示例#1
0
// NewIndepGraph constructs a new Graph given a DataGroup.
func NewIndepGraph(data []*utils.VarData, pval float64) *Graph {
	igraph := Graph{make(map[int][]int), nil}
	n := len(data)

	// IDs and Reverse IDs.
	ids := make([]int, n)
	rids := make(map[int]int)

	for i := 0; i < n; i++ {
		ids[i] = data[i].Varid
		rids[ids[i]] = i
		igraph.adjlist[ids[i]] = []int{}
	}

	sys.Println("Constructing independence graph...")
	// Construct the indepedency graph by adding an edge if there exists a dependency relation.
	for i := 0; i < n; i++ {
		for j := i + 1; j < n; j++ {
			v1, v2 := ids[i], ids[j]

			// Initialize the count matrix mdata.
			//sys.Println("Initializing count matrix...")
			p, q := data[i].Categories, data[j].Categories
			mdata := make([][]int, p+1)
			for k := 0; k < p+1; k++ {
				mdata[k] = make([]int, q+1)
			}

			// len(data[i].Data) == len(data[j].Data) by definition.
			m := len(data[i].Data)
			for k := 0; k < m; k++ {
				mdata[data[i].Data[k]][data[j].Data[k]]++
			}

			//sys.Println("Counting totals and assigning to edges...")
			// Total on the x axis, y axis and x+y respectively.
			tx, ty, tt := make([]int, q), 0, 0
			//sys.Println("Y-axis...")
			for x := 0; x < p; x++ {
				ty = 0
				for y := 0; y < q; y++ {
					ty += mdata[x][y]
					tx[y] += mdata[x][y]
				}
				mdata[x][q] = ty
			}
			// Compute total on the x axis.
			//sys.Println("X-axis...")
			for y := 0; y < q; y++ {
				mdata[p][y] = tx[y]
				tt += tx[y]
			}
			// Total total.
			mdata[p][q] = tt

			// Checks if variables i, j are independent.
			//sys.Println("Checking for pairwise independence...")
			indep := GTest(p, q, mdata, n*(n-1)/2, pval)

			//sys.Printf("%t\n", indep)
			// If not independent, then add an undirected edge i-j.
			if !indep {
				//sys.Println("Not independent. Creating edge...")
				igraph.adjlist[v1] = append(igraph.adjlist[v1], v2)
				igraph.adjlist[v2] = append(igraph.adjlist[v2], v1)
			} //else {
			//sys.Println("Independent. No edges.")
			//}
		}
	}

	// utils.Union-utils.Find to discriminate each set of connected variables that are fully disconnected of
	// another set of connected set of variables
	sys.Println("utils.Finding disconnected subgraphs...")

	// Set of utils.Union-utils.Find trees.
	sets := make([]*utils.UFNode, n)

	// At first every vertex has its own set.
	for i := 0; i < n; i++ {
		sets[i] = utils.MakeSet(ids[i])
	}

	sys.Println("Preparing to test each vertex of the independence graph for disconnectivity...")
	// If a vertex u has an edge with another vertex v, then union sets that contain u and v.
	for i := 0; i < n; i++ {
		v1 := ids[i]
		m := len(igraph.adjlist[v1])
		for j := 0; j < m; j++ {
			v2 := igraph.adjlist[v1][j]
			rv2 := rids[v2]

			if utils.Find(sets[i]) == utils.Find(sets[rv2]) {
				continue
			}

			utils.Union(sets[i], sets[rv2])
		}
	}

	igraph.Kset = nil
	for i := 0; i < n; i++ {
		if sets[i] == sets[i].Pa {
			igraph.Kset = append(igraph.Kset, utils.UFVarids(sets[i]))
		}
	}

	return &igraph
}
示例#2
0
文件: gens.go 项目: RenatoGeh/gospn
// Gens Learning Algorithm
// Based on the article
//	Learning the Structure of Sum Product Networks
//	Robert Gens and Pedro Domingos
//	International Conference on Machine Learning 30 (ICML 2013)
func Gens(sc map[int]Variable, data []map[int]int, kclusters int, pval, eps float64, mp int) spn.SPN {
	n := len(sc)

	sys.Printf("Sample size: %d, scope size: %d\n", len(data), n)

	// If the data's scope is unary, then we return a leaf (i.e. a univariate distribution).
	if n == 1 {
		sys.Println("Creating new leaf...")

		// m number of instantiations.
		m := len(data)
		// pr is the univariate probability distribution.
		var tv *Variable
		for _, v := range sc {
			tv = &v
		}
		counts := make([]int, tv.Categories)
		for i := 0; i < m; i++ {
			counts[data[i][tv.Varid]]++
		}

		leaf := spn.NewGaussian(tv.Varid, counts)
		//sys.Println("Leaf created.")
		return leaf
	}

	// Else we check for independent subsets of variables. We separate variables in k partitions,
	// where every partition is pairwise indepedent with each other.
	//sys.Println("Preparing to create new product node...")

	sys.Println("Creating VarDatas for Independency Test...")
	vdata, l := make([]*utils.VarData, n), 0
	for _, v := range sc {
		tn := len(data)
		// tdata is the transpose of data[k].
		tdata := make([]int, tn)
		for j := 0; j < tn; j++ {
			tdata[j] = data[j][v.Varid]
		}
		vdata[l] = utils.NewVarData(v.Varid, v.Categories, tdata)
		l++
	}

	sys.Println("Creating new Independency graph...")
	// Independency graph.
	igraph := indep.NewUFIndepGraph(vdata, pval)
	vdata = nil

	// If true, then we can partition the set of variables in data into independent subsets. This
	// means we can create a product node (since product nodes' children have disjoint scopes).
	if len(igraph.Kset) > 1 {
		sys.Println("Found independency. Separating independent sets.")

		//sys.Println("Found independency between variables. Creating new product node...")
		// prod is the new product node. m is the number of disjoint sets. kset is a shortcut.
		prod, m, kset := spn.NewProduct(), len(igraph.Kset), &igraph.Kset
		tn := len(data)
		for i := 0; i < m; i++ {
			// Data slices of the relevant vectors.
			tdata := make([]map[int]int, tn)
			// Number of variables in set of variables kset[i].
			s := len((*kset)[i])
			for j := 0; j < tn; j++ {
				tdata[j] = make(map[int]int)
				for l := 0; l < s; l++ {
					// Get the instanciations of variables in kset[i].
					//sys.Printf("[%d][%d] => %v vs %v | %v vs %v\n", j, k, (*kset)[i][k], len(data[j]), len(tdata[j]), k)
					k := (*kset)[i][l]
					tdata[j][k] = data[j][k]
				}
			}
			// Create new scope with new variables.
			nsc := make(map[int]Variable)
			for j := 0; j < s; j++ {
				t := (*kset)[i][j]
				nsc[t] = Variable{t, sc[t].Categories}
			}
			//sys.Printf("LENGTH: %d\n", len(tdata))
			//sys.Println("Product node created. Recursing...")
			// Adds the recursive calls as children of this new product node.
			prod.AddChild(Gens(nsc, tdata, kclusters, pval, eps, mp))
		}
		return prod
	}
	igraph = nil

	// Else we perform k-clustering on the instances.
	sys.Println("No independency found. Preparing for clustering...")

	m := len(data)
	mdata := make([][]int, m)
	for i := 0; i < m; i++ {
		lc := len(data[i])
		mdata[i] = make([]int, lc)
		l := 0
		keys := make([]int, lc)
		for k := range data[i] {
			keys[l] = k
			l++
		}
		sort.Ints(keys)
		for j := 0; j < lc; j++ {
			mdata[i][j] = data[i][keys[j]]
		}
	}

	var clusters []map[int][]int
	if kclusters > 0 {
		sys.Printf("data: %d, mdata: %d\n", len(data), len(mdata))
		if len(mdata) < kclusters {
			//Fully factorized form.
			//All instances are approximately the same.
			prod := spn.NewProduct()
			m := len(data)
			for _, v := range sc {
				counts := make([]int, v.Categories)
				for i := 0; i < m; i++ {
					counts[data[i][v.Varid]]++
				}
				leaf := spn.NewGaussian(v.Varid, counts)
				prod.AddChild(leaf)
			}
			return prod
		}
		clusters = cluster.KMeansV(kclusters, mdata)
	} else if kclusters == -1 {
		clusters = cluster.DBSCAN(mdata, eps, mp)
	} else {
		clusters = cluster.OPTICS(mdata, eps, mp)
	}
	k := len(clusters)
	//sys.Printf("Clustering similar instances with %d clusters.\n", k)
	if k == 1 {
		// Fully factorized form.
		// All instances are approximately the same.
		prod := spn.NewProduct()
		m := len(data)
		for _, v := range sc {
			counts := make([]int, v.Categories)
			for i := 0; i < m; i++ {
				counts[data[i][v.Varid]]++
			}
			leaf := spn.NewGaussian(v.Varid, counts)
			counts = nil
			prod.AddChild(leaf)
		}
		return prod
	}
	mdata = nil

	sys.Println("Reformating clusters to appropriate format and creating sum node...")

	sum := spn.NewSum()
	for i := 0; i < k; i++ {
		ni := len(clusters[i])
		ndata := make([]map[int]int, ni)

		l := 0
		for k := range clusters[i] {
			ndata[l] = make(map[int]int)
			for index, value := range data[k] {
				ndata[l][index] = value
			}
			l++
		}

		nsc := make(map[int]Variable)
		for k, v := range sc {
			nsc[k] = v
		}

		//sys.Println("Created new sum node child. Recursing...")
		sum.AddChildW(Gens(nsc, ndata, kclusters, pval, eps, mp), float64(ni)/float64(len(data)))
	}

	clusters = nil
	return sum
}