# AI Class: Bayes Networks

October 23, 2011

The second week of the online Stanford AI class was about probability, reasoning when there is uncertainty and, more specifically Bayes networks. I don’t much want to talk about the theory behind these things here since that’s covered in a lot of detail on the linked Wikipedia page, in the lectures and in AIMA.

Instead, I want to present a mildly amusing, although not very efficient, Haskell implementation of Bayes networks. It’s often said that if you know the full joint probability distribution function (PDF) for a system, you can calculate any marginal or conditional probabilities you want. Well, Haskell is a functional programming language, a PDF is a function, so can we represent the PDF explicitly and use it for calculating? The answer, of course, is yes.

The idea here is to implement something that will allow us to write the two-test cancer problem from the lectures as:

import BayesNet

data Event = C | T1 | T2 deriving (Eq, Ord, Show)

bn = fromList [(C, [], [0.01]),
(T1, [C], [0.9,0.2]),
(T2, [C], [0.9,0.2])]

where the entries in the list passed to the BayesNet.fromList function are triples giving the label for a node in the network, a list of other nodes that it is conditional on (i.e. nodes at the other end of incoming edges) and the probability table for the node. If a node $A$ is conditional on nodes $B$ and $C$, the probability table entries are stored in the order $P(A|+B,+C)$, $P(A|+B,-C)$, $P(A|-B,+C)$, $P(A|-B,-C)$. Given this definition, we can then calculate $P(C|T1,T2)$ as

p_3_20 = prob bn C [(T1,True),(T2,True)]

and $P(C|T1,\neg T2)$ as

p_3_21 = prob bn C [(T1,True),(T2,False)]

## Data structures

A Bayesian network is basically just a directed acyclic graph with probability tables of the appropriate size associated with each node. In my Haskell code, I treat Bayesian networks as an abstract data type, exporting only a way to construct a network from a simple list-based description, and functions to calculate probability values given a network. (You can imagine lots of other possible things you might want to do, including updating networks, calculating conditional independence relationships, and so on, but here, we’re going to concentrate on the basics.)

module BayesNet(fromList, prob, jointProb, jointProbTF) where

import qualified Data.Map as M
import Data.List

The internal representation of a node in the network is as a list of nodes on which this node is conditional, and a probability table. Nodes are parameterised by type e (“event”) and the type of probability values is parameterised too, by type p, so that we can use, for instance, rational values if we want. (I’ll show an example of this later on, but basically, we just want to impose the type class constraint Fractional p everywhere to make sure that the probability values that get passed in are numbers with a fractional part.)

data BayesNode e p = BayesNode { cond :: [e], ps :: [p] }
deriving (Eq, Ord, Show)

A Bayesian network is then just a map from node labels to nodes.

newtype BayesNet e p = BayesNet (M.Map e (BayesNode e p))
deriving (Eq, Ord, Show)

We can generate Bayesian network values from a simple list representation, which is a list of nodes of the form:

  (event, conditions, probabilities)

where:

• event is a label for the node (of type e in all the function type signatures here);
• conditions is a list of the events on which this event is conditional (i.e. a list of type [e]); and
• probabilities is a table of probability values, stored as a flat list. The type of these values (represented as type variable p everywhere) can be any fractional numeric type. The values are stored in lexical order of the truth value assignment to the conditions variables, where True sorts before False. For instance, if conditions is [R,S], then the probability values are in the order +R,+S; +R,-S; -R,+S; -R,-S.

Creating a network from its list representation is simple. The only small thing we need to do is to check that the probability table has the right number of entries, dependent on the number of conditional variables. It would be interesting to try to apply this constraint at the type level. No idea how to do that. It’s probably easy in something like Agda, with dependent types, or Qi, where you can write programs at the type level. In Haskell, I guess it might require Template Haskell. I don’t know though. In any case, let’s keep things simple here:

fromList :: (Ord e, Fractional p) => [(e, [e], [p])] -> BayesNet e p
fromList = BayesNet . (foldl doOne M.empty)
where doOne m (ev, cond, ps) =
if (length ps /= 2^(length cond))
then error "Invalid length for probability table"
else M.insert ev (BayesNode cond ps) m

## Probability calculations

Given a Bayesian network, we want to use it to calculate probabilities. A couple of special cases, first the probability that a single event is true, given conditions (true or false) on a set of other events.

prob :: (Ord e, Fractional p) => BayesNet e p -> e -> [(e,Bool)] -> p
prob bn ev cond = jointProb bn [ev] cond

Then, the joint probability that a set of events is true, given conditions (true or false) on a set of other events.

jointProb :: (Ord e, Fractional p) => BayesNet e p -> [e] -> [(e,Bool)] -> p
jointProb bn evs cond = jointProbTF bn (zip evs $repeat True) cond Then the general case: the probability that a set of events is true or false, as specified, given conditions (true or false) on a set of other events. We do this by calculating the joint PDF of the whole network, then enumerating the possible assignments of truth values to the free variables in the numerator and denominator of the representation of $P(X | Y) = P(X ^ Y) / P(Y)$, applying the joint PDF to each of these variable assignments, summing the results and forming the fraction representing the conditional probability. jointProbTF :: (Ord e, Fractional p) => BayesNet e p -> [(e,Bool)] -> [(e,Bool)] -> p jointProbTF bn@(BayesNet m) evs cond = eval (cond ++ evs) / eval cond where eval = sum . (map (jointPDF bn)) . (enumerate bn) All the work here is being done in the computation of the joint PDF, which represented just as a regular Haskell function, and the enumeration of the possibilities (remember that we’re only dealing with binary random variables throughout, just as in the lectures). ## The joint PDF The joint PDF for the network is: $P(B,E,A,J,M) = P(B) P(E) P(A|B,E) P(J|A) P(M|A)$ where we have one factor per node in the network, each of which is conditioned on the variables in the nodes connected to the incoming edges. In the code below, the joint PDF is represented as a function that takes a map from node labels to Boolean values and returns a probability value. To calculate the joint PDF of the whole network, we form the product of the individual PDF factors for each node in the network, applying each of these factor functions to the input variable assignment, and forming the product. jointPDF :: (Ord e, Fractional p) => BayesNet e p -> (M.Map e Bool -> p) jointPDF bn@(BayesNet m) = (\vals -> product$ zipWith (applyFactor vals) (M.keys m) factors)
where factors = map (jointPDFFactor bn) (M.keys m)
applyFactor vs k f = f (vs M.! k) (map (vs M.!) (cond $m M.! k)) We then need to produce the constituent functions for the individual factors in the PDF. Thes functions, for a factor of the form $P(X | Y)$ are represented by a function that takes a single Boolean value representing the value of $X$, and a list of Boolean values representing the values of $Y$, and returns $P(X | Y)$. To do this, we need to know the predecessors of the node in question in the graph of the network, we need to extract the correct value from the node’s probability table, and we need to deal with complementary probability values. jointPDFFactor :: (Ord e, Fractional p) => BayesNet e p -> e -> (Bool -> [Bool] -> p) jointPDFFactor bn@(BayesNet m) ev = (\b bs -> let pval = pvals !! (length pvals - idx - 1) idx = foldl (\i b -> (if b then 1 else 0) + 2 * i) 0 bs in if b then pval else (1 - pval)) where pvals = ps (m M.! ev) ## Enumerating cases The other element we need in order to calculate probabilities is to be able to enumerate the possible assignments of Boolean truth values to variables in the network, given that some variables may have their values fixed by the requirements of the calculation. Here, we assume that there are no extra logical constraints on the values that variables may take. In many more realistic problems, there may be consistency requirements that eliminate some possible assignments (see The Wumpus World Revisited, Section 13.6 of AIMA for a simple example where this is the case). Given that caveat, state enumeration is quite simple: enumerate :: (Ord e, Fractional p) => BayesNet e p -> [(e,Bool)] -> [M.Map e Bool] enumerate bn@(BayesNet m) fixed = map compose msks where base = M.fromList fixed vars = (M.keys m) \\ (map fst fixed) msks = masks (length vars) compose = (M.union base) . M.fromList . (zip vars) We have a little helper to generate combinations of Boolean values: masks :: Int -> [[Bool]] masks 0 = [[]] masks 1 = [[False], [True]] masks n = map (False :) xs' ++ map (True :) xs' where xs' = masks (n - 1) ## Applications Given the definitions above, the two test cancer example works as expected. We can also deal with Sebastian’s happiness example. The necessary definition of the Bayes network is: import BayesNet import Data.Ratio data Event = S | R | H deriving (Eq, Ord, Show) bn = fromList [(S, [], [7 % 10]), (R, [], [1 % 100]), (H, [S, R], [1, 7 % 10, 9 % 10, 1 % 10])] Here, I’ve made the probability values in the Bayes network be rational numbers (remember that we can use any instance of typeclass Fractional for this). We can then answer some of the questions Sebastian posed in the lecture. First we load the definition into GHCi: *Main> :load "happiness.hs" [1 of 2] Compiling BayesNet ( BayesNet.hs, interpreted ) [2 of 2] Compiling Main ( happiness.hs, interpreted ) Ok, modules loaded: BayesNet, Main. Then we ask the value for $P(R|S)$: *Main> prob bn R [(S,True)] Loading package array-0.3.0.2 ... linking ... done. Loading package containers-0.4.0.0 ... linking ... done. 1 % 100 The answer is just $P(R)$ because $R$ and $S$ are independent. Notice that we get the result as a rational here. What about $P(R|H,S)$? Just as easy: *Main> prob bn R [(H,True),(S,True)] 10 % 703 *Main> fromRational$ prob bn R [(H,True),(S,True)]
1.422475106685633e-2

Here, I’ve converted the result from a rational to a floating point for comparison with the next result, which is $P(R|H)$:

*Main> prob bn R [(H,True)]
97 % 5245
*Main> fromRational \$ prob bn R [(H,True)]
1.8493803622497616e-2

Here, $P(R|H) > P(R|H,S)$, demonstrating the “explaining away” effect.

For sure, you can do the homework questions using the same setup.

## Conclusions

This is not a good way to do probability calculations on Bayes networks in general. There are much better approaches available than enumeration. My goal here was more to investigate how easy it would be to construct an explicit programmatic representation of the full joint PDF of a Bayes network. Whether writing all this code to answer three homework problems is an efficient use of time, I’ll leave for the reader to decide…

The code is in: BayesNet.hs, cancer.hs and happiness.hs. There’s also code implementing the earthquake alarm example from the lectures in alarm.hs.