mml

Class Graphs.Motifs

java.lang.Object

la.la.Value

la.la.Function

la.la.Function.Native

mml.UPModel

mml.Graphs

mml.Graphs.Motifs

All Implemented Interfaces:

java.lang.Comparable<Value>

Direct Known Subclasses:

MotifA, MotifD

Enclosing class:

Graphs

public abstract static class Graphs.Motifs
extends Graphs

UnParameterised Models based on the notion of frequent sub-graphs (motifs, patterns) and that can calculate the message-length contribution of a set of motifs. Also see Graphs.Motifs.M.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	Graphs.Motifs.M Fully parameterised Models based around the notion of frequent sub-graphs (patterns motifs).

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
protected Model	mdlMotif The Model used for each individual motifs (subGraph, pattern) in a Graphs.Motifs.M-Model.
protected Discretes.M	mdlNmotifs The (prior) Model of the number of motifs (motifs, patterns) in a Graphs.Motifs.M Model.
int	verbosity Whether (verbosity>0) or not (verbosity==0) to Print tracing information.

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

Modifier	Constructor and Description
protected	Motifs(Value dp) Constructor only for use by subclasses of this class; it does not set gType or upmV.

Method Summary

Modifier and Type	Method and Description
Graphs.Motifs.M	greedy(Value ps, Vector motifs, Value ss) Given candidate 'motifs' and ss=stats(Gs), estimate mdlV and then return greedy(motifs, mdlV, ss).
Graphs.Motifs.M	greedy(Vector motifs, Discretes.M mdlV, Value ss) Greedy search for a subset of some given 'motifs' that minimises the message length under this Motif Model of Graphs.
double	msgMotifs(Graph[] ms) Return the cost, in nits, of stating 'N' motifs m[0], ..., m[N-1] (including stating N) as part of some fully parameterised Model.
double	msgMotifs(Vector vm) Return the cost, in nits, of stating 'N' motifs m0, ..., mN-1 (including stating N).
abstract Graphs.Motifs.M	sp2Model(double msg1, double msg2, Value sp) Given two-part message lengths msg1 & msg2, and statistical parameter sp, return a fully parameterised M-Model.

Methods inherited from class mml.Graphs

ds2mdlV, gType, stats, stats, upmV, vStats

Methods inherited from class mml.UPModel

apply, defnParams, estimator, main, 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

verbosity

public int verbosity

Whether (verbosity>0) or not (verbosity==0) to Print tracing information. Presently the values 0,1,2 print increasing amounts of tracing information.

mdlNmotifs

protected Discretes.M mdlNmotifs

The (prior) Model of the number of motifs (motifs, patterns) in a Graphs.Motifs.M Model. Anything sensible will prefer "few" to "many". NB. must be set by constructor of non-abstract subclass.

mdlMotif

protected Model mdlMotif

The Model used for each individual motifs (subGraph, pattern) in a Graphs.Motifs.M-Model. NB. must be set by the constructor of non-abstract subclass.

Constructor Detail

Motifs

protected Motifs(Value dp)

Constructor only for use by subclasses of this class; it does not set gType or upmV.

Method Detail

msgMotifs

public double msgMotifs(Graph[] ms)

Return the cost, in nits, of stating 'N' motifs m[0], ..., m[N-1] (including stating N) as part of some fully parameterised Model.

msgMotifs

public double msgMotifs(Vector vm)

Return the cost, in nits, of stating 'N' motifs m₀, ..., m_N-1 (including stating N). Also see Graphs.Motifs.

greedy

public Graphs.Motifs.M greedy(Vector motifs,
                              Discretes.M mdlV,
                              Value ss)

Greedy search for a subset of some given 'motifs' that minimises the message length under this Motif Model of Graphs. It requires motifs, a Model of |V|, and statistics ss=stats(Gs). Greedy may be used select from a given list of proposed motifs or used within a Motif Model's estimator.

greedy

public Graphs.Motifs.M greedy(Value ps,
                              Vector motifs,
                              Value ss)

Given candidate 'motifs' and ss=stats(Gs), estimate mdlV and then return greedy(motifs, mdlV, ss).

sp2Model

public abstract Graphs.Motifs.M sp2Model(double msg1,
                                         double msg2,
                                         Value sp)

Description copied from class: UPModel

Given two-part message lengths msg1 & msg2, and statistical parameter sp, return a fully parameterised M-Model. If 'this' UPModel produces a Model m, then sp2Model(m.msg1(), m.msg2(), m.statParams()) must be equivalent to m. Also see apply(sp).

Specified by:

sp2Model in class UPModel