Back to the table of contents Previous Next ## Bayesian belief network exampleThis document shows an example of how to use MCMC to do Bayesian inference with a belief network in Waffles. As an example, we will build a belief network for ranking professional golfers. Let's start by downloading the golf dataset from mldata.org. This dataset records the number of swings used by 604 professional golfers at 42 different tournaments. Ranking the golfers is a challenging problem because not every golfer participated in every tournament, and not every tournament has the same difficulty. We can rank a golfer by attributing the number of swings used by each golfer to two causes: 1- the difficulty of the
tournament, and 2- error on the part of the golfer. Here is a belief network that was designed for this purpose: Our first task is to instantiate this network. Here is some code to do this: GBayesNet bn; // Make the 4 nodes that are not on a plate GBNNormal* pTournMean = bn.newNormal(); pTournMean->setMeanAndVariance(0, bn.newConst(72.0), bn.newConst(2.0)); GBNInverseGamma* pTournVar = bn.newInverseGamma(); pTournVar->setAlphaAndBeta(0, bn.newConst(18), bn.newConst(66.667)); GBNInverseGamma* pGolferVar = bn.newInverseGamma(); pGolferVar->setAlphaAndBeta(0, bn.newConst(18), bn.newConst(66.667)); GBNInverseGamma* pInstVar = bn.newInverseGamma(); pInstVar->setAlphaAndBeta(0, bn.newConst(83), bn.newConst(714.29)); // Make the 42 tournament nodes vector<GBNNormal*> tourns; for(size_t i = 0; i < 42; i++) { GBNNormal* pTourn = bn.newNormal(); pTourn->setMeanAndVariance(0, pTournMean, pTournVar); tourns.push_back(pTourn); } // Make the 604 golfer nodes vector<GBNNormal*> golfers; for(size_t i = 0; i < 604; i++) { GBNNormal* pGolfer = bn.newNormal(); pGolfer->setMeanAndVariance(0, bn.newConst(0), pGolferVar); golfers.push_back(pGolfer); } // Make the 5700 swing nodes GMatrix data; data.loadArff("golfdata.arff"); for(size_t i = 0; i < data.rows(); i++) { double* pRow = data[i]; GBNSum* pSum = bn.newSum(); size_t tourn = (size_t)pRow[2] - 1; if(tourn >= 42) throw Ex("tournament out of range"); size_t golfer = (size_t)pRow[0]; if(golfer >= 604) throw Ex("golfer out of range"); pSum->addParent(tourns[tourn]); pSum->addParent(golfers[golfer]); GBNNormal* pInst = bn.newNormal(); pInst->setMeanAndVariance(0, pSum, pInstVar); pInst->setObserved(pRow[1]); }Now, we are ready to use MCMC to do some inference. We will begin by doing some burn-in iterations: for(size_t i = 0; i < 50000; i++) bn.sample();Then, we can draw some samples to represent the joint distribution. We will store these samples in a matrix: GMatrix results(0, 604); for(size_t i = 0; i < 50000; i++) { bn.sample(); double* pRow = results.newRow(); for(size_t j = 0; j < 604; j++) *(pRow++) = golfers[j]->currentValue(); }Finally, let's examine the results. I computed the median "error" of each golfer, then sorted by this value, and printed the first 10 lines. GMatrix digest(604, 2); for(size_t i = 0; i < 604; i++) { digest[i][0] = i; digest[i][1] = results.columnMedian(i); } digest.sort(1); for(size_t i = 0; i < 10; i++) { ((const GArffRelation&)data.relation()).printAttrValue(cout, 0, digest[i][0]); cout << " " << digest[i][1] << "\n"; }Here are my results: VijaySingh -3.89276 TigerWoods -3.7662 ErnieEls -3.39097 PhilMickelson -3.38151 StewartCink -3.04885 JayHaas -2.92062 SergioGarcia -2.89011 ScottVerplank -2.81684 RetiefGoosen -2.77541 PadraigHaringtn -2.76943Some Wikipedia searches confirm that these guys are pretty-good golfers, so I think these results are approximately correct. I probably didn't need to do so many iterations, but I find it is often easier to just use overkill rather than to make mixing plots to figure out the minimum number of iterations that are really necessary. Previous Next Back to the table of contents |