mml

Class MotifD

java.lang.Object

la.la.Value

la.la.Function

la.la.Function.Native

mml.UPModel

mml.Graphs

mml.Graphs.Motifs

mml.MotifD

All Implemented Interfaces:

java.lang.Comparable<Value>

public class MotifD
extends Graphs.Motifs

The UnParameterised 'MotifD' Model of Graphs. The fully parameterised Model is M. Also see MotifA.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	MotifD.M The fully parameterised MotifD Model of Graphs.

Nested classes/interfaces inherited from class mml.Graphs

Graphs.GERadaptive, Graphs.GERfixed, Graphs.IndependentEdges, Graphs.Motifs, Graphs.Skewed

Nested classes/interfaces inherited from class mml.UPModel

UPModel.Est, UPModel.Transform

Nested classes/interfaces inherited from class la.la.Function.Native

Function.Native.WithInverse

Nested classes/interfaces inherited from class la.la.Function

Function.Cts2Cts, Function.Cts2Cts2Cts, Function.CtsD2CtsD, Function.HasInverse, Function.Native, Function.Native2, Function.Native3

Nested classes/interfaces inherited from class la.la.Value

Value.Atomic, Value.Bool, Value.Char, Value.Chars, Value.Cts, Value.Defer, Value.Discrete, Value.Enum, Value.Inc_Or, Value.Int, Value.Lambda, Value.List, Value.Maybe, Value.Option, Value.Real, Value.Scannable, Value.Structured, Value.Triv, Value.Tuple

Field Summary

Fields

Modifier and Type	Field and Description
int	sgMaxV Bounds [sgMinV, sgMaxV] on |V| for the motifs (patterns) that the estimator will search for (but not necessarily find).
int	sgMinV Bounds [sgMinV, sgMaxV] on |V| for the motifs (patterns) that the estimator will search for (but not necessarily find).
Discretes.Bounded	upmE The UnParameterised (Adaptive) Model over the probability of existence of possible Edges outside instances of motifs.

Fields inherited from class mml.Graphs.Motifs

mdlMotif, mdlNmotifs, verbosity

Fields inherited from class mml.Graphs

gType, upmV

Fields inherited from class mml.UPModel

dp

Fields inherited from class la.la.Value

C, comparator, CR, E, eight, ffalse, five, fiveR, four, fourR, half, negCR, negOne, negOneR, negTenR, nilVal, nine, None, one, oneR, PI, PIby2, point01, point1, point5, point9, quarter, seven, six, ten, tenR, three, threeR, triv, ttrue, two, twoR, zero, zeroR

Constructor Summary

Constructors

Constructor and Description
MotifD(Value dp) Problem definition parameters, dp = ⟨gType, upmV, ⟨sgMinV, sgMaxV⟩⟩.

Method Summary

Modifier and Type	Method and Description
protected boolean	clearV(Graph g, java.util.BitSet free, Graph.Induced instnc, java.util.BitSet of_instnc) ?Obsolete; 'instnc' only uses Vertices in 'free'?
protected boolean	clearV2(Graph g, java.util.BitSet free, Graph.Induced instnc, java.util.BitSet of_instnc) ?Obsolete; 'instnc' only uses Vertex-pairs (V2) in 'free'?
UPModel.Est	estimator(Value ps) Return an Estimator for a MotifD Model.
static void	main(java.lang.String[] argv) Developer's debugging tests; main() will "go away" one day.
MotifD.M	sp2Model(double msg1, double msg2, Value sp) Return a fully parameterised MotifD Model.
Vector	stats(boolean add, Value ss0, Value ss1) Combine sufficient statisticses 'ss0' and 'ss1' additively (add=true), or remove ss1 from ss0 (add=false).
Vector	stats(Vector ds, int lo, int hi) Sufficient statistics are elements [lo, hi) of the data-set ds itself.

Methods inherited from class mml.Graphs.Motifs

greedy, greedy, msgMotifs, msgMotifs

Methods inherited from class mml.Graphs

ds2mdlV, gType, upmV, vStats

Methods inherited from class mml.UPModel

apply, defnParams, stats, stats, toString, transform

Methods inherited from class la.la.Function

bOp, fromBop, fromUop, type, uOp

Methods inherited from class la.la.Value

AoM, bOp, compareTo, cons, cts, elt, errMsg, error, force, isTuple, just, n, nElts, nlAoM, pair, print, quad, real, RTE, triple, tuple, UOE, x

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

upmE

public final Discretes.Bounded upmE

The UnParameterised (Adaptive) Model over the probability of existence of possible Edges outside instances of motifs. That is, the Model of entries in the adjacency matrix, A[,], that are not covered by any instance of a motif. Also see mdlE.

sgMinV

public final int sgMinV

Bounds [sgMinV, sgMaxV] on |V| for the motifs (patterns) that the estimator will search for (but not necessarily find). Also see mdlMotif.

sgMaxV

public final int sgMaxV

Bounds [sgMinV, sgMaxV] on |V| for the motifs (patterns) that the estimator will search for (but not necessarily find). Also see mdlMotif.

Constructor Detail

MotifD

public MotifD(Value dp)

Problem definition parameters, dp = ⟨gType, upmV, ⟨sgMinV, sgMaxV⟩⟩.

Method Detail

stats

public Vector stats(Vector ds,
                    int lo,
                    int hi)

Sufficient statistics are elements [lo, hi) of the data-set ds itself.

Overrides:

stats in class Graphs

stats

public Vector stats(boolean add,
                    Value ss0,
                    Value ss1)

Description copied from class: UPModel

Combine sufficient statisticses 'ss0' and 'ss1' additively (add=true), or remove ss1 from ss0 (add=false). Also see stats(ds,lo,hi).

Overrides:

stats in class Graphs

sp2Model

public MotifD.M sp2Model(double msg1,
                         double msg2,
                         Value sp)

Return a fully parameterised MotifD Model.

Specified by:

sp2Model in class Graphs.Motifs

estimator

public UPModel.Est estimator(Value ps)

Return an Estimator for a MotifD Model. Parameters 'ps' are for upmV.estimator(ps). Estimating mdlV is standard but finding good motifs is hard so heuristics are used. The time complexity should be approximately O(#G.V.d^sgMaxV-1), given a data-set of #G Graphs of average size V and average degree d.

Overrides:

estimator in class UPModel

clearV

protected boolean clearV(Graph g,
                         java.util.BitSet free,
                         Graph.Induced instnc,
                         java.util.BitSet of_instnc)

?Obsolete; 'instnc' only uses Vertices in 'free'?

clearV2

protected boolean clearV2(Graph g,
                          java.util.BitSet free,
                          Graph.Induced instnc,
                          java.util.BitSet of_instnc)

?Obsolete; 'instnc' only uses Vertex-pairs (V2) in 'free'?

main

public static void main(java.lang.String[] argv)

Developer's debugging tests; main() will "go away" one day. Also see Test.main(argv)