bayes_table


Bayesian updates using the table method

This notebook demonstrates a way of doing simple Bayesian updates using the table method, with a Pandas DataFrame as the table.

Copyright 2018 Allen Downey

MIT License: https://opensource.org/licenses/MIT


In [1]:
# Configure Jupyter so figures appear in the notebook
%matplotlib inline

# Configure Jupyter to display the assigned value after an assignment
%config InteractiveShell.ast_node_interactivity='last_expr_or_assign'

import numpy as np
import pandas as pd

As an example, I'll use the "cookie problem", which is a version of a classic probability "urn problem".

Suppose there are two bowls of cookies.

  • Bowl #1 has 10 chocolate and 30 vanilla.

  • Bowl #2 has 20 of each.

You choose a bowl at random, and then pick a cookie at random. The cookie turns out to be vanilla. What is the probability that the bowl you picked from is Bowl #1?

The BayesTable class

Here's the class that represents a Bayesian table.


In [2]:
class BayesTable(pd.DataFrame):
    def __init__(self, hypo, prior=1):
        columns = ['hypo', 'prior', 'likelihood', 'unnorm', 'posterior']
        super().__init__(columns=columns)
        self.hypo = hypo
        self.prior = prior
    
    def mult(self):
        self.unnorm = self.prior * self.likelihood
        
    def norm(self):
        nc = np.sum(self.unnorm)
        self.posterior = self.unnorm / nc
        return nc
    
    def update(self):
        self.mult()
        return self.norm()
    
    def reset(self):
        return BayesTable(self.hypo, self.posterior)

Here's an instance that represents the two hypotheses: you either chose from Bowl 1 or Bowl 2:


In [3]:
table = BayesTable(['Bowl 1', 'Bowl 2'])


Out[3]:
hypo prior likelihood unnorm posterior
0 Bowl 1 1 NaN NaN NaN
1 Bowl 2 1 NaN NaN NaN

Since we didn't specify prior probabilities, the default value is equal priors for all hypotheses.

Now we can specify the likelihoods:

  • The likelihood of getting a vanilla cookie from Bowl 1 is 3/4.

  • The likelihood of getting a vanilla cookie from Bowl 2 is 1/2.

Here's how we plug the likelihoods in:


In [4]:
table.likelihood = [3/4, 1/2]
table


Out[4]:
hypo prior likelihood unnorm posterior
0 Bowl 1 1 0.75 NaN NaN
1 Bowl 2 1 0.50 NaN NaN

The next step is to multiply the priors by the likelihoods, which yields the unnormalized posteriors.


In [5]:
table.mult()
table


Out[5]:
hypo prior likelihood unnorm posterior
0 Bowl 1 1 0.75 0.75 NaN
1 Bowl 2 1 0.50 0.50 NaN

Now we can compute the normalized posteriors; norm returns the normalization constant.


In [6]:
table.norm()


Out[6]:
1.25

In [7]:
table


Out[7]:
hypo prior likelihood unnorm posterior
0 Bowl 1 1 0.75 0.75 0.6
1 Bowl 2 1 0.50 0.50 0.4

We can read the posterior probabilities from the last column: the probability that you chose from Bowl 1 is 60%.

Resetting

Suppose you put the first cookie back, stir the bowl, and select another cookie from the same bowl.

If this second cookie is chocolate, what is the probability, now, that you are drawing from Bowl 1?

To solve this problem, we want a new table where the priors in the new table are the posteriors from the old table. That's what the reset method computes:


In [8]:
table2 = table.reset()


Out[8]:
hypo prior likelihood unnorm posterior
0 Bowl 1 0.6 NaN NaN NaN
1 Bowl 2 0.4 NaN NaN NaN

Here are the likelihoods for the second update.


In [9]:
table2.likelihood = [1/4, 1/2]

We could run mult and norm again, or run update, which does both steps.


In [10]:
table2.update()


Out[10]:
0.35

Here are the results.


In [11]:
table2


Out[11]:
hypo prior likelihood unnorm posterior
0 Bowl 1 0.6 0.25 0.15 0.428571
1 Bowl 2 0.4 0.50 0.20 0.571429

But the result is the same.