Initializing from previous runs¶

The user can use the ensemble parameters from a prior MOSFiT run to draw their initial conditions for a new run using the -w option. Assuming that LSQ12dlf-mysuffix.json contains results from a previous run, the user can draw walker positions from it by passing it to the -w option:

mosfit -e LSQ12dlf -m slsn -w LSQ12dlf-suffix.json


If the file contains more walkers than requested by the new run, walker positions will be drawn verbatim from the input file, otherwise walker positions will be “jittered” by a small amount so no two walkers share identical parameters.

Note that while the outputs of nested sampling runs can be initialized from, they cannot themselves be initialized from previous runs, as the nested sampling approach must sample from the full prior volume.