0. Observation¶
Today I will use the data set which is called 'Wine Quality Data Set'. And 50 number of Ph column of this dataset will be used. This dataset can be obtained from the following link.
In [2]:
import numpy as np
from scipy.stats import t
from scipy.stats import norm
from scipy.stats import gamma
import matplotlib.pyplot as plt
from sklearn.datasets import load_boston
from mpl_toolkits.mplot3d import Axes3D
import pandas as pd
%matplotlib inline
plt.style.use('dark_background')
In [14]:
# observation pH of red wine data
N=50
obs_data = pd.read_csv('./winequality/winequality-red.csv',
sep=';').sample(N,random_state=16).pH.values
plt.hist(obs_data,bins=13)
plt.xlim(2.5,4)
plt.title('Observation num={}'.format(N),fontsize=16)
plt.show()
2. Model and Prior distribution¶
- Model
Assume the observation follows univariate gaussian distribution.
- Prior distribution
Because conjugate prior for precision and mean of univariate gaussian distribution is gauss-gamma distribution. Gauss-gamma distribution is gonna be applied as prior distribution here.
In [7]:
def gauss_gamma_pdf(X, m, beta, a, b):
"""
X : consists of mean and lambda
"""
X = X.reshape(2,-1)
gamma_prob = gamma.pdf(
X[1],
a=a,
scale=1/b
)
norm_prob = norm.pdf(
X[0],
loc=m,
scale=np.sqrt(1/(beta * X[1]))
)
return gamma_prob * norm_prob
In [9]:
# parameter of gauss-gamma distribution
m = 0
beta=2
a=5
b=6
x = np.linspace(-4,4,101)
y = np.linspace(0,3,101) + 1e-10
xx, yy = np.meshgrid(x,y)
prob = gauss_gamma_pdf(
np.vstack([xx.ravel(), yy.ravel()]),
m=m, beta=beta, a=a, b=b
)
# plot gauss gamma distribution
contourf = plt.contourf(xx,yy,prob.reshape(xx.shape))
plt.colorbar(contourf)
plt.xlabel('mu',fontsize=14)
plt.ylabel('lambda',fontsize=14)
plt.title('plot of gauss-gamma distribution',fontsize=16)
plt.show()
It looks like 'ONIGIRI' in convenience store in Japan...:)
3. Posterior distribution¶
Posterior distribution looks like following.
$$\begin{eqnarray}p(\mu, \lambda | X) &\propto& p(X| \mu, \lambda^{-1}) p(\lambda, \mu) \\ &=& \prod^{N}_{n=1}N(x_n|\mu, \lambda^{-1})NG(\mu, \lambda | m, \beta, a,b)\end{eqnarray}$$With calculation, we will get the following result,
$$\begin{eqnarray}p(\mu, \lambda|X) &=& NG(\mu, \lambda | \hat{m}, \hat{\beta}, \hat{a},\hat{b}) \\ &=& N(\mu|\hat{m}, (\hat{\beta}\lambda)^{-1})Gam(\lambda|\hat{a},\hat{b})\end{eqnarray}$$$$\hat{\beta} = N + \beta$$$$\hat{m} = \frac{1}{\hat{\beta}}\left( \sum_{n=1}^{N} x_n + \beta m\right)$$$$\hat{a} = \frac{N}{2} + a$$$$\hat{b} = \frac{1}{2}\left(\sum^{N}_{n=1}x_n^2 + \beta m^2 - \hat{\beta}\hat{m}^2 \right) + b$$In [10]:
def post_dist(X, mu_0, beta, a, b):
"""
X : observation
followings are parameters of prior normal-gamma
mu_0, beta, a, b
"""
a_hat = (1/2) * X.shape[0] + a
beta_hat = beta + X.shape[0]
mu_hat = (X.sum() + beta * mu_0) / beta_hat
b_hat = (1/2) * (-beta_hat * (mu_hat **2) + \
(X**2).sum() + beta_hat*(mu_0**2)) + b
return mu_hat, beta_hat, a_hat, b_hat
In [11]:
# parameter of prior distribution
m = 0
beta=2
a=5
b=6
# compute parameter of posterior distribution
mu_hat, beta_hat, a_hat, b_hat = post_dist(
obs_data, mu_0=m, beta=beta, a=a, b=b)
print('Parameter of posterior distribution : ')
print('Mean : ', mu_hat)
print('Beta : ', beta_hat)
print('a : ', a_hat)
print('b : ', b_hat)
x = np.linspace(-4,4,101)
y = np.linspace(0,3,101) + 1e-10
xx, yy = np.meshgrid(x,y)
plt.figure(figsize=(15,5))
for i, (mu, beta, a, b) in enumerate(zip(
[m,mu_hat], [beta, beta_hat], [a, a_hat],[b, b_hat])):
prob_post = gauss_gamma_pdf(
np.vstack([xx.ravel(), yy.ravel()]),
m=mu, beta=beta, a=a, b=b
)
# plot gauss gamma distribution
plt.subplot(1,2,i+1)
contourf = plt.contourf(xx,yy,prob_post.reshape(xx.shape))
plt.colorbar(contourf)
plt.xlabel('mu',fontsize=14)
plt.ylabel('lambda',fontsize=14)
title = 'prior' if i ==0 else 'posterior'
plt.title('plot of gauss-gamma distribution ({})'.format(title),
fontsize=16)
plt.show()
4. Predictive distribution¶
For predictive distribution, parameters $\mu$ and $\lambda$ is supporsed to be integrated out by calculating following.
$$ p(x_* ) = \int \int p(x_*| \mu, \lambda) d\mu d\lambda$$
Or from bayesian theorem, following can be also calculated.
As a result, we got student-T distribution. $$ p(x_*) = st(x_*|\mu_s, \lambda_s, \nu)$$ $$\begin{eqnarray}\mu_s &=& m\\ \lambda_s &=& \frac{\beta a }{(1+\beta)b}\\ \nu_s &=& 2a \end{eqnarray}$$
Here, not only predictive distribution but showing comparison with maximum likelihood estimation :)
In [12]:
from scipy.stats import t
class predictive_t():
def __init__(self, m, beta, a, b):
self.mu = m
self.lam = (beta * a) / ((1+beta)*b)
self.nu = 2 * a
def pdf(self, X):
return t.pdf(X,df=self.nu, loc =mu, scale = 1/np.sqrt(self.lam))
In [13]:
# data to plot predictive distribution of t
pred_t = predictive_t(m=mu_hat,beta=beta_hat,a=a_hat,b=b_hat)
X = np.linspace(0,6,101)
y_pred = pred_t.pdf(X)
# data to plot observations
y_mle = norm.pdf(X,
loc=obs_data.sum() / obs_data.shape[0],
scale= np.sqrt(obs_data.var())
)
plt.figure(figsize=(10,5))
plt.plot(X,y_mle,label='Maximum Likelihood Estimation')
plt.plot(X,y_pred,label='Predictive distribution\n(Bayesian Inference)')
plt.legend(fontsize=14)
plt.title('Comparison predictive distribution and Maximum Likelihood Estimation',
fontsize=16)
plt.show()
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