tests/ExampleTree.R

In CRF: Conditional Random Fields

library(CRF)

nNodes <- 100
nStates <- 4

adj <-
structure(c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
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1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0), .Dim = c(100L, 100L))

crf <- make.crf(adj, nStates)

crf$node.pot[4,] <- c(.9, .09, .009, .001)
crf$node.pot[-4,] <- 1

trans <- array(dim=c(4, 4))
trans[1,] <- c(0.9890, 0.0099, 0.0010, 0.0001)
trans[2,] <- c(0.1309, 0.8618, 0.0066, 0.0007)
trans[3,] <- c(0.0420, 0.0841, 0.8682, 0.0057)
trans[4,] <- c(0.0667, 0.0333, 0.1667, 0.7333)

queue <- c(4)
done.nodes <- c()
done.edges <- c()
while (length(queue) > 0)
{
	n <- queue[1]
	e <- crf$adj.edges[[n]]
	e <- e[!e %in% done.edges]
	e1 <- e[crf$edges[e,1] == n]
	for (i in e1) crf$edge.pot[[i]][,] <- trans
	e2 <- e[crf$edges[e,2] == n]
	for (i in e2) crf$edge.pot[[i]][,] <- t(trans)
	done.nodes <- c(done.nodes, n)
	done.edges <- c(done.edges, e1, e2)
	queue <- c(queue[-1], crf$adj.nodes[[n]])
	queue <- queue[!queue %in% done.nodes]
}

answer <-
structure(list(decode = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), node.bel = structure(c(0.910308819836526, 
0.911010874568674, 0.912883867401247, 0.9, 0.907320044555024, 
0.912883867401247, 0.91160347075071, 0.908490212589711, 0.9042832062, 
0.908490212589711, 0.912883867401247, 0.912103876374476, 0.914127109426, 
0.911010874568674, 0.908490212589711, 0.905931515438836, 0.907320044555024, 
0.910308819836526, 0.912526606630899, 0.91160347075071, 0.913840680215625, 
0.912526606630899, 0.908490212589711, 0.910308819836526, 0.909476755453772, 
0.913185926407476, 0.912883867401247, 0.912883867401247, 0.91160347075071, 
0.912883867401247, 0.91160347075071, 0.911010874568674, 0.91160347075071, 
0.912103876374476, 0.913995722969885, 0.913185926407476, 0.912103876374476, 
0.907320044555024, 0.91160347075071, 0.91160347075071, 0.913441424019237, 
0.907320044555024, 0.913441424019237, 0.909476755453772, 0.913840680215625, 
0.912526606630899, 0.913185926407476, 0.91160347075071, 0.909476755453772, 
0.913441424019237, 0.907320044555024, 0.905931515438836, 0.913840680215625, 
0.91160347075071, 0.913185926407476, 0.913995722969885, 0.905931515438836, 
0.910308819836526, 0.913185926407476, 0.913185926407476, 0.911010874568674, 
0.909476755453772, 0.913185926407476, 0.907320044555024, 0.913657633677552, 
0.91160347075071, 0.905931515438836, 0.913441424019237, 0.913840680215625, 
0.9023257, 0.91160347075071, 0.910308819836526, 0.912526606630899, 
0.912103876374476, 0.908490212589711, 0.907320044555024, 0.91160347075071, 
0.912103876374476, 0.909476755453772, 0.913441424019237, 0.913657633677552, 
0.91160347075071, 0.911010874568674, 0.912883867401247, 0.912103876374476, 
0.905931515438836, 0.908490212589711, 0.909476755453772, 0.913185926407476, 
0.912103876374476, 0.908490212589711, 0.912883867401247, 0.911010874568674, 
0.910308819836526, 0.911010874568674, 0.907320044555024, 0.9042832062, 
0.913185926407476, 0.912103876374476, 0.912103876374476, 0.0779372016316757, 
0.0771261148119761, 0.0749775286283519, 0.09, 0.081410940315857, 
0.0749775286283519, 0.0764435363569473, 0.0800475722188414, 0.08496361592, 
0.0800475722188414, 0.0749775286283519, 0.0758689336941176, 0.0735748478206177, 
0.0771261148119761, 0.0800475722188414, 0.083033032768672, 0.081410940315857, 
0.0779372016316757, 0.0753850825546116, 0.0764435363569473, 0.0738949427826766, 
0.0753850825546116, 0.0800475722188414, 0.0779372016316757, 0.078901282896636, 
0.0746341379956691, 0.0749775286283519, 0.0749775286283519, 0.0764435363569473, 
0.0749775286283519, 0.0764435363569473, 0.0771261148119761, 0.0764435363569473, 
0.0758689336941176, 0.0737213456422645, 0.0746341379956691, 0.0758689336941176, 
0.081410940315857, 0.0764435363569473, 0.0764435363569473, 0.0743447214100827, 
0.081410940315857, 0.0743447214100827, 0.078901282896636, 0.0738949427826766, 
0.0753850825546116, 0.0746341379956691, 0.0764435363569473, 0.078901282896636, 
0.0743447214100827, 0.081410940315857, 0.083033032768672, 0.0738949427826766, 
0.0764435363569473, 0.0746341379956691, 0.0737213456422645, 0.083033032768672, 
0.0779372016316757, 0.0746341379956691, 0.0746341379956691, 0.0771261148119761, 
0.078901282896636, 0.0746341379956691, 0.081410940315857, 0.074100720088625, 
0.0764435363569473, 0.083033032768672, 0.0743447214100827, 0.0738949427826766, 
0.0872622, 0.0764435363569473, 0.0779372016316757, 0.0753850825546116, 
0.0758689336941176, 0.0800475722188414, 0.081410940315857, 0.0764435363569473, 
0.0758689336941176, 0.078901282896636, 0.0743447214100827, 0.074100720088625, 
0.0764435363569473, 0.0771261148119761, 0.0749775286283519, 0.0758689336941176, 
0.083033032768672, 0.0800475722188414, 0.078901282896636, 0.0746341379956691, 
0.0758689336941176, 0.0800475722188414, 0.0749775286283519, 0.0771261148119761, 
0.0779372016316757, 0.0771261148119761, 0.081410940315857, 0.08496361592, 
0.0746341379956691, 0.0758689336941176, 0.0758689336941176, 0.0109521583525101, 
0.0110670216561422, 0.0113531107139509, 0.009, 0.0104310474358567, 
0.0113531107139509, 0.0111611227943571, 0.0106405568489174, 0.00986031504, 
0.0106405568489174, 0.0113531107139509, 0.0112382223661015, 0.011515549037391, 
0.0110670216561422, 0.0106405568489174, 0.010174608824428, 0.0104310474358567, 
0.0109521583525101, 0.0113013843901413, 0.0111611227943571, 0.0114814461390273, 
0.0113013843901413, 0.0106405568489174, 0.0109521583525101, 0.0108119060911639, 
0.0113954480040508, 0.0113531107139509, 0.0113531107139509, 0.0111611227943571, 
0.0113531107139509, 0.0111611227943571, 0.0110670216561422, 0.0111611227943571, 
0.0112382223661015, 0.0115002534152921, 0.0113954480040508, 0.0112382223661015, 
0.0104310474358567, 0.0111611227943571, 0.0111611227943571, 0.0114300732760162, 
0.0104310474358567, 0.0114300732760162, 0.0108119060911639, 0.0114814461390273, 
0.0113013843901413, 0.0113954480040508, 0.0111611227943571, 0.0108119060911639, 
0.0114300732760162, 0.0104310474358567, 0.010174608824428, 0.0114814461390273, 
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Tree <- list()
Tree$crf <- crf
Tree$answer <- answer
save(Tree, file="Tree.RData")