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zhangce · Sep 7, 2013 · 280d406 · 280d406
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diff --git a/deepdive/bin/common/Elementary.class b/deepdive/bin/common/Elementary.class
diff --git a/deepdive/bin/lda/Main/Main.class b/deepdive/bin/lda/Main/Main.class
diff --git a/deepdive/bin/lda/Utils/CommandOptions.class b/deepdive/bin/lda/Utils/CommandOptions.class
diff --git a/deepdive/bin/python/DStruct/Extractor.class b/deepdive/bin/python/DStruct/Extractor.class
diff --git a/deepdive/bin/python/DStruct/Factor.class b/deepdive/bin/python/DStruct/Factor.class
diff --git a/deepdive/bin/python/DStruct/Relation.class b/deepdive/bin/python/DStruct/Relation.class
diff --git a/deepdive/bin/python/DStruct/VariableGroup.class b/deepdive/bin/python/DStruct/VariableGroup.class
diff --git a/deepdive/bin/python/Main/ElementaryInterface.class b/deepdive/bin/python/Main/ElementaryInterface.class
diff --git a/deepdive/bin/python/Main/Main.class b/deepdive/bin/python/Main/Main.class
diff --git a/deepdive/bin/python/Utils/CommandOptions.class b/deepdive/bin/python/Utils/CommandOptions.class
diff --git a/deepdive/bin/python/Utils/Config.class b/deepdive/bin/python/Utils/Config.class
diff --git a/deepdive/bin/python/Utils/DB.class b/deepdive/bin/python/Utils/DB.class
diff --git a/deepdive/bin/python/Utils/INIParser.class b/deepdive/bin/python/Utils/INIParser.class
diff --git a/deepdive/bin/sql/main/Main.class b/deepdive/bin/sql/main/Main.class
diff --git a/deepdive/bin/sql/main/SQLCommandOptions.class b/deepdive/bin/sql/main/SQLCommandOptions.class
diff --git a/deepdive/bin/tuffy/db/RDB$1.class b/deepdive/bin/tuffy/db/RDB$1.class
diff --git a/deepdive/bin/tuffy/db/RDB.class b/deepdive/bin/tuffy/db/RDB.class
diff --git a/deepdive/bin/tuffy/db/SQLMan.class b/deepdive/bin/tuffy/db/SQLMan.class
diff --git a/deepdive/bin/tuffy/db/package.html b/deepdive/bin/tuffy/db/package.html
@@ -0,0 +1,8 @@
+<html>
+<head>
+<title>package</title>
+</head>
+<body>
+Provides interfaces to the RDBMS. Currently only supports PostgreSQL.
+</body>
+</html>
diff --git a/deepdive/bin/tuffy/ground/Grounding.class b/deepdive/bin/tuffy/ground/Grounding.class
diff --git a/deepdive/bin/tuffy/ground/KBMC$AtomCutSet$Stratum.class b/deepdive/bin/tuffy/ground/KBMC$AtomCutSet$Stratum.class
diff --git a/deepdive/bin/tuffy/ground/KBMC$AtomCutSet.class b/deepdive/bin/tuffy/ground/KBMC$AtomCutSet.class
diff --git a/deepdive/bin/tuffy/ground/KBMC.class b/deepdive/bin/tuffy/ground/KBMC.class
diff --git a/deepdive/bin/tuffy/ground/package.html b/deepdive/bin/tuffy/ground/package.html
@@ -0,0 +1,28 @@
+<html>
+<head>
+<title>package</title>
+</head>
+<body>
+Provides facilities for grounding MLNs, including KBMC, SQL-based grounding, and MRF partitioning.
+
+<p>
+Grounding will be conducted in three phases:
+<ul>
+<li> Ground relevant atoms: This phase is done by class KBMC. In this phase, a rough sift
+of atoms results from a partially grounded predicate tables. In these tables (one
+for each predicate), those definitely not useful atoms are not grounded.
+<li> Pick active atoms: This phase is done by class Grounding. In this phase, all
+atoms that will not violate any clauses by default are further eliminated
+on the basis of the first phase. These eliminated atoms will not play any role
+in following inference or learning, therefore grounding them out will make no sense.
+<li> Ground active clauses: This phase is done by class Grounding. In this phase, clauses
+are grounded according to picked active atoms in the second phase. Clauses relying on
+exactly the same atoms will be merged together to form GClause for efficiency 
+consideration.
+</ul>
+</p>
+
+
+
+</body>
+</html>
diff --git a/deepdive/bin/tuffy/ground/package_grounding.jpeg b/deepdive/bin/tuffy/ground/package_grounding.jpeg
diff --git a/deepdive/bin/tuffy/ground/partition/Bucket.class b/deepdive/bin/tuffy/ground/partition/Bucket.class
diff --git a/deepdive/bin/tuffy/ground/partition/Component.class b/deepdive/bin/tuffy/ground/partition/Component.class
diff --git a/deepdive/bin/tuffy/ground/partition/Partition.class b/deepdive/bin/tuffy/ground/partition/Partition.class
diff --git a/deepdive/bin/tuffy/ground/partition/PartitionScheme.class b/deepdive/bin/tuffy/ground/partition/PartitionScheme.class
diff --git a/deepdive/bin/tuffy/ground/partition/Partitioning.class b/deepdive/bin/tuffy/ground/partition/Partitioning.class
diff --git a/deepdive/bin/tuffy/ground/partition/package.html b/deepdive/bin/tuffy/ground/partition/package.html
@@ -0,0 +1,8 @@
+<html>
+<head>
+<title>package</title>
+</head>
+<body>
+Data structures and algorithms for MRF partitioning.
+</body>
+</html>
diff --git a/deepdive/bin/tuffy/helper/Stats$ClauseCostComparator.class b/deepdive/bin/tuffy/helper/Stats$ClauseCostComparator.class
diff --git a/deepdive/bin/tuffy/helper/Stats.class b/deepdive/bin/tuffy/helper/Stats.class
diff --git a/deepdive/bin/tuffy/helper/package.html b/deepdive/bin/tuffy/helper/package.html
@@ -0,0 +1,8 @@
+<html>
+<head>
+<title>package</title>
+</head>
+<body>
+Misc functionalities to help develop MLN programs.
+</body>
+</html>
diff --git a/deepdive/bin/tuffy/infer/DataMover.class b/deepdive/bin/tuffy/infer/DataMover.class
diff --git a/deepdive/bin/tuffy/infer/InferBucket$CompWorker.class b/deepdive/bin/tuffy/infer/InferBucket$CompWorker.class
diff --git a/deepdive/bin/tuffy/infer/InferBucket.class b/deepdive/bin/tuffy/infer/InferBucket.class
diff --git a/deepdive/bin/tuffy/infer/InferComponent.class b/deepdive/bin/tuffy/infer/InferComponent.class
diff --git a/deepdive/bin/tuffy/infer/InferPartitioned.class b/deepdive/bin/tuffy/infer/InferPartitioned.class
diff --git a/deepdive/bin/tuffy/infer/MRF$1.class b/deepdive/bin/tuffy/infer/MRF$1.class
diff --git a/deepdive/bin/tuffy/infer/MRF$2.class b/deepdive/bin/tuffy/infer/MRF$2.class
diff --git a/deepdive/bin/tuffy/infer/MRF$INIT_STRATEGY.class b/deepdive/bin/tuffy/infer/MRF$INIT_STRATEGY.class
diff --git a/deepdive/bin/tuffy/infer/MRF$myDouble.class b/deepdive/bin/tuffy/infer/MRF$myDouble.class
diff --git a/deepdive/bin/tuffy/infer/MRF.class b/deepdive/bin/tuffy/infer/MRF.class
diff --git a/deepdive/bin/tuffy/infer/PGInfer.class b/deepdive/bin/tuffy/infer/PGInfer.class
diff --git a/deepdive/bin/tuffy/infer/ds/GAtom.class b/deepdive/bin/tuffy/infer/ds/GAtom.class
diff --git a/deepdive/bin/tuffy/infer/ds/GClause.class b/deepdive/bin/tuffy/infer/ds/GClause.class
diff --git a/deepdive/bin/tuffy/infer/ds/KeyBlock.class b/deepdive/bin/tuffy/infer/ds/KeyBlock.class
diff --git a/deepdive/bin/tuffy/infer/ds/package.html b/deepdive/bin/tuffy/infer/ds/package.html
@@ -0,0 +1,8 @@
+<html>
+<head>
+<title>package</title>
+</head>
+<body>
+Data structures used to represent MRFs.
+</body>
+</html>
diff --git a/deepdive/bin/tuffy/infer/package.html b/deepdive/bin/tuffy/infer/package.html
@@ -0,0 +1,26 @@
+<html>
+<head>
+<title>package</title>
+</head>
+<body>
+Provides MLN inference algorithms. Currently supports MAP inference and 
+Marginal inference.
+
+<p>
+By default this package deals with inference in memory. It first loads from
+database about information of MLN groundings. Then, it forms a MRF by taking
+GAtom and GClause as elements. Once this MRF is formed, this package will not
+interact with DBMS.
+</p>
+
+<p>
+Marginal and MAP inference on this in-memory structure follow classic scheme.
+There are indices from GClause to GAtom, vice versa. Therefore, the change
+of GAtom's truth assignment will influence GClause's truth value. Together with the
+sign of GClause's weight, whether a GClause is violated in current truth assignment
+setting can be tracked. The WalkSAT or MCSAT subroutines are then invoked. 
+</p>
+
+
+</body>
+</html>
diff --git a/deepdive/bin/tuffy/infer/package_infer.jpeg b/deepdive/bin/tuffy/infer/package_infer.jpeg
diff --git a/deepdive/bin/tuffy/learn/DNLearner.class b/deepdive/bin/tuffy/learn/DNLearner.class
diff --git a/deepdive/bin/tuffy/learn/Learner.class b/deepdive/bin/tuffy/learn/Learner.class
diff --git a/deepdive/bin/tuffy/learn/Main.class b/deepdive/bin/tuffy/learn/Main.class
diff --git a/deepdive/bin/tuffy/learn/MultiCoreSGDLearner.class b/deepdive/bin/tuffy/learn/MultiCoreSGDLearner.class
diff --git a/deepdive/bin/tuffy/learn/NaiveDNLearner.class b/deepdive/bin/tuffy/learn/NaiveDNLearner.class
diff --git a/deepdive/bin/tuffy/learn/NaiveGDLearner.class b/deepdive/bin/tuffy/learn/NaiveGDLearner.class
diff --git a/deepdive/bin/tuffy/learn/SGDLearner.class b/deepdive/bin/tuffy/learn/SGDLearner.class
diff --git a/deepdive/bin/tuffy/learn/package.html b/deepdive/bin/tuffy/learn/package.html
@@ -0,0 +1,24 @@
+<html>
+<head>
+<title>package</title>
+</head>
+<body>
+Provides weight learning in Tuffy.
+
+<p>
+This package provide frameworks for weight learning. You can write
+your own learner by materializing several functions of the abstract class
+Learner. An example in this package is DNLearner, which implements 
+a Diagonal Newton optimizer. This materialized class only need to tell
+the learner how to update the weight according to the gradient and Hessian.
+</p>
+
+<p>
+This package deals with in memory MRF directly, and has nothing
+to do with DBMS. The flow of learning involves repetitive invocations of MCSAT (see
+package infer), which will update the expectation of clause violation/satisfaction
+under current weight settings. 
+</p>
+
+</body>
+</html>
diff --git a/deepdive/bin/tuffy/main/Infer.class b/deepdive/bin/tuffy/main/Infer.class
diff --git a/deepdive/bin/tuffy/main/Main.class b/deepdive/bin/tuffy/main/Main.class
diff --git a/deepdive/bin/tuffy/main/NonPartInfer.class b/deepdive/bin/tuffy/main/NonPartInfer.class
diff --git a/deepdive/bin/tuffy/main/PartInfer.class b/deepdive/bin/tuffy/main/PartInfer.class
diff --git a/deepdive/bin/tuffy/main/package.html b/deepdive/bin/tuffy/main/package.html
@@ -0,0 +1,8 @@
+<html>
+<head>
+<title>package</title>
+</head>
+<body>
+Entrances to Tuffy.
+</body>
+</html>
diff --git a/deepdive/bin/tuffy/mln/Atom$AtomType.class b/deepdive/bin/tuffy/mln/Atom$AtomType.class
diff --git a/deepdive/bin/tuffy/mln/Atom.class b/deepdive/bin/tuffy/mln/Atom.class
diff --git a/deepdive/bin/tuffy/mln/Clause$ClauseInstance.class b/deepdive/bin/tuffy/mln/Clause$ClauseInstance.class
diff --git a/deepdive/bin/tuffy/mln/Clause.class b/deepdive/bin/tuffy/mln/Clause.class
diff --git a/deepdive/bin/tuffy/mln/Literal$VarClique.class b/deepdive/bin/tuffy/mln/Literal$VarClique.class
diff --git a/deepdive/bin/tuffy/mln/Literal.class b/deepdive/bin/tuffy/mln/Literal.class
diff --git a/deepdive/bin/tuffy/mln/MarkovLogicNetwork.class b/deepdive/bin/tuffy/mln/MarkovLogicNetwork.class
diff --git a/deepdive/bin/tuffy/mln/Predicate$FunctionalDependency.class b/deepdive/bin/tuffy/mln/Predicate$FunctionalDependency.class
diff --git a/deepdive/bin/tuffy/mln/Predicate.class b/deepdive/bin/tuffy/mln/Predicate.class
diff --git a/deepdive/bin/tuffy/mln/Term.class b/deepdive/bin/tuffy/mln/Term.class
diff --git a/deepdive/bin/tuffy/mln/Tuple.class b/deepdive/bin/tuffy/mln/Tuple.class
diff --git a/deepdive/bin/tuffy/mln/Type.class b/deepdive/bin/tuffy/mln/Type.class
diff --git a/deepdive/bin/tuffy/mln/package.html b/deepdive/bin/tuffy/mln/package.html
@@ -0,0 +1,36 @@
+<html>
+<head>
+<title>package</title>
+</head>
+<body>
+
+This package builds the data structure of MLN.
+
+<p>
+This package defines the data structure representing logics, e.g., 
+Atom, Predicate, Term, etc. Also, it bridges these objects to
+relational tables in DBMS.
+</p>
+
+<p>
+Following figure illustrates the relationship between classes in this
+package, and the relationship between class and database table. For example,
+from this figure, we can see that, an Atom object is formed by a Tuple object
+and a Predicate object. And a Predicate object is associated with two
+database tables.
+</p>
+
+<p>
+There are four kinds of database tables. type_TypeName table saves the constant
+ID of type TypeName. pred_PredicateName table saves grounded instances of predicate 
+PredicateName.
+act_pred_PredicateName table saves the active atoms of predicate PredicateName.
+ClauseName_instances table saves instances of clause ClauseName. Here by instance,
+it means the possible binding from meta-variable to constant. By such bindings, you
+can get clauses as the same as your input program.
+</p>
+
+
+
+</body>
+</html>
diff --git a/deepdive/bin/tuffy/mln/package_mln.jpeg b/deepdive/bin/tuffy/mln/package_mln.jpeg
diff --git a/deepdive/bin/tuffy/parse/CommandOptions$InferDataStore.class b/deepdive/bin/tuffy/parse/CommandOptions$InferDataStore.class
diff --git a/deepdive/bin/tuffy/parse/CommandOptions$MAPInferAlgo.class b/deepdive/bin/tuffy/parse/CommandOptions$MAPInferAlgo.class
diff --git a/deepdive/bin/tuffy/parse/CommandOptions.class b/deepdive/bin/tuffy/parse/CommandOptions.class
diff --git a/deepdive/bin/tuffy/parse/Config.g b/deepdive/bin/tuffy/parse/Config.g
@@ -0,0 +1,38 @@
+grammar Config;
+options {language=Java; output=AST; backtrack=false; memoize=false;}
+
+@lexer::header {
+package tuffy.parse;
+}
+
+@parser::header{
+package tuffy.parse;
+import java.util.Hashtable;
+import tuffy.mln.*;
+import tuffy.util.*;
+}
+
+@parser::members {
+public Hashtable<String, String> map = new Hashtable<String, String>();
+}
+
+WS  :   (' ' 
+        | '\r'
+        | '\n'
+        | '\t'
+        ) {$channel=HIDDEN;}
+    ;
+
+COMMENT
+    :   (('#' ~('\n'|'\r')* '\r'? '\n')) {$channel=HIDDEN;}
+    ;
+
+SPAN: ('a'..'z'|'A'..'Z'|'0'..'9'|'_'|'-'|':'|'/'|'\\'|'\.')+;
+
+config :  (state)+ EOF;
+
+state : id=SPAN '=' value=SPAN
+      {
+          map.put($id.text, $value.text);
+      }
+      ;
diff --git a/deepdive/bin/tuffy/parse/Config.tokens b/deepdive/bin/tuffy/parse/Config.tokens
@@ -0,0 +1,5 @@
+WS=4
+SPAN=6
+COMMENT=5
+T__7=7
+'='=7
diff --git a/deepdive/bin/tuffy/parse/ConfigLexer.class b/deepdive/bin/tuffy/parse/ConfigLexer.class
diff --git a/deepdive/bin/tuffy/parse/ConfigParser$config_return.class b/deepdive/bin/tuffy/parse/ConfigParser$config_return.class
diff --git a/deepdive/bin/tuffy/parse/ConfigParser$state_return.class b/deepdive/bin/tuffy/parse/ConfigParser$state_return.class
diff --git a/deepdive/bin/tuffy/parse/ConfigParser.class b/deepdive/bin/tuffy/parse/ConfigParser.class
diff --git a/deepdive/bin/tuffy/parse/InputParser.class b/deepdive/bin/tuffy/parse/InputParser.class