# The xfit class¶

This document describes the `xfit`

class. `xfit`

is a toolbox that helps you find neuron or network models satisfying arbitrary constraints. It is a bridge
between the Global Optimization Toolbox in MATLAB and the xolotl neuron and network simulator

The first step in using `xfit`

is to create a `xfit`

object using:

xf = xfit('particleswarm');

## Properties¶

Every xfit object has the following properties. To access a property, use dot notation, e.g.:

xf.x

You can view all the properties of an xfit object
using the built-in `properties`

command:

properties(xf)

`best_cost`

¶

The best cost holds the lowest value computed by the simulation function during an optimization procedure. This is a read-only property.

`data`

¶

Default | Allowed values | Type |
---|---|---|

[] | any | any |

The `data`

property can hold any user-defined data. You may want to use this if your cost function required additional data to measure the cost. For example, if you want to fit a neuron to a specifiy voltage trace, you would store it here.

`engine`

¶

This option determines the optimization algorithm used.

Engine Name | Engine Keyword |
---|---|

Pattern Search | `patternsearch` |

Particle Swarm | `particleswarm` |

Genetic Algorithm | `ga` |

`lb`

& `ub`

¶

Default | Allowed values | Type |
---|---|---|

[] | vectors | double |

`lb`

and `ub`

are x 1 vectors of numerical lower bound and upper bound values. During optimization, parameters are bounded between their upper and lower bounds.

`nonlcon`

¶

Nonlinear inequality and equaity constraints, only supported for engines that support them. To understand how to use these constraints, look at MATLAB's documentation here

`options`

¶

This property is a struct that holds options for the selected optimization engine. It is automatically generated from MATLAB's built-in optimoptions function.

`parameter_names`

¶

Default | Allowed values | Type |
---|---|---|

[] | any | cell |

This cell array of character vectors contains the names of xolotl parameters to optimize over.
The `find`

method of xolotl is the best way to populate this list.
`seed`

, `lb`

, and `ub`

share one-to-one correspondence with `parameter_names`

, so all should be the same dimensions.

`seed`

¶

Default | Allowed values | Type |
---|---|---|

[] | vector | double |

The seed is an x 1 vector of numerical parameter values for starting an optimization protocol, where is the number of parameters to optimize over.

`SimFcn`

¶

Default | Allowed values | Type |
---|---|---|

[] | any | function_handle |

A function handle to the simulation function used to evaluate the model cost. The simulation function can be any MATLAB function, provided that the following are true:

- The first output must be the cost, which is a positive, real-valued scalar.
- The function accepts two arguments, the first of which is a xolotl object.

The function thus has the (minimal) signature:

function [cost, ...] = functionName(xolotl_object, data)

When xfit performs a parameter optimization routine,
it calls the `SimFcn`

using the xolotl object stored in the `x`

property, which has been set up with trial parameters.

`timestamp`

¶

This property keeps track of the duration of a simulation. This is a read-only property.

`x`

¶

Default | Allowed values | Type |
---|---|---|

[] | scalar values | xolotl |

This property contains a xolotl object. Since xfit uses xolotl to run actual simulations, this is necessary for all projects.

## Methods¶

### evaluate¶

**Syntax**

c = evaluate(self,params);

**Description**

Updates parameters in the xolotl object using
`params`

(a vector), evaluate the cost function,
and return a cost (a double).

It is assumed that you have the following things configured in the xfit object:

`x`

(the xolotl object)`SimFcn`

`parameter_names`

See Also

### fit¶

**Syntax**

best_fit_params = xf.fit;

**Description**

Assuming `xf`

is a `xfit`

object, runs the optimization
algorithm in an effort to minimze the cost function using
specified conditions. Returns a vector of the best-fit
parameters. Only the last (best-fit) value is returned.

The best-fit value is also used to update the seed.

See Also

### save¶

**Syntax**

xf.save()

**Description**

Assuming `xf`

is a `xfit`

object, save results of
this optimization run in a database called

See Also

### show¶

**Syntax**

xf.show()

**Description**

Assuming `xf`

is a `xfit`

object, and you have run the xfit
algorithm many times and run `xf.save`

, and you have been
saving results to a `.xfit`

file, then this method runs
the user-defined `ShowFcn`

and goes over all the results
If `ShowFcn`

is not defined, then it simply plots the result

See Also