# Source code for astropy.stats.info_theory

```
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
This module contains simple functions for model selection.
"""
import numpy as np
__all__ = ['bayesian_info_criterion', 'bayesian_info_criterion_lsq',
'akaike_info_criterion', 'akaike_info_criterion_lsq']
__doctest_requires__ = {'bayesian_info_criterion_lsq': ['scipy'],
'akaike_info_criterion_lsq': ['scipy']}
[docs]def bayesian_info_criterion(log_likelihood, n_params, n_samples):
r""" Computes the Bayesian Information Criterion (BIC) given the log of the
likelihood function evaluated at the estimated (or analytically derived)
parameters, the number of parameters, and the number of samples.
The BIC is usually applied to decide whether increasing the number of free
parameters (hence, increasing the model complexity) yields significantly
better fittings. The decision is in favor of the model with the lowest
BIC.
BIC is given as
.. math::
\mathrm{BIC} = k \ln(n) - 2L,
in which :math:`n` is the sample size, :math:`k` is the number of free
parameters, and :math:`L` is the log likelihood function of the model
evaluated at the maximum likelihood estimate (i. e., the parameters for
which L is maximized).
When comparing two models define
:math:`\Delta \mathrm{BIC} = \mathrm{BIC}_h - \mathrm{BIC}_l`, in which
:math:`\mathrm{BIC}_h` is the higher BIC, and :math:`\mathrm{BIC}_l` is
the lower BIC. The higher is :math:`\Delta \mathrm{BIC}` the stronger is
the evidence against the model with higher BIC.
The general rule of thumb is:
:math:`0 < \Delta\mathrm{BIC} \leq 2`: weak evidence that model low is
better
:math:`2 < \Delta\mathrm{BIC} \leq 6`: moderate evidence that model low is
better
:math:`6 < \Delta\mathrm{BIC} \leq 10`: strong evidence that model low is
better
:math:`\Delta\mathrm{BIC} > 10`: very strong evidence that model low is
better
For a detailed explanation, see [1]_ - [5]_.
Parameters
----------
log_likelihood : float
Logarithm of the likelihood function of the model evaluated at the
point of maxima (with respect to the parameter space).
n_params : int
Number of free parameters of the model, i.e., dimension of the
parameter space.
n_samples : int
Number of observations.
Returns
-------
bic : float
Bayesian Information Criterion.
Examples
--------
The following example was originally presented in [1]_. Consider a
Gaussian model (mu, sigma) and a t-Student model (mu, sigma, delta).
In addition, assume that the t model has presented a higher likelihood.
The question that the BIC is proposed to answer is: "Is the increase in
likelihood due to larger number of parameters?"
>>> from astropy.stats.info_theory import bayesian_info_criterion
>>> lnL_g = -176.4
>>> lnL_t = -173.0
>>> n_params_g = 2
>>> n_params_t = 3
>>> n_samples = 100
>>> bic_g = bayesian_info_criterion(lnL_g, n_params_g, n_samples)
>>> bic_t = bayesian_info_criterion(lnL_t, n_params_t, n_samples)
>>> bic_g - bic_t # doctest: +FLOAT_CMP
2.1948298140119391
Therefore, there exist a moderate evidence that the increasing in
likelihood for t-Student model is due to the larger number of parameters.
References
----------
.. [1] Richards, D. Maximum Likelihood Estimation and the Bayesian
Information Criterion.
<https://hea-www.harvard.edu/astrostat/Stat310_0910/dr_20100323_mle.pdf>
.. [2] Wikipedia. Bayesian Information Criterion.
<https://en.wikipedia.org/wiki/Bayesian_information_criterion>
.. [3] Origin Lab. Comparing Two Fitting Functions.
<http://www.originlab.com/doc/Origin-Help/PostFit-CompareFitFunc>
.. [4] Liddle, A. R. Information Criteria for Astrophysical Model
Selection. 2008. <https://arxiv.org/pdf/astro-ph/0701113v2.pdf>
.. [5] Liddle, A. R. How many cosmological parameters? 2008.
<https://arxiv.org/pdf/astro-ph/0401198v3.pdf>
"""
return n_params*np.log(n_samples) - 2.0*log_likelihood
[docs]def bayesian_info_criterion_lsq(ssr, n_params, n_samples):
r"""
Computes the Bayesian Information Criterion (BIC) assuming that the
observations come from a Gaussian distribution.
In this case, BIC is given as
.. math::
\mathrm{BIC} = n\ln\left(\dfrac{\mathrm{SSR}}{n}\right) + k\ln(n)
in which :math:`n` is the sample size, :math:`k` is the number of free
parameters and :math:`\mathrm{SSR}` stands for the sum of squared residuals
between model and data.
This is applicable, for instance, when the parameters of a model are
estimated using the least squares statistic. See [1]_ and [2]_.
Parameters
----------
ssr : float
Sum of squared residuals (SSR) between model and data.
n_params : int
Number of free parameters of the model, i.e., dimension of the
parameter space.
n_samples : int
Number of observations.
Returns
-------
bic : float
Examples
--------
Consider the simple 1-D fitting example presented in the Astropy
modeling webpage [3]_. There, two models (Box and Gaussian) were fitted to
a source flux using the least squares statistic. However, the fittings
themselves do not tell much about which model better represents this
hypothetical source. Therefore, we are going to apply to BIC in order to
decide in favor of a model.
>>> import numpy as np
>>> from astropy.modeling import models, fitting
>>> from astropy.stats.info_theory import bayesian_info_criterion_lsq
>>> # Generate fake data
>>> np.random.seed(0)
>>> x = np.linspace(-5., 5., 200)
>>> y = 3 * np.exp(-0.5 * (x - 1.3)**2 / 0.8**2)
>>> y += np.random.normal(0., 0.2, x.shape)
>>> # Fit the data using a Box model.
>>> # Bounds are not really needed but included here to demonstrate usage.
>>> t_init = models.Trapezoid1D(amplitude=1., x_0=0., width=1., slope=0.5,
... bounds={"x_0": (-5., 5.)})
>>> fit_t = fitting.LevMarLSQFitter()
>>> t = fit_t(t_init, x, y)
>>> # Fit the data using a Gaussian
>>> g_init = models.Gaussian1D(amplitude=1., mean=0, stddev=1.)
>>> fit_g = fitting.LevMarLSQFitter()
>>> g = fit_g(g_init, x, y)
>>> # Compute the mean squared errors
>>> ssr_t = np.sum((t(x) - y)*(t(x) - y))
>>> ssr_g = np.sum((g(x) - y)*(g(x) - y))
>>> # Compute the bics
>>> bic_t = bayesian_info_criterion_lsq(ssr_t, 4, x.shape[0])
>>> bic_g = bayesian_info_criterion_lsq(ssr_g, 3, x.shape[0])
>>> bic_t - bic_g # doctest: +FLOAT_CMP
30.644474706065466
Hence, there is a very strong evidence that the Gaussian model has a
significantly better representation of the data than the Box model. This
is, obviously, expected since the true model is Gaussian.
References
----------
.. [1] Wikipedia. Bayesian Information Criterion.
<https://en.wikipedia.org/wiki/Bayesian_information_criterion>
.. [2] Origin Lab. Comparing Two Fitting Functions.
<http://www.originlab.com/doc/Origin-Help/PostFit-CompareFitFunc>
.. [3] Astropy Models and Fitting
<http://docs.astropy.org/en/stable/modeling>
"""
return bayesian_info_criterion(-0.5 * n_samples * np.log(ssr / n_samples),
n_params, n_samples)
[docs]def akaike_info_criterion(log_likelihood, n_params, n_samples):
r"""
Computes the Akaike Information Criterion (AIC).
Like the Bayesian Information Criterion, the AIC is a measure of
relative fitting quality which is used for fitting evaluation and model
selection. The decision is in favor of the model with the lowest AIC.
AIC is given as
.. math::
\mathrm{AIC} = 2(k - L)
in which :math:`n` is the sample size, :math:`k` is the number of free
parameters, and :math:`L` is the log likelihood function of the model
evaluated at the maximum likelihood estimate (i. e., the parameters for
which L is maximized).
In case that the sample size is not "large enough" a correction is
applied, i.e.
.. math::
\mathrm{AIC} = 2(k - L) + \dfrac{2k(k+1)}{n - k - 1}
Rule of thumb [1]_:
:math:`\Delta\mathrm{AIC}_i = \mathrm{AIC}_i - \mathrm{AIC}_{min}`
:math:`\Delta\mathrm{AIC}_i < 2`: substantial support for model i
:math:`3 < \Delta\mathrm{AIC}_i < 7`: considerably less support for model i
:math:`\Delta\mathrm{AIC}_i > 10`: essentially none support for model i
in which :math:`\mathrm{AIC}_{min}` stands for the lower AIC among the
models which are being compared.
For detailed explanations see [1]_-[6]_.
Parameters
----------
log_likelihood : float
Logarithm of the likelihood function of the model evaluated at the
point of maxima (with respect to the parameter space).
n_params : int
Number of free parameters of the model, i.e., dimension of the
parameter space.
n_samples : int
Number of observations.
Returns
-------
aic : float
Akaike Information Criterion.
Examples
--------
The following example was originally presented in [2]_. Basically, two
models are being compared. One with six parameters (model 1) and another
with five parameters (model 2). Despite of the fact that model 2 has a
lower AIC, we could decide in favor of model 1 since the difference (in
AIC) between them is only about 1.0.
>>> n_samples = 121
>>> lnL1 = -3.54
>>> n1_params = 6
>>> lnL2 = -4.17
>>> n2_params = 5
>>> aic1 = akaike_info_criterion(lnL1, n1_params, n_samples)
>>> aic2 = akaike_info_criterion(lnL2, n2_params, n_samples)
>>> aic1 - aic2 # doctest: +FLOAT_CMP
0.9551029748283746
Therefore, we can strongly support the model 1 with the advantage that
it has more free parameters.
References
----------
.. [1] Cavanaugh, J. E. Model Selection Lecture II: The Akaike
Information Criterion.
<http://machinelearning102.pbworks.com/w/file/fetch/47699383/ms_lec_2_ho.pdf>
.. [2] Mazerolle, M. J. Making sense out of Akaike's Information
Criterion (AIC): its use and interpretation in model selection and
inference from ecological data.
<http://theses.ulaval.ca/archimede/fichiers/21842/apa.html>
.. [3] Wikipedia. Akaike Information Criterion.
<https://en.wikipedia.org/wiki/Akaike_information_criterion>
.. [4] Origin Lab. Comparing Two Fitting Functions.
<http://www.originlab.com/doc/Origin-Help/PostFit-CompareFitFunc>
.. [5] Liddle, A. R. Information Criteria for Astrophysical Model
Selection. 2008. <https://arxiv.org/pdf/astro-ph/0701113v2.pdf>
.. [6] Liddle, A. R. How many cosmological parameters? 2008.
<https://arxiv.org/pdf/astro-ph/0401198v3.pdf>
"""
# Correction in case of small number of observations
if n_samples/float(n_params) >= 40.0:
aic = 2.0 * (n_params - log_likelihood)
else:
aic = (2.0 * (n_params - log_likelihood) +
2.0 * n_params * (n_params + 1.0) /
(n_samples - n_params - 1.0))
return aic
[docs]def akaike_info_criterion_lsq(ssr, n_params, n_samples):
r"""
Computes the Akaike Information Criterion assuming that the observations
are Gaussian distributed.
In this case, AIC is given as
.. math::
\mathrm{AIC} = n\ln\left(\dfrac{\mathrm{SSR}}{n}\right) + 2k
In case that the sample size is not "large enough", a correction is
applied, i.e.
.. math::
\mathrm{AIC} = n\ln\left(\dfrac{\mathrm{SSR}}{n}\right) + 2k +
\dfrac{2k(k+1)}{n-k-1}
in which :math:`n` is the sample size, :math:`k` is the number of free
parameters and :math:`\mathrm{SSR}` stands for the sum of squared residuals
between model and data.
This is applicable, for instance, when the parameters of a model are
estimated using the least squares statistic.
Parameters
----------
ssr : float
Sum of squared residuals (SSR) between model and data.
n_params : int
Number of free parameters of the model, i.e., the dimension of the
parameter space.
n_samples : int
Number of observations.
Returns
-------
aic : float
Akaike Information Criterion.
Examples
--------
This example is based on Astropy Modeling webpage, Compound models
section.
>>> import numpy as np
>>> from astropy.modeling import models, fitting
>>> from astropy.stats.info_theory import akaike_info_criterion_lsq
>>> np.random.seed(42)
>>> # Generate fake data
>>> g1 = models.Gaussian1D(.1, 0, 0.2) # changed this to noise level
>>> g2 = models.Gaussian1D(.1, 0.3, 0.2) # and added another Gaussian
>>> g3 = models.Gaussian1D(2.5, 0.5, 0.1)
>>> x = np.linspace(-1, 1, 200)
>>> y = g1(x) + g2(x) + g3(x) + np.random.normal(0., 0.2, x.shape)
>>> # Fit with three Gaussians
>>> g3_init = (models.Gaussian1D(.1, 0, 0.1)
... + models.Gaussian1D(.1, 0.2, 0.15)
... + models.Gaussian1D(2., .4, 0.1))
>>> fitter = fitting.LevMarLSQFitter()
>>> g3_fit = fitter(g3_init, x, y)
>>> # Fit with two Gaussians
>>> g2_init = (models.Gaussian1D(.1, 0, 0.1) +
... models.Gaussian1D(2, 0.5, 0.1))
>>> g2_fit = fitter(g2_init, x, y)
>>> # Fit with only one Gaussian
>>> g1_init = models.Gaussian1D(amplitude=2., mean=0.3, stddev=.5)
>>> g1_fit = fitter(g1_init, x, y)
>>> # Compute the mean squared errors
>>> ssr_g3 = np.sum((g3_fit(x) - y)**2.0)
>>> ssr_g2 = np.sum((g2_fit(x) - y)**2.0)
>>> ssr_g1 = np.sum((g1_fit(x) - y)**2.0)
>>> akaike_info_criterion_lsq(ssr_g3, 9, x.shape[0]) # doctest: +FLOAT_CMP
-660.41075962620482
>>> akaike_info_criterion_lsq(ssr_g2, 6, x.shape[0]) # doctest: +FLOAT_CMP
-662.83834510232043
>>> akaike_info_criterion_lsq(ssr_g1, 3, x.shape[0]) # doctest: +FLOAT_CMP
-647.47312032659499
Hence, from the AIC values, we would prefer to choose the model g2_fit.
However, we can considerably support the model g3_fit, since the
difference in AIC is about 2.4. We should reject the model g1_fit.
References
----------
.. [1] Akaike Information Criteria
<http://avesbiodiv.mncn.csic.es/estadistica/ejemploaic.pdf>
.. [2] Hu, S. Akaike Information Criterion.
<http://www4.ncsu.edu/~shu3/Presentation/AIC.pdf>
.. [3] Origin Lab. Comparing Two Fitting Functions.
<http://www.originlab.com/doc/Origin-Help/PostFit-CompareFitFunc>
"""
return akaike_info_criterion(-0.5 * n_samples * np.log(ssr / n_samples),
n_params, n_samples)
```