Curve Fitting — Fityk 0.9.7 manual

# Curve Fitting

## Nonlinear Optimization

This is the core. We have a set of observations (data points), to which we want to fit a model that depends on adjustable parameters. Let me quote Numerical Recipes, chapter 15.0, page 656):

> The basic approach in all cases is usually the same: You choose or design a figure-of-merit function (merit function, for short) that measures the agreement between the data and the model with a particular choice of parameters. The merit function is conventionally arranged so that small values represent close agreement. The parameters of the model are then adjusted to achieve a minimum in the merit function, yielding best-fit parameters. The adjustment process is thus a problem in minimization in many dimensions. [...] however, there exist special, more efficient, methods that are specific to modeling, and we will discuss these in this chapter. There are important issues that go beyond the mere finding of best-fit parameters. Data are generally not exact. They are subject to measurement errors (called noise in the context of signal-processing). Thus, typical data never exactly fit the model that is being used, even when that model is correct. We need the means to assess whether or not the model is appropriate, that is, we need to test the goodness-of-fit against some useful statistical standard. We usually also need to know the accuracy with which parameters are determined by the data set. In other words, we need to know the likely errors of the best-fit parameters. Finally, it is not uncommon in fitting data to discover that the merit function is not unimodal, with a single minimum. In some cases, we may be interested in global rather than local questions. Not, “how good is this fit?” but rather, “how sure am I that there is not a very much better fit in some corner of parameter space?”

Our function of merit is the weighted sum of squared residuals (WSSR), also called chi-square:

Weights are based on standard deviations, . You can learn why squares of residuals are minimized e.g. from chapter 15.1 of Numerical Recipes.

So we are looking for a global minimum of . This field of numerical research (looking for a minimum or maximum) is usually called optimization; it is non-linear and global optimization. Fityk implements three very different optimization methods. All are well-known and described in many standard textbooks.

The standard deviations of the best-fit parameters are given by the square root of the corresponding diagonal elements of the covariance matrix. The covariance matrix is based on standard deviations of data points. Formulae can be found e.g. in GSL Manual, chapter Least-Squares Fitting. Fitting Overview (weighted data version).

## Fitting Related Commands

To fit model to data, use command

fit [+] [number-of-iterations] [@n ...]

The plus sign (+) prevents initialization of the fitting method. It is used to continue the previous fitting where it left off (if the previous fitting was stopped before it converged).

All non-linear fitting methods are iterative. number-of-iterations is the maximum number of iterations. There are also other stopping criteria, so the number of executed iterations can be smaller.

Like with all commands, the generic dataset specification (`@n: fit`) can be used, but in special cases the datasets can be given at the end of the command. The difference is that `fit @*` fits all datasets simultaneously, while `@*: fit` fits all datasets one by one, separately.

The fitting method can be set using the set command:

    set fitting_method = method

where method is one of: `levenberg_marquardt`, `nelder_mead_simplex`, `genetic_algorithms`.

All non-linear fitting methods are iterative, and there are two common stopping criteria:

- the number of iterations; it can be specified after the `fit` command.
- and the number of evaluations of the objective function (WSSR); set using the option max_wssr_evaluations (0=unlimited).

There are also other criteria, different for each method.

On Unix, fitting can be interrupted by sending the `INT` signal to the program. This is usually done by pressing Ctrl-C in the terminal.

Setting `set fit_replot = 1` will plot a model after every iteration, to visualize progress.

`info fit` shows measures of goodness-of-fit, including , reduced and R-squared:

Values of all parameters are stored before and after fitting (if they change). This enables simple undo/redo functionality. If in the meantime some functions or variables where added or removed, the program can still load the old parameters, but the result can be unexpected. The following history-related commands are provided:

fit undo
  move back to the previous parameters (undo fitting).
fit redo
  move forward in the parameter history
info fit_history
  show number of items in the history
fit history n
  load the n-th set of parameters from history
fit clear_history
  clear the history

## Uncertainty of Parameters

From the book J. Wolberg, Data Analysis Using the Method of Least Squares: Extracting the Most Information from Experiments, Springer, 2006, p.50:

> (...) we turn to the task of determining the uncertainties associated with the ‘s. The usual measures of uncertainty are standard deviation (i.e., σ) or variance (i.e., σ2) so we seek an expression that allows us to estimate the ‘s. It can be shown (...) that the following expression gives us an unbiased estimate of :

Note that is a square root of the value above. In this formula n-p, the number of (active) data points minus the number of independent parameters, is equal to the number of degrees of freedom. S is another symbol for (the latter symbol is used e.g. in Numerical Recipes).

Terms of the C matrix are given as (p. 47 in the same book):

above is often called a standard error. Having standard errors, it is easy to calculate confidence intervals. Now another book will be cited: H. Motulsky and A. Christopoulos, Fitting Models to Biological Data Using Linear and Nonlinear Regression: A Practical Guide to Curve Fitting, Oxford University Press, 2004. This book can be downloaded for free as a manual to GraphPad Prism 4.

> The standard errors reported by most nonlinear regression programs (...) are “approximate” or “asymptotic”. Accordingly, the confidence intervals computed using these errors should also be considered approximate.

> It would be a mistake to assume that the “95% confidence intervals” reported by nonlinear regression have exactly a 95% chance of enclosing the true parameter values. The chance that the true value of the parameter is within the reported confidence interval may not be exactly 95%. Even so, the asymptotic confidence intervals will give you a good sense of how precisely you have determined the value of the parameter.

> The calculations only work if nonlinear regression has converged on a sensible fit. If the regression converged on a false minimum, then the sum-of-squares as well as the parameter values will be wrong, so the reported standard error and confidence intervals won’t be helpful.

In Fityk:

- `info errors` shows values of .
- `info cov` shows the matrix C–1.
- Individual symmetric errors of simple-variables can be accessed as `$variable.error` or e.g. `%func.height.error`.

In the GUI

select Fit ‣ Info from the menu to see uncertainties and the covariance matrix.

Note

In Fityk 0.9.0 and earlier `info errors` reported values of , which makes sense if the standard deviations of y‘s are set accurately. This formula is derived in Numerical Recipes.

## Levenberg-Marquardt

This is a standard nonlinear least-squares routine, and involves computing the first derivatives of functions. For a description of the L-M method see Numerical Recipes, chapter 15.5 or Siegmund Brandt, Data Analysis, chapter 10.15. Essentially, it combines an inverse-Hessian method with a steepest descent method by introducing a λ factor. When λ is equal to 0, the method is equivalent to the inverse-Hessian method. When λ increases, the shift vector is rotated toward the direction of steepest descent and the length of the shift vector decreases. (The shift vector is a vector that is added to the parameter vector.) If a better fit is found on iteration, λ is decreased – it is divided by the value of lm_lambda_down_factor option (default: 10). Otherwise, λ is multiplied by the value of lm_lambda_up_factor (default: 10). The initial λ value is equal to lm_lambda_start (default: 0.0001).

The Marquardt method has two stopping criteria other than the common criteria.

- If it happens twice in sequence, that the relative change of the value of the objective function (WSSR) is smaller than the value of the lm_stop_rel_change option, the fit is considered to have converged and is stopped.
- If λ is greater than the value of the lm_max_lambda option (default: 10^15), usually when due to limited numerical precision WSSR is no longer changing, the fitting is also stopped.

## Nelder-Mead Downhill Simplex

To quote chapter 4.8.3, p. 86 of Peter Gans, Data Fitting in the Chemical Sciences by the Method of Least Squares:

> A simplex is a geometrical entity that has n+1 vertices corresponding to variations in n parameters. For two parameters the simplex is a triangle, for three parameters the simplex is a tetrahedron and so forth. The value of the objective function is calculated at each of the vertices. An iteration consists of the following process. Locate the vertex with the highest value of the objective function and replace this vertex by one lying on the line between it and the centroid of the other vertices. Four possible replacements can be considered, which I call contraction, short reflection, reflection and expansion.[...] It starts with an arbitrary simplex. Neither the shape nor position of this are critically important, except insofar as it may determine which one of a set of multiple minima will be reached. The simplex than expands and contracts as required in order to locate a valley if one exists. Then the size and shape of the simplex is adjusted so that progress may be made towards the minimum. Note particularly that if a pair of parameters are highly correlated, both will be simultaneously adjusted in about the correct proportion, as the shape of the simplex is adapted to the local contours.[...] Unfortunately it does not provide estimates of the parameter errors, etc. It is therefore to be recommended as a method for obtaining initial parameter estimates that can be used in the standard least squares method.

This method is also described in previously mentioned Numerical Recipes (chapter 10.4) and Data Analysis (chapter 10.8).

There are a few options for tuning this method. One of these is a stopping criterium nm_convergence. If the value of the expression 2(M−m)/(M+m), where M and m are the values of the worst and best vertices respectively (values of objective functions of vertices, to be precise!), is smaller then the value of nm_convergence option, fitting is stopped. In other words, fitting is stopped if all vertices are almost at the same level.

The remaining options are related to initialization of the simplex. Before starting iterations, we have to choose a set of points in space of the parameters, called vertices. Unless the option nm_move_all is set, one of these points will be the current point – values that parameters have at this moment. All but this one are drawn as follows: each parameter of each vertex is drawn separately. It is drawn from a distribution that has its center in the center of the domain of the parameter, and a width proportional to both width of the domain and value of the nm_move_factor parameter. Distribution shape can be set using the option nm_distribution as one of: `uniform`, `gaussian`, `lorentzian` and `bound`. The last one causes the value of the parameter to be either the greatest or smallest value in the domain of the parameter – one of the two bounds of the domain (assuming that nm_move_factor is equal 1).

## Genetic Algorithms

[TODO]

### Navigation

- next
- previous
- Home
- Wiki
- Manual