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cora/README

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+This directory contains the a selection of the Cora dataset (www.research.whizbang.com/data).
+
+The Cora dataset consists of Machine Learning papers. These papers are classified into one of the following seven classes:
+		Case_Based
+		Genetic_Algorithms
+		Neural_Networks
+		Probabilistic_Methods
+		Reinforcement_Learning
+		Rule_Learning
+		Theory
+
+The papers were selected in a way such that in the final corpus every paper cites or is cited by atleast one other paper. There are 2708 papers in the whole corpus. 
+
+After stemming and removing stopwords we were left with a vocabulary of size 1433 unique words. All words with document frequency less than 10 were removed.
+
+
+THE DIRECTORY CONTAINS TWO FILES:
+
+The .content file contains descriptions of the papers in the following format:
+
+		<paper_id> <word_attributes>+ <class_label>
+
+The first entry in each line contains the unique string ID of the paper followed by binary values indicating whether each word in the vocabulary is present (indicated by 1) or absent (indicated by 0) in the paper. Finally, the last entry in the line contains the class label of the paper.
+
+The .cites file contains the citation graph of the corpus. Each line describes a link in the following format:
+
+		<ID of cited paper> <ID of citing paper>
+
+Each line contains two paper IDs. The first entry is the ID of the paper being cited and the second ID stands for the paper which contains the citation. The direction of the link is from right to left. If a line is represented by "paper1 paper2" then the link is "paper2->paper1". 

cora/cora.cites

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gnn.go

@@ -0,0 +1,108 @@
+package main
+
+import (
+	"math"
+)
+
+const (
+	HIDDEN int = 200
+)
+
+type (
+	Parameter struct {
+		Wo, Wi, B Matrix
+	}
+
+	Layer struct {
+		d       int
+		f       func(Matrix) Matrix
+		p       Parameter
+		O, I, E Matrix
+	}
+)
+
+func ReLU(A Matrix) Matrix {
+	for i := 0; i < A.N(); i++ {
+		for j := 0; j < A.M(); j++ {
+			A[i][j] = math.Max(0, A[i][j])
+		}
+	}
+	return A
+}
+
+func Softmax(A Matrix) Matrix {
+	for i := 0; i < A.N(); i++ {
+		max, sum := 0., 0.
+		for j := 0; j < A.M(); j++ {
+			max = math.Max(max, A[i][j])
+		}
+		for j := 0; j < A.M(); j++ {
+			A[i][j] = math.Exp(A[i][j] - max)
+			sum += A[i][j]
+		}
+		for j := 0; j < A.M(); j++ {
+			A[i][j] /= sum
+		}
+	}
+	return A
+}
+
+func GetEmbedding(G Graph, u, k int, l []Layer) Vector {
+	if k == 0 {
+		return G.X[u]
+	}
+	l[k].E = Multiply(Matrix{GetEmbedding(G, u, k-1, l)}, l[k].p.B)
+	l[k-1].O, l[k-1].I = MakeMatrix(1, l[k-1].d), MakeMatrix(1, l[k-1].d)
+	Do, Di := 0, 0
+	for v, w := range G.A[u] {
+		if w == 1 {
+			l[k-1].O.Add(Matrix{GetEmbedding(G, v, k-1, l)})
+			Do++
+		} else {
+			l[k-1].I.Add(Matrix{GetEmbedding(G, v, k-1, l)})
+			Di++
+		}
+	}
+	if Do > 0 {
+		l[k-1].O.Divide(float64(Do))
+		l[k].E.Add(Multiply(l[k-1].O, l[k].p.Wo))
+	}
+	if Di > 0 {
+		l[k-1].I.Divide(float64(Di))
+		l[k].E.Add(Multiply(l[k-1].I, l[k].p.Wi))
+	}
+	return l[k].f(l[k].E)[0]
+}
+
+func Train(G Graph) []Layer {
+	p1 := Parameter{MakeRandomMatrix(1433, HIDDEN), MakeRandomMatrix(1433, HIDDEN), MakeRandomMatrix(1433, HIDDEN)}
+	p2 := Parameter{MakeRandomMatrix(HIDDEN, 7), MakeRandomMatrix(HIDDEN, 7), MakeRandomMatrix(HIDDEN, 7)}
+	l := []Layer{{d: 1433}, {d: HIDDEN, f: ReLU, p: p1}, {d: 7, f: Softmax, p: p2}}
+	for u, X := range G.X {
+		GetEmbedding(G, u, 2, l)
+		delta := MakeMatrix(1, 7)
+		delta[0][nodeLabel[u]] = 1
+		delta.Sub(l[2].E)
+		DWo2, DWi2, DB2 := Multiply(l[1].O.Transpose(), delta), Multiply(l[1].I.Transpose(), delta), Multiply(l[1].E.Transpose(), delta)
+		DWo2.Divide(10)
+		DWi2.Divide(10)
+		DB2.Divide(10)
+		delta = Multiply(delta, l[2].p.B.Transpose())
+		for i := 0; i < HIDDEN; i++ {
+			if l[1].E[0][i] == 0 {
+				delta[0][i] = 0
+			}
+		}
+		DWo1, DWi1, DB1 := Multiply(l[0].O.Transpose(), delta), Multiply(l[0].I.Transpose(), delta), Multiply(Matrix{X}.Transpose(), delta)
+		DWo1.Divide(10)
+		DWi1.Divide(10)
+		DB1.Divide(10)
+		l[2].p.Wo.Add(DWo2)
+		l[2].p.Wi.Add(DWi2)
+		l[2].p.B.Add(DB2)
+		l[1].p.Wo.Add(DWo1)
+		l[1].p.Wi.Add(DWi1)
+		l[1].p.B.Add(DB1)
+	}
+	return l
+}

go.mod

@@ -0,0 +1,3 @@
+module gnn
+
+go 1.18

graph.go

@@ -0,0 +1,30 @@
+package main
+
+type (
+	AdjacencyMatrix map[int]map[int]int
+
+	Graph struct {
+		X map[int]Vector
+		A AdjacencyMatrix
+	}
+)
+
+func (A AdjacencyMatrix) Modify(u, v, w int) {
+	if A[u] == nil {
+		A[u] = make(map[int]int)
+	}
+	A[u][v] = w
+}
+
+func MakeGraph() Graph {
+	return Graph{make(map[int]Vector), make(AdjacencyMatrix)}
+}
+
+func (G Graph) AddNode(u int, V Vector) {
+	G.X[u] = V
+}
+
+func (G Graph) AddEdge(u, v int) {
+	G.A.Modify(u, v, 1)
+	G.A.Modify(v, u, -1)
+}

main.go

@@ -0,0 +1,73 @@
+package main
+
+import (
+	"fmt"
+	"os"
+)
+
+var labelName = []string{
+	"Case_Based",
+	"Genetic_Algorithms",
+	"Neural_Networks",
+	"Probabilistic_Methods",
+	"Reinforcement_Learning",
+	"Rule_Learning",
+	"Theory",
+}
+
+var nodeLabel = make(map[int]int)
+
+func main() {
+	file, err := os.Open("cora/cora.content")
+	if err != nil {
+		panic(err)
+	}
+	G := MakeGraph()
+	for i := 0; i < 2708; i++ {
+		var u int
+		fmt.Fscan(file, &u)
+		V := MakeVector(1433)
+		for j := 0; j < 1433; j++ {
+			fmt.Fscan(file, &V[j])
+		}
+		G.AddNode(u, V)
+		var label string
+		fmt.Fscan(file, &label)
+		for j := 0; j < 7; j++ {
+			if labelName[j] == label {
+				nodeLabel[u] = j
+				break
+			}
+		}
+		if i%100 == 0 {
+			fmt.Println("reading node", i)
+		}
+	}
+	file.Close()
+	file, err = os.Open("cora/cora.cites")
+	if err != nil {
+		panic(err)
+	}
+	for i := 0; i < 5429; i++ {
+		var u, v int
+		fmt.Fscan(file, &u, &v)
+		G.AddEdge(u, v)
+	}
+	file.Close()
+	l := Train(G)
+	cnt, tot := 0, 0
+	for u := range G.X {
+		GetEmbedding(G, u, 2, l)
+		id, max := 0, 0.
+		for i := 0; i < 7; i++ {
+			if l[2].E[0][i] > max {
+				id, max = i, l[2].E[0][i]
+			}
+		}
+		if nodeLabel[u] == id {
+			cnt++
+		}
+		tot++
+	}
+	fmt.Println(cnt, "/", tot)
+}

matrix.go

@@ -0,0 +1,86 @@
+package main
+
+type Matrix []Vector
+
+func MakeMatrix(n, m int) Matrix {
+	M := make(Matrix, n)
+	for i := 0; i < n; i++ {
+		M[i] = MakeVector(m)
+	}
+	return M
+}
+
+func MakeRandomMatrix(n, m int) Matrix {
+	M := make(Matrix, n)
+	for i := 0; i < n; i++ {
+		M[i] = MakeRandomVector(m)
+	}
+	return M
+}
+
+func (A Matrix) N() int {
+	return len(A)
+}
+
+func (A Matrix) M() int {
+	return A[0].N()
+}
+
+func (A Matrix) Transpose() Matrix {
+	B := MakeMatrix(A.M(), A.N())
+	for i := 0; i < A.N(); i++ {
+		for j := 0; j < A.M(); j++ {
+			B[j][i] = A[i][j]
+		}
+	}
+	return B
+}
+
+func (A Matrix) Add(B Matrix) {
+	if A.N() != B.N() || A.M() != B.M() {
+		panic("Incompatible Dimensions")
+	}
+	for i := 0; i < A.N(); i++ {
+		for j := 0; j < A.M(); j++ {
+			A[i][j] += B[i][j]
+		}
+	}
+}
+
+func (A Matrix) Sub(B Matrix) {
+	if A.N() != B.N() || A.M() != B.M() {
+		panic("Incompatible Dimensions")
+	}
+	for i := 0; i < A.N(); i++ {
+		for j := 0; j < A.M(); j++ {
+			A[i][j] -= B[i][j]
+		}
+	}
+}
+
+func (A Matrix) Divide(b float64) {
+	for i := 0; i < A.N(); i++ {
+		for j := 0; j < A.M(); j++ {
+			A[i][j] /= b
+		}
+	}
+}
+
+func Multiply(A, B Matrix) Matrix {
+	if A.M() != B.N() {
+		panic("Incompatible Dimensions")
+	}
+	C := MakeMatrix(A.N(), B.M())
+	for i := 0; i < A.N(); i++ {
+		for j := 0; j < A.M(); j++ {
+			if A[i][j] != 0 {
+				for k := 0; k < B.M(); k++ {
+					if B[j][k] != 0 {
+						C[i][k] += A[i][j] * B[j][k]
+					}
+				}
+			}
+		}
+	}
+	return C
+}

test.out

@@ -0,0 +1,29 @@
+reading node 0
+reading node 100
+reading node 200
+reading node 300
+reading node 400
+reading node 500
+reading node 600
+reading node 700
+reading node 800
+reading node 900
+reading node 1000
+reading node 1100
+reading node 1200
+reading node 1300
+reading node 1400
+reading node 1500
+reading node 1600
+reading node 1700
+reading node 1800
+reading node 1900
+reading node 2000
+reading node 2100
+reading node 2200
+reading node 2300
+reading node 2400
+reading node 2500
+reading node 2600
+reading node 2700
+2288 / 2708

vector.go

@@ -0,0 +1,23 @@
+package main
+
+import "math/rand"
+
+type Vector []float64
+
+func MakeVector(n int) Vector {
+	return make(Vector, n)
+}
+
+func MakeRandomVector(n int) Vector {
+	V := make(Vector, n)
+	for i := 0; i < n; i++ {
+		for V[i] == 0 {
+			V[i] = rand.NormFloat64()
+		}
+	}
+	return V
+}
+
+func (V Vector) N() int {
+	return len(V)
+}