// BronKerbosch returns the set of maximal cliques of the undirected graph g.
func BronKerbosch(g graph.Undirected) [][]graph.Node {
nodes := g.Nodes()
// The algorithm used here is essentially BronKerbosch3 as described at
// http://en.wikipedia.org/w/index.php?title=Bron%E2%80%93Kerbosch_algorithm&oldid=656805858
p := make(internal.Set, len(nodes))
for _, n := range nodes {
p.Add(n)
}
x := make(internal.Set)
var bk bronKerbosch
order, _ := VertexOrdering(g)
for _, v := range order {
neighbours := g.From(v)
nv := make(internal.Set, len(neighbours))
for _, n := range neighbours {
nv.Add(n)
}
bk.maximalCliquePivot(g, []graph.Node{v}, make(internal.Set).Intersect(p, nv), make(internal.Set).Intersect(x, nv))
p.Remove(v)
x.Add(v)
}
return bk
}
func benchmarkWalkAllDepthFirst(b *testing.B, g graph.Undirected) {
n := len(g.Nodes())
b.ResetTimer()
var dft DepthFirst
for i := 0; i < b.N; i++ {
dft.WalkAll(g, nil, nil, nil)
}
if dft.visited.Len() != n {
b.Fatalf("unexpected number of nodes visited: want: %d got %d", n, dft.visited.Len())
}
}
// WalkAll calls Walk for each unvisited node of the graph g using edges independent
// of their direction. The functions before and after are called prior to commencing
// and after completing each walk if they are non-nil respectively. The function
// during is called on each node as it is traversed.
func (b *BreadthFirst) WalkAll(g graph.Undirected, before, after func(), during func(graph.Node)) {
b.Reset()
for _, from := range g.Nodes() {
if b.Visited(from) {
continue
}
if before != nil {
before()
}
b.Walk(g, from, func(n graph.Node, _ int) bool {
if during != nil {
during(n)
}
return false
})
if after != nil {
after()
}
}
}
// Q returns the modularity Q score of the graph g subdivided into the
// given communities at the given resolution. If communities is nil, the
// unclustered modularity score is returned. The resolution parameter
// is γ as defined in Reichardt and Bornholdt doi:10.1103/PhysRevE.74.016110.
// Q will panic if g has any edge with negative edge weight.
//
// graph.Undirect may be used as a shim to allow calculation of Q for
// directed graphs.
func Q(g graph.Undirected, communities [][]graph.Node, resolution float64) float64 {
nodes := g.Nodes()
weight := weightFuncFor(g)
// Calculate the total edge weight of the graph
// and the table of penetrating edge weight sums.
var m2 float64
k := make(map[int]float64, len(nodes))
for _, u := range nodes {
w := weight(u, u)
for _, v := range g.From(u) {
w += weight(u, v)
}
m2 += w
k[u.ID()] = w
}
if communities == nil {
var q float64
for _, u := range nodes {
kU := k[u.ID()]
q += weight(u, u) - resolution*kU*kU/m2
}
return q / m2
}
// Iterate over the communities, calculating
// the non-self edge weights for the upper
// triangle and adjust the diagonal.
var q float64
for _, c := range communities {
for i, u := range c {
kU := k[u.ID()]
q += weight(u, u) - resolution*kU*kU/m2
for _, v := range c[i+1:] {
q += 2 * (weight(u, v) - resolution*kU*k[v.ID()]/m2)
}
}
}
return q / m2
}
// VertexOrdering returns the vertex ordering and the k-cores of
// the undirected graph g.
func VertexOrdering(g graph.Undirected) (order []graph.Node, cores [][]graph.Node) {
nodes := g.Nodes()
// The algorithm used here is essentially as described at
// http://en.wikipedia.org/w/index.php?title=Degeneracy_%28graph_theory%29&oldid=640308710
// Initialize an output list L.
var l []graph.Node
// Compute a number d_v for each vertex v in G,
// the number of neighbors of v that are not already in L.
// Initially, these numbers are just the degrees of the vertices.
dv := make(map[int]int, len(nodes))
var (
maxDegree int
neighbours = make(map[int][]graph.Node)
)
for _, n := range nodes {
adj := g.From(n)
neighbours[n.ID()] = adj
dv[n.ID()] = len(adj)
if len(adj) > maxDegree {
maxDegree = len(adj)
}
}
// Initialize an array D such that D[i] contains a list of the
// vertices v that are not already in L for which d_v = i.
d := make([][]graph.Node, maxDegree+1)
for _, n := range nodes {
deg := dv[n.ID()]
d[deg] = append(d[deg], n)
}
// Initialize k to 0.
k := 0
// Repeat n times:
s := []int{0}
for _ = range nodes { // TODO(kortschak): Remove blank assignment when go1.3.3 is no longer supported.
// Scan the array cells D[0], D[1], ... until
// finding an i for which D[i] is nonempty.
var (
i int
di []graph.Node
)
for i, di = range d {
if len(di) != 0 {
break
}
}
// Set k to max(k,i).
if i > k {
k = i
s = append(s, make([]int, k-len(s)+1)...)
}
// Select a vertex v from D[i]. Add v to the
// beginning of L and remove it from D[i].
var v graph.Node
v, d[i] = di[len(di)-1], di[:len(di)-1]
l = append(l, v)
s[k]++
delete(dv, v.ID())
// For each neighbor w of v not already in L,
// subtract one from d_w and move w to the
// cell of D corresponding to the new value of d_w.
for _, w := range neighbours[v.ID()] {
dw, ok := dv[w.ID()]
if !ok {
continue
}
for i, n := range d[dw] {
if n.ID() == w.ID() {
d[dw][i], d[dw] = d[dw][len(d[dw])-1], d[dw][:len(d[dw])-1]
dw--
d[dw] = append(d[dw], w)
break
}
}
dv[w.ID()] = dw
}
}
for i, j := 0, len(l)-1; i < j; i, j = i+1, j-1 {
l[i], l[j] = l[j], l[i]
}
cores = make([][]graph.Node, len(s))
offset := len(l)
for i, n := range s {
cores[i] = l[offset-n : offset]
offset -= n
}
return l, cores
}
// reduce returns a reduced graph constructed from g divided
// into the given communities. The communities value is mutated
// by the call to reduce. If communities is nil and g is a
// ReducedUndirected, it is returned unaltered.
func reduce(g graph.Undirected, communities [][]graph.Node) *ReducedUndirected {
if communities == nil {
if r, ok := g.(*ReducedUndirected); ok {
return r
}
nodes := g.Nodes()
// TODO(kortschak) This sort is necessary really only
// for testing. In practice we would not be using the
// community provided by the user for a Q calculation.
// Probably we should use a function to map the
// communities in the test sets to the remapped order.
sort.Sort(ordered.ByID(nodes))
communities = make([][]graph.Node, len(nodes))
for i := range nodes {
communities[i] = []graph.Node{node(i)}
}
weight := weightFuncFor(g)
r := ReducedUndirected{
nodes: make([]community, len(nodes)),
edges: make([][]int, len(nodes)),
weights: make(map[[2]int]float64),
communities: communities,
}
communityOf := make(map[int]int, len(nodes))
for i, n := range nodes {
r.nodes[i] = community{id: i, nodes: []graph.Node{n}}
communityOf[n.ID()] = i
}
for _, u := range nodes {
var out []int
uid := communityOf[u.ID()]
for _, v := range g.From(u) {
vid := communityOf[v.ID()]
if vid != uid {
out = append(out, vid)
}
if uid < vid {
// Only store the weight once.
r.weights[[2]int{uid, vid}] = weight(u, v)
}
}
r.edges[uid] = out
}
return &r
}
// Remove zero length communities destructively.
var commNodes int
for i := 0; i < len(communities); {
comm := communities[i]
if len(comm) == 0 {
communities[i] = communities[len(communities)-1]
communities[len(communities)-1] = nil
communities = communities[:len(communities)-1]
} else {
commNodes += len(comm)
i++
}
}
r := ReducedUndirected{
nodes: make([]community, len(communities)),
edges: make([][]int, len(communities)),
weights: make(map[[2]int]float64),
}
r.communities = make([][]graph.Node, len(communities))
for i := range r.communities {
r.communities[i] = []graph.Node{node(i)}
}
if g, ok := g.(*ReducedUndirected); ok {
// Make sure we retain the truncated
// community structure.
g.communities = communities
r.parent = g
}
weight := weightFuncFor(g)
communityOf := make(map[int]int, commNodes)
for i, comm := range communities {
r.nodes[i] = community{id: i, nodes: comm}
for _, n := range comm {
communityOf[n.ID()] = i
}
}
for uid, comm := range communities {
var out []int
for i, u := range comm {
r.nodes[uid].weight += weight(u, u)
for _, v := range comm[i+1:] {
r.nodes[uid].weight += 2 * weight(u, v)
}
for _, v := range g.From(u) {
vid := communityOf[v.ID()]
found := false
for _, e := range out {
if e == vid {
found = true
break
}
}
if !found && vid != uid {
out = append(out, vid)
}
if uid < vid {
// Only store the weight once.
r.weights[[2]int{uid, vid}] += weight(u, v)
}
}
}
r.edges[uid] = out
}
return &r
}