tuffy.mln
Class MarkovLogicNetwork

java.lang.Object
  tuffy.mln.MarkovLogicNetwork

All Implemented Interfaces:

java.lang.Cloneable

public class MarkovLogicNetwork
extends java.lang.Object
implements java.lang.Cloneable

An MLN. Holds the symbol table.

Field Summary

private java.util.ArrayList<Predicate>	clusteringPredicates
(package private) java.util.ArrayList<ConjunctiveQuery>	datalogRules
private RDB	db The db connection associated with this MLN.
java.util.HashSet<ConjunctiveQuery>	dedupalogRules
private int	id
private static int	idGen
(package private) java.util.ArrayList<ConjunctiveQuery>	intermediateRules
private java.util.ArrayList<Clause>	listClauses List of normalized clauses.
private java.util.ArrayList<Predicate>	listPred List of all predicates appearing in this MLN.
private java.util.HashMap<java.lang.String,java.lang.Integer>	mapConstantID Map from string name to integer constant ID.
private java.util.Hashtable<java.lang.String,Function>	nameMapFunc
private java.util.Hashtable<java.lang.String,Predicate>	nameMapPred Map from string name to Predicate object.
private java.util.Hashtable<java.lang.String,Type>	nameMapType Map from string name to Type object.
private InputParser	parser Parser of input.
(package private) java.util.ArrayList<ConjunctiveQuery>	postprocRules
java.lang.String	relAtomPart
java.lang.String	relAtoms
java.lang.String	relClausePart
java.lang.String	relClauses Database tables storing intermediate data.
private java.util.HashSet<Clause>	relevantClauses List of clauses marked as relevant.
java.lang.String	relTrueAtoms
private java.util.HashMap<Predicate,java.util.ArrayList<ConjunctiveQuery>>	scopes
private java.util.ArrayList<ConjunctiveQuery>	scopingRules
private java.util.Hashtable<java.lang.String,Clause>	sigMap Map from signature of clauses to Clause object.
private java.util.HashMap<Clause,Clause>	unnormal2normal
java.util.ArrayList<Clause>	unnormalizedClauses List of unnormalized clauses.

Constructor Summary

MarkovLogicNetwork()
Constructor of MLN.

Method Summary

boolean	applyAllScopes() Execute all scoping rules
private void	applyScopeForPred(Predicate p) Execute the scoping rules for a predicate
boolean	cleanUp() Clean up temporary data in DB and working dir, including 1) drop schema in PostgreSQL; 2) remove directory.
java.lang.Object	clone()
void	closeFiles() Close all file handles used by each predicate in listPred.
void	executeAllDatalogRules() Execute all Datalog rules
void	executeAllIntermediateRules()
void	executeAllPostprocRules() Execute all Postprocessing rules
void	finalizeClauseDefinitions(RDB adb) Finalize the definitions of all clauses, i.e., prepare the database table used by each clause, including 1) instance table for each clause; 2) SQL needed to ground this clause.
java.util.ArrayList<ConjunctiveQuery>	getAllDatalogRules()
java.util.ArrayList<Clause>	getAllNormalizedClauses() Return all normalized clauses.
java.util.HashSet<Predicate>	getAllPred() Return the set of all predicates.
java.util.ArrayList<Predicate>	getAllPredOrderByName()
java.util.ArrayList<Clause>	getAllUnnormalizedClauses() Return all unnormalized clauses as read from the input file.
Clause	getClauseById(int id) Get the clause object by integer ID.
RDB	getDB()
Function	getFunctionByName(java.lang.String name) Get a function by its name; can be built-in.
int	getID()
Type	getOrCreateTypeByName(java.lang.String name) Return the type of a given name; create if this type does not exist.
Predicate	getPredByName(java.lang.String name) Return the predicate of the given name; null if such predicate does not exist.
RDB	getRDB() Returns the RDB used by this MLN.
java.util.HashSet<Clause>	getRelevantClauses() Returns the set of relevant clauses.
int	getSymbolID(java.lang.String symbol, Type type) Return assigned ID of a constant symbol.
boolean	isScoped(Predicate p) Test whether a predicate is scoped
void	loadEvidences(java.lang.String[] evidFiles) Parse multiple MLN evidence files.
void	loadPrograms(java.lang.String[] progFiles) Parse multiple MLN program files.
void	loadProgramsButNotNormalizeClauses(java.lang.String[] progFiles)
void	loadQueries(java.lang.String[] queryFiles) Parse multiple MLN query files.
private void	materializeAllTypes(RDB adb) Call materialize() for all types.
void	materializeTables() Stores constants and evidence into database table.
void	normalizeClauses() Normalize all clauses.
void	parseQueryCommaList(java.lang.String queryAtoms) Read in the query atoms provided by the command line.
void	prepareDB(RDB adb) Prepare the database for each predicate and clause.
void	registerClause(Clause c) Registers a new, unnormalized clause.
void	registerDatalogRule(ConjunctiveQuery cq) Add a datalog rule
void	registerIntermediateRule(ConjunctiveQuery cq)
void	registerPostprocRule(ConjunctiveQuery cq)
void	registerPred(Predicate p) Register a new predicate.
void	registerScopingRule(ConjunctiveQuery cq) Add a scoping rule
void	setClauseAsRelevant(Clause c) Marks a clause as relevant.
void	setDB(RDB adb)
void	storeAllEvidence() Store all evidences into the database by flushing the "buffers".
void	storeAllQueries() Ground and store all query atoms.

Methods inherited from class java.lang.Object

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

Field Detail

idGen

private static int idGen

id

private int id

db

private RDB db

The db connection associated with this MLN.

relClauses

public java.lang.String relClauses

Database tables storing intermediate data.

relAtoms

public java.lang.String relAtoms

relTrueAtoms

public java.lang.String relTrueAtoms

relClausePart

public java.lang.String relClausePart

relAtomPart

public java.lang.String relAtomPart

parser

private InputParser parser

Parser of input.

listPred

private java.util.ArrayList<Predicate> listPred

List of all predicates appearing in this MLN.

nameMapPred

private java.util.Hashtable<java.lang.String,Predicate> nameMapPred

Map from string name to Predicate object.

nameMapFunc

private java.util.Hashtable<java.lang.String,Function> nameMapFunc

nameMapType

private java.util.Hashtable<java.lang.String,Type> nameMapType

Map from string name to Type object.

relevantClauses

private java.util.HashSet<Clause> relevantClauses

List of clauses marked as relevant.

unnormal2normal

private java.util.HashMap<Clause,Clause> unnormal2normal

listClauses

private java.util.ArrayList<Clause> listClauses

List of normalized clauses.

unnormalizedClauses

public java.util.ArrayList<Clause> unnormalizedClauses

List of unnormalized clauses.

sigMap

private java.util.Hashtable<java.lang.String,Clause> sigMap

Map from signature of clauses to Clause object. For the definition of ``signature'', see Clause.normalize().

mapConstantID

private java.util.HashMap<java.lang.String,java.lang.Integer> mapConstantID

Map from string name to integer constant ID.

scopes

private java.util.HashMap<Predicate,java.util.ArrayList<ConjunctiveQuery>> scopes

scopingRules

private java.util.ArrayList<ConjunctiveQuery> scopingRules

clusteringPredicates

private java.util.ArrayList<Predicate> clusteringPredicates

dedupalogRules

public java.util.HashSet<ConjunctiveQuery> dedupalogRules

datalogRules

java.util.ArrayList<ConjunctiveQuery> datalogRules

intermediateRules

java.util.ArrayList<ConjunctiveQuery> intermediateRules

postprocRules

java.util.ArrayList<ConjunctiveQuery> postprocRules

Constructor Detail

MarkovLogicNetwork

public MarkovLogicNetwork()

Constructor of MLN. parser will be constructed here.

Method Detail

getDB

public RDB getDB()

clone

public java.lang.Object clone()
                       throws java.lang.CloneNotSupportedException

Overrides:

clone in class java.lang.Object

Throws:

java.lang.CloneNotSupportedException

getAllDatalogRules

public java.util.ArrayList<ConjunctiveQuery> getAllDatalogRules()

getRDB

public RDB getRDB()

Returns the RDB used by this MLN.

getID

public int getID()

setClauseAsRelevant

public void setClauseAsRelevant(Clause c)

Marks a clause as relevant. Called by KBMC.

See Also:

KBMC.run()

getRelevantClauses

public java.util.HashSet<Clause> getRelevantClauses()

Returns the set of relevant clauses.

registerClause

public void registerClause(Clause c)

Registers a new, unnormalized clause.

Parameters:

c - the clause to be registered

registerScopingRule

public void registerScopingRule(ConjunctiveQuery cq)

Add a scoping rule

Parameters:

cq -

registerDatalogRule

public void registerDatalogRule(ConjunctiveQuery cq)

Add a datalog rule

Parameters:

cq -

registerPostprocRule

public void registerPostprocRule(ConjunctiveQuery cq)

registerIntermediateRule

public void registerIntermediateRule(ConjunctiveQuery cq)

isScoped

public boolean isScoped(Predicate p)

Test whether a predicate is scoped

applyScopeForPred

private void applyScopeForPred(Predicate p)

Execute the scoping rules for a predicate

Parameters:

p - the target predicate

executeAllDatalogRules

public void executeAllDatalogRules()

Execute all Datalog rules

executeAllPostprocRules

public void executeAllPostprocRules()

Execute all Postprocessing rules

executeAllIntermediateRules

public void executeAllIntermediateRules()

applyAllScopes

public boolean applyAllScopes()

Execute all scoping rules

Returns:

true iff there is at least one scoping rule

getClauseById

public Clause getClauseById(int id)

Get the clause object by integer ID. Accepts negative id, and will translate it into positive. Does not accept zero id or id larger than the number of clauses, and will return null.

Parameters:

id - ID of wanted clause.

normalizeClauses

public void normalizeClauses()

Normalize all clauses. If the signature of this clause is as the same as some some existing clauses in listClauses, then Clause.absorb(Clause) this new clause. If not absorbed, this new clause is set an ID sequentially and a name Clause$id. Predicates in this clause is registered by Predicate.addRelatedClause(Clause).

See Also:

Clause.normalize(), Clause.absorb(Clause)

finalizeClauseDefinitions

public void finalizeClauseDefinitions(RDB adb)

Finalize the definitions of all clauses, i.e., prepare the database table used by each clause, including 1) instance table for each clause; 2) SQL needed to ground this clause. Call this when all clauses have been parsed.

getOrCreateTypeByName

public Type getOrCreateTypeByName(java.lang.String name)

Return the type of a given name; create if this type does not exist.

materializeAllTypes

private void materializeAllTypes(RDB adb)

Call materialize() for all types. This will put the domain members of each type into corresponding database tables.

See Also:

Type.storeConstantList(RDB)

getAllPred

public java.util.HashSet<Predicate> getAllPred()

Return the set of all predicates.

getAllPredOrderByName

public java.util.ArrayList<Predicate> getAllPredOrderByName()

registerPred

public void registerPred(Predicate p)

Register a new predicate. Here by ``register'' it means 1) set ID for this predicate sequentially; 2) push it into listPred; 3) building the map from predicate name to this predicate.

getPredByName

public Predicate getPredByName(java.lang.String name)

Return the predicate of the given name; null if such predicate does not exist.

getFunctionByName

public Function getFunctionByName(java.lang.String name)

Get a function by its name; can be built-in.

Parameters:

name -

getAllUnnormalizedClauses

public java.util.ArrayList<Clause> getAllUnnormalizedClauses()

Return all unnormalized clauses as read from the input file.

getAllNormalizedClauses

public java.util.ArrayList<Clause> getAllNormalizedClauses()

Return all normalized clauses.

getSymbolID

public int getSymbolID(java.lang.String symbol,
                       Type type)

Return assigned ID of a constant symbol. If this symbol is a new one, a new ID will be assigned to it, and the symbol table will be updated.

storeAllQueries

public void storeAllQueries()

Ground and store all query atoms.

See Also:

Predicate.addQuery(Atom), Predicate.groundAndStoreAtom(Atom)

storeAllEvidence

public void storeAllEvidence()

Store all evidences into the database by flushing the "buffers". These tuples are pushed into the relational table Predicate.getRelName() in the database.

closeFiles

public void closeFiles()

Close all file handles used by each predicate in listPred.

loadPrograms

public void loadPrograms(java.lang.String[] progFiles)

Parse multiple MLN program files.

Parameters:

progFiles - list of MLN program files (in Alchemy format)

loadProgramsButNotNormalizeClauses

public void loadProgramsButNotNormalizeClauses(java.lang.String[] progFiles)

loadEvidences

public void loadEvidences(java.lang.String[] evidFiles)

Parse multiple MLN evidence files. If file size is larger than 1MB, then uses a file stream incrementally parse this file. Can also accept .gz file (see GZIPInputStream.GZIPInputStream(InputStream)).

Parameters:

evidFiles - list of MLN evidence files (in Alchemy format)

loadQueries

public void loadQueries(java.lang.String[] queryFiles)

Parse multiple MLN query files.

Parameters:

queryFiles - list of MLN query files (in Alchemy format)

parseQueryCommaList

public void parseQueryCommaList(java.lang.String queryAtoms)

Read in the query atoms provided by the command line.

prepareDB

public void prepareDB(RDB adb)

Prepare the database for each predicate and clause.

See Also:

Predicate.prepareDB(RDB), finalizeClauseDefinitions(RDB)

setDB

public void setDB(RDB adb)

cleanUp

public boolean cleanUp()

Clean up temporary data in DB and working dir, including 1) drop schema in PostgreSQL; 2) remove directory.

Returns:

true on success

materializeTables

public void materializeTables()

Stores constants and evidence into database table.

See Also:

materializeAllTypes(RDB), storeAllEvidence()