Construction & inference in C#

// --------------------------------------------------------------------------------------------------------------------
// <copyright file="NetworkExample.cs" company="Bayes Server">
//   Copyright (C) Bayes Server.  All rights reserved.
// </copyright>
// --------------------------------------------------------------------------------------------------------------------

namespace BayesServer.HelpSamples
    using System;

    using BayesServer.Inference.RelevanceTree;

    public static class NetworkExample
        public static void Main()
            // In this example we programatically create a simple Bayesian network.
            // Note that you can automatically define nodes from data using
            // classes in BayesServer.Data.Discovery, 
            // and you can automatically learn the parameters using classes in
            // BayesServer.Learning.Parameters,
            // however here we build a Bayesian network from scratch.

            var network = new Network("Demo");

            // add the nodes (variables)

            var aTrue = new State("True");
            var aFalse = new State("False");
            var a = new Node("A", aTrue, aFalse);

            var bTrue = new State("True");
            var bFalse = new State("False");
            var b = new Node("B", bTrue, bFalse);

            var cTrue = new State("True");
            var cFalse = new State("False");
            var c = new Node("C", cTrue, cFalse);

            var dTrue = new State("True");
            var dFalse = new State("False");
            var d = new Node("D", dTrue, dFalse);


            // add some directed links

            network.Links.Add(new Link(a, b));
            network.Links.Add(new Link(a, c));
            network.Links.Add(new Link(b, d));
            network.Links.Add(new Link(c, d));

            // at this point we have fully specified the structural (graphical) specification of the Bayesian Network.

            // We must define the necessary probability distributions for each node.

            // Each node in a Bayesian Network requires a probability distribution conditioned on it's parents.

            // NewDistribution() can be called on a Node to create the appropriate probability distribution for a node
            // or it can be created manually.

            // The interface IDistribution has been designed to represent both discrete and continuous variables,

            // As we are currently dealing with discrete distributions, we will use the
            // Table class.

            // To access the discrete part of a distribution, we use IDistribution.Table.

            // The Table class is used to define distributions over a number of discrete variables.

            var tableA = a.NewDistribution().Table;     // access the table property of the Distribution
            // IMPORTANT
            // Note that calling Node.NewDistribution() does NOT assign the distribution to the node.
            // A distribution cannot be assigned to a node until it is correctly specified.
            // If a distribution becomes invalid  (e.g. a parent node is added), it is automatically set to null.

            tableA[aTrue] = 0.1;
            tableA[aFalse] = 0.9;

            // now tableA is correctly specified we can assign it to Node A;
            a.Distribution = tableA;

            // node B has node A as a parent, therefore its distribution will be P(B|A)

            var tableB = b.NewDistribution().Table;
            tableB[aTrue, bTrue] = 0.2;
            tableB[aTrue, bFalse] = 0.8;
            tableB[aFalse, bTrue] = 0.15;
            tableB[aFalse, bFalse] = 0.85;
            b.Distribution = tableB;

            // specify P(C|A)
            var tableC = c.NewDistribution().Table;
            tableC[aTrue, cTrue] = 0.3;
            tableC[aTrue, cFalse] = 0.7;
            tableC[aFalse, cTrue] = 0.4;
            tableC[aFalse, cFalse] = 0.6;
            c.Distribution = tableC;

            // specify P(D|B,C)
            var tableD = d.NewDistribution().Table;

            // we could specify the values individually as above, or we can use a TableIterator as follows
            var iteratorD = new TableIterator(tableD, new Node[] { b, c, d });
            iteratorD.CopyFrom(new double[] { 0.4, 0.6, 0.55, 0.45, 0.32, 0.68, 0.01, 0.99 });
            d.Distribution = tableD;

            // The network is now fully specified

            // If required the network can be saved...

            if (false)   // change this to true to save the network
                // network.Save("fileName.bayes");  // replace 'fileName.bayes' with your own path and uncomment start of line

            // Now we will calculate P(A|D=True), i.e. the probability of A given the evidence that D is true

            // use the factory design pattern to create the necessary inference related objects
            var factory = new RelevanceTreeInferenceFactory();
            var inference = factory.CreateInferenceEngine(network);
            var queryOptions = factory.CreateQueryOptions();
            var queryOutput = factory.CreateQueryOutput();

            // we could have created these objects explicitly instead, but as the number of algorithms grows
            // this makes it easier to switch between them

            inference.Evidence.SetState(dTrue);  // set D = True

            var queryA = new Table(a);
            inference.Query(queryOptions, queryOutput); // note that this can raise an exception (see help for details)

            Console.WriteLine("P(A|D=True) = {" + queryA[aTrue] + "," + queryA[aFalse] + "}.");

            // Expected output ...
            // P(A|D=True) = {0.0980748663101604,0.90192513368984}

            // to perform another query we reuse all the objects

            // now lets calculate P(A|D=True, C=True)

            // we will also return the log-likelihood of the case
            queryOptions.LogLikelihood = true; // only request the log-likelihood if you really need it, as extra computation is involved

            inference.Query(queryOptions, queryOutput);
            Console.WriteLine(string.Format("P(A|D=True, C=True) = [{0},{1}], log-likelihood = {2}.", queryA[aTrue], queryA[aFalse], queryOutput.LogLikelihood.Value));
            // Expected output ...
            // P(A|D=True, C=True) = {0.0777777777777778,0.922222222222222}, log-likelihood = -2.04330249506396.

            // Note that we can also calculate joint queries such as P(A,B|D=True,C=True)