Starting /v/sally/v12/lucid/non-dbcs/lisp ...
;;; Lucid Common Lisp/SPARC
;;; Development Environment Version 4.1, 12 October 1992
;;; Copyright (C) 1985, 1986, 1987, 1988, 1989, 1990, 1991, 1992 by Lucid, Inc.
;;; All Rights Reserved
;;;
;;; This software product contains confidential and trade secret information
;;; belonging to Lucid, Inc.  It may not be copied for any reason other than
;;; for archival and backup purposes.
;;;
;;; Lucid and Lucid Common Lisp are trademarks of Lucid, Inc.  Other brand
;;; or product names are trademarks or registered trademarks of their
;;; respective holders.


;;***** loading neither *****

> 
> (load "neither-sys.lisp")
;;; Loading source file "neither-sys.lisp"
;;; Loading source file "/u/baffes/neither/mcl-defsystem.lisp"
;;; Warning: File "/u/baffes/neither/mcl-defsystem.lisp" does not begin with IN-PACKAGE.  Loading into package "USER"

;  - Compiling defsystem "neither" 
;    - Compiling module "neither-structs" 
;      - Compiling source file "/u/baffes/neither/structures.lisp" 
;;; You are using the compiler in DEVELOPMENT mode (compilation-speed = 3)
;;; If you want faster code at the expense of longer compile time,
;;; you should use the production mode of the compiler, which can be obtained
;;; by evaluating (proclaim '(optimize (compilation-speed 0)))
;;; Generation of full safety checking code is enabled (safety = 3)
;;; Optimization of tail calls is disabled (speed = 2)
;;; Reading source file "/u/baffes/neither/structures.lisp"
;;; Expanding Reserved Memory
;;; GC: 94850 words [379400 bytes] of dynamic storage in use.
;;; 363900 words [1455600 bytes] of free storage available before a GC.
;;; 822650 words [3290600 bytes] of free storage available if GC is disabled.
;;; Writing binary file "/u/baffes/neither/structures.sbin"

;      - Loading binary file "/u/baffes/neither/structures.sbin" 
;      - Compiling source file "/u/baffes/neither/data-utilities.lisp" 
;;; Reading source file "/u/baffes/neither/data-utilities.lisp"
;;; While compiling CHECK-THEORY-ANTECEDENTS
;;; Warning: Free variable *AUGMENTED-FEATURE-NAMES* assumed to be special
;;; Writing binary file "/u/baffes/neither/data-utilities.sbin"

;      - Loading binary file "/u/baffes/neither/data-utilities.sbin" 
;;; Warning: Redefining Function APPEND-SYMBOLS whose source-file was not recorded

;      - Compiling source file "/u/baffes/neither/pfoil.lisp" 
;;; Reading source file "/u/baffes/neither/pfoil.lisp"
;;; While compiling MAXIMUM-CATEGORY-LABEL
;;; Warning: Free variable *TIE-BREAKER* assumed to be special
;;; Writing binary file "/u/baffes/neither/pfoil.sbin"

;      - Loading binary file "/u/baffes/neither/pfoil.sbin" 
;    - Compiling module "neither-code" 
;      - Compiling source file "/u/baffes/neither/debug.lisp" 
;;; Reading source file "/u/baffes/neither/debug.lisp"
;;; Writing binary file "/u/baffes/neither/debug.sbin"

;      - Loading binary file "/u/baffes/neither/debug.sbin" 
;      - Compiling source file "/u/baffes/neither/deduce.lisp" 
;;; Reading source file "/u/baffes/neither/deduce.lisp"
;;; Writing binary file "/u/baffes/neither/deduce.sbin"

;      - Loading binary file "/u/baffes/neither/deduce.sbin" 
;      - Compiling source file "/u/baffes/neither/abduce.lisp" 
;;; Reading source file "/u/baffes/neither/abduce.lisp"
;;; Writing binary file "/u/baffes/neither/abduce.sbin"

;      - Loading binary file "/u/baffes/neither/abduce.sbin" 
;      - Compiling source file "/u/baffes/neither/rule-retract.lisp" 
;;; Reading source file "/u/baffes/neither/rule-retract.lisp"
;;; Writing binary file "/u/baffes/neither/rule-retract.sbin"

;      - Loading binary file "/u/baffes/neither/rule-retract.sbin" 
;      - Compiling source file "/u/baffes/neither/io.lisp" 
;;; Reading source file "/u/baffes/neither/io.lisp"
;;; Writing binary file "/u/baffes/neither/io.sbin"

;      - Loading binary file "/u/baffes/neither/io.sbin" 
;      - Compiling source file "/u/baffes/neither/label.lisp" 
;;; Reading source file "/u/baffes/neither/label.lisp"
;;; Writing binary file "/u/baffes/neither/label.sbin"

;      - Loading binary file "/u/baffes/neither/label.sbin" 
;      - Compiling source file "/u/baffes/neither/pfoil-glue.lisp" 
;;; Reading source file "/u/baffes/neither/pfoil-glue.lisp"
;;; Writing binary file "/u/baffes/neither/pfoil-glue.sbin"

;      - Loading binary file "/u/baffes/neither/pfoil-glue.sbin" 
;      - Compiling source file "/u/baffes/neither/induce.lisp" 
;;; Reading source file "/u/baffes/neither/induce.lisp"
;;; Writing binary file "/u/baffes/neither/induce.sbin"

;      - Loading binary file "/u/baffes/neither/induce.sbin" 
;      - Compiling source file "/u/baffes/neither/subset.lisp" 
;;; Reading source file "/u/baffes/neither/subset.lisp"
;;; Writing binary file "/u/baffes/neither/subset.sbin"

;      - Loading binary file "/u/baffes/neither/subset.sbin" 
;      - Compiling source file "/u/baffes/neither/generalize.lisp" 
;;; Reading source file "/u/baffes/neither/generalize.lisp"
;;; Writing binary file "/u/baffes/neither/generalize.sbin"

;      - Loading binary file "/u/baffes/neither/generalize.sbin" 
;      - Compiling source file "/u/baffes/neither/specialize.lisp" 
;;; Reading source file "/u/baffes/neither/specialize.lisp"
;;; Writing binary file "/u/baffes/neither/specialize.sbin"

;      - Loading binary file "/u/baffes/neither/specialize.sbin" 
;      - Compiling source file "/u/baffes/neither/model.lisp" 
;;; Reading source file "/u/baffes/neither/model.lisp"
;;; Writing binary file "/u/baffes/neither/model.sbin"

;      - Loading binary file "/u/baffes/neither/model.sbin" 
;      - Compiling source file "/u/baffes/neither/neither.lisp" 
;;; Reading source file "/u/baffes/neither/neither.lisp"
;;; While compiling LEAVE-ONE-OUT-TEST
;;; Warning: Free variable *NURSE-ERROR-MAXES* assumed to be special
;;; Writing binary file "/u/baffes/neither/neither.sbin"

;      - Loading binary file "/u/baffes/neither/neither.sbin" 
;  - Providing system neither
;;; Warning: The following functions are not known to be defined:
;;;          ANTECEDENTS was referenced by CHECK-THEORY-ANTECEDENTS,
;;;             FIND-CONSEQUENT-IN-THEORY
;;;          DOMAIN was referenced by CHECK-THEORY-ANTECEDENTS
;;;          PCVAR-P was referenced by CHECK-THEORY-ANTECEDENTS
;;;          CONSEQUENT was referenced by CHECK-THEORY-ANTECEDENTS
;;;          FIND-RULES was referenced by FIND-CONSEQUENT-IN-THEORY
;;;          SET-EQUAL was referenced by EQUAL-OR-AV
;;;          BRULE-ANTECEDENTS was referenced by COUNT-ANTECEDENTS,
;;;             PRINT-THEORY, LITERAL-COUNT
;;;          BRULE-CONSEQUENT was referenced by GROUP-RULES,
;;;             PRINT-THEORY
;;;          PROVE was referenced by PROVABLE-EXAMPLE-CATEGORIES
;;;          MAXIMUM-LABEL was referenced by TEST-PFOIL
;;;          MAKE-BRULE was referenced by PFOIL-RULES
#P"/tmp_mnt/v/frisbee/v1/baffes/neither/neither-sys.lisp"


;;***** loading a data file for use by neither *****


> (load-neither-data "dna.lisp")
;;; Loading source file "dna.lisp"
;;; Warning: Redefining Function EXAMPLE-PREPARATION-HOOK which used to be defined in "io.lisp"
NIL


;;***** setting the trace flags before running neither *****


> (trace-neither-status)
NEITHER trace flag values:
   *trace-deduce*  = NIL
   *trace-genl*    = NIL
   *trace-pos-fix* = NIL
   *trace-spec*    = NIL
   *trace-neg-fix* = NIL
NIL
> (trace-neither :genl t :spec t)
NIL


;;***** training neither with the theory and examples in the input file *****


> (progn (setf result (train-neither *theory* *raw-examples* t)) nil)
Preparing examples with DNA example preparation hook
Examples are now in *neither-examples* and theories in *neither-theory*

Generalizing Theory...

*Attempting to make the following generalizations
  To make the following examples provable:
    example 4
    example 5
    example 9
    example 24
    example 27
  in rule:
    0:CONFORMATION <- (P-45 A) (P-44 A) (P-41 A)
  increase threshold by: 2 ... succeeded.
  To make the following examples provable:
    example 4
    example 5
  in rule:
    0:MINUS_35 <- (P-36 T) (P-35 T) (P-34 G) (P-32 C) (P-31 A)
  increase threshold by: 2 ... succeeded.
  To make the following examples provable:
    example 4
    example 5
    example 22
    example 24
  in rule:
    0:MINUS_10 <- (P-12 T) (P-11 A) (P-7 T)
  increase threshold by: 2 ... succeeded.

*Attempting to make the following generalizations
  To make the following examples provable:
    example 2
    example 28
    example 31
    example 40
    example 43
    example 44
    example 51
    example 52
  in rule:
    2:MINUS_35 <- (P-36 T) (P-35 T) (P-34 G) (P-32 C) (P-31 A)
  increase threshold by: 1 ... succeeded.

*Attempting to make the following generalizations
  To make the following examples provable:
    example 20
    example 21
    example 33
    example 35
  in rule:
    0:MINUS_10 <- (P-13 T) (P-12 A) (P-10 A) (P-8 T)
  increase threshold by: 2 ... succeeded.

*Attempting to make the following generalizations
  To make the following examples provable:
    example 17
  in rule:
    2:MINUS_10 <- (P-13 T) (P-12 A) (P-10 A) (P-8 T)
  increase threshold by: 1 ... failed.
  in rule:
    2:MINUS_10 <- (P-13 T) (P-12 A) (P-10 A) (P-8 T)
  remove the following:
    (P-8 T) ... failed.

*Attempting to make the following generalizations
  To make the following examples provable:
    example 16
  in rule:
    0:CONFORMATION <- (P-47 C) (P-46 A) (P-45 A) (P-43 T) (P-42 T) (P-40 A) (P-39 C) (P-22 G) (P-18 T) (P-16 C) (P-8 G) (P-7 C) (P-6 G) (P-5 C) (P-4 C) (P-2 C) (P-1 C)
  increase threshold by: 3 ... succeeded.

*Attempting to make the following generalizations
  To make the following examples provable:
    example 6
  in rule:
    0:CONFORMATION <- (P-49 A) (P-44 T) (P-27 T) (P-22 A) (P-18 T) (P-16 T) (P-15 G) (P-1 A)
  increase threshold by: 5 ... failed.
  in rule:
    0:CONFORMATION <- (P-49 A) (P-44 T) (P-27 T) (P-22 A) (P-18 T) (P-16 T) (P-15 G) (P-1 A)
  remove the following:
    (P-1 A)
    (P-16 T)
    (P-18 T)
    (P-22 A)
    (P-44 T) ... succeeded.

*Attempting to make the following generalizations
  To make the following examples provable:
    example 1
    example 42
  in rule:
    0:CONFORMATION <- (P-49 A) (P-27 T) (P-15 G)
  increase threshold by: 2 ... failed.
  in rule:
    0:CONFORMATION <- (P-49 A) (P-27 T) (P-15 G)
  remove the following:
    (P-15 G)
    (P-49 A) ... failed.

*Attempting to make the following generalizations
  To make the following examples provable:
    example 0
  in rule:
    0:CONFORMATION <- (P-49 A) (P-27 T) (P-15 G)
  increase threshold by: 1 ... failed.
  in rule:
    0:CONFORMATION <- (P-49 A) (P-27 T) (P-15 G)
  remove the following:
    (P-27 T) ... failed.

*Attempting to make the following generalizations
  To make the following examples provable:
    example 3
  in rule:
    0:CONFORMATION <- (P-49 A) (P-27 T) (P-15 G)
  increase threshold by: 2 ... failed.
  in rule:
    0:CONFORMATION <- (P-49 A) (P-27 T) (P-15 G)
  remove the following:
    (P-15 G)
    (P-27 T) ... failed.

Induction being called with the following examples:
  positives = 42 1 0 3
  negatives = 67 80 84 87 90

+Adding the following rule(s) to the theory
(0 CONFORMATION <- (P-48 C))
(0 CONFORMATION <- (P-42 T))

Induction being called with the following examples:
  positives = 17
  negatives = 82 97

+Adding the following rule(s) to the theory
(2 MINUS_10 <- (P-13 T) (P-12 A) (P-10 A) (P-49 A))

Specializing Theory...
NIL


;;***** testing neither on the training examples (should get all correct) *****


> (test-neither *raw-examples* result nil)
  Example 0(): PROMOTER proven to be (PROMOTER)
  Example 1(): PROMOTER proven to be (PROMOTER)
  Example 2(): PROMOTER proven to be (PROMOTER)
  Example 3(): PROMOTER proven to be (PROMOTER)
  Example 4(): PROMOTER proven to be (PROMOTER)
  Example 5(): PROMOTER proven to be (PROMOTER)
  Example 6(): PROMOTER proven to be (PROMOTER)
  Example 7(): PROMOTER proven to be (PROMOTER)
  Example 8(): PROMOTER proven to be (PROMOTER)
  Example 9(): PROMOTER proven to be (PROMOTER)
  Example 10(): PROMOTER proven to be (PROMOTER)
  Example 11(): PROMOTER proven to be (PROMOTER)
  Example 12(): PROMOTER proven to be (PROMOTER)
  Example 13(): PROMOTER proven to be (PROMOTER)
  Example 14(): PROMOTER proven to be (PROMOTER)
  Example 15(): PROMOTER proven to be (PROMOTER)
  Example 16(): PROMOTER proven to be (PROMOTER)
  Example 17(): PROMOTER proven to be (PROMOTER)
  Example 18(): PROMOTER proven to be (PROMOTER)
  Example 19(): PROMOTER proven to be (PROMOTER)
  Example 20(): PROMOTER proven to be (PROMOTER)
  Example 21(): PROMOTER proven to be (PROMOTER)
  Example 22(): PROMOTER proven to be (PROMOTER)
  Example 23(): PROMOTER proven to be (PROMOTER)
  Example 24(): PROMOTER proven to be (PROMOTER)
  Example 25(): PROMOTER proven to be (PROMOTER)
  Example 26(): PROMOTER proven to be (PROMOTER)
  Example 27(): PROMOTER proven to be (PROMOTER)
  Example 28(): PROMOTER proven to be (PROMOTER)
  Example 29(): PROMOTER proven to be (PROMOTER)
  Example 30(): PROMOTER proven to be (PROMOTER)
  Example 31(): PROMOTER proven to be (PROMOTER)
  Example 32(): PROMOTER proven to be (PROMOTER)
  Example 33(): PROMOTER proven to be (PROMOTER)
  Example 34(): PROMOTER proven to be (PROMOTER)
  Example 35(): PROMOTER proven to be (PROMOTER)
  Example 36(): PROMOTER proven to be (PROMOTER)
  Example 37(): PROMOTER proven to be (PROMOTER)
  Example 38(): PROMOTER proven to be (PROMOTER)
  Example 39(): PROMOTER proven to be (PROMOTER)
  Example 40(): PROMOTER proven to be (PROMOTER)
  Example 41(): PROMOTER proven to be (PROMOTER)
  Example 42(): PROMOTER proven to be (PROMOTER)
  Example 43(): PROMOTER proven to be (PROMOTER)
  Example 44(): PROMOTER proven to be (PROMOTER)
  Example 45(): PROMOTER proven to be (PROMOTER)
  Example 46(): PROMOTER proven to be (PROMOTER)
  Example 47(): PROMOTER proven to be (PROMOTER)
  Example 48(): PROMOTER proven to be (PROMOTER)
  Example 49(): PROMOTER proven to be (PROMOTER)
  Example 50(): PROMOTER proven to be (PROMOTER)
  Example 51(): PROMOTER proven to be (PROMOTER)
  Example 52(): PROMOTER proven to be (PROMOTER)
  Example 53(): NEGATIVE proven to be NIL
  Example 54(): NEGATIVE proven to be NIL
  Example 55(): NEGATIVE proven to be NIL
  Example 56(): NEGATIVE proven to be NIL
  Example 57(): NEGATIVE proven to be NIL
  Example 58(): NEGATIVE proven to be NIL
  Example 59(): NEGATIVE proven to be NIL
  Example 60(): NEGATIVE proven to be NIL
  Example 61(): NEGATIVE proven to be NIL
  Example 62(): NEGATIVE proven to be NIL
  Example 63(): NEGATIVE proven to be NIL
  Example 64(): NEGATIVE proven to be NIL
  Example 65(): NEGATIVE proven to be NIL
  Example 66(): NEGATIVE proven to be NIL
  Example 67(): NEGATIVE proven to be NIL
  Example 68(): NEGATIVE proven to be NIL
  Example 69(): NEGATIVE proven to be NIL
  Example 70(): NEGATIVE proven to be NIL
  Example 71(): NEGATIVE proven to be NIL
  Example 72(): NEGATIVE proven to be NIL
  Example 73(): NEGATIVE proven to be NIL
  Example 74(): NEGATIVE proven to be NIL
  Example 75(): NEGATIVE proven to be NIL
  Example 76(): NEGATIVE proven to be NIL
  Example 77(): NEGATIVE proven to be NIL
  Example 78(): NEGATIVE proven to be NIL
  Example 79(): NEGATIVE proven to be NIL
  Example 80(): NEGATIVE proven to be NIL
  Example 81(): NEGATIVE proven to be NIL
  Example 82(): NEGATIVE proven to be NIL
  Example 83(): NEGATIVE proven to be NIL
  Example 84(): NEGATIVE proven to be NIL
  Example 85(): NEGATIVE proven to be NIL
  Example 86(): NEGATIVE proven to be NIL
  Example 87(): NEGATIVE proven to be NIL
  Example 88(): NEGATIVE proven to be NIL
  Example 89(): NEGATIVE proven to be NIL
  Example 90(): NEGATIVE proven to be NIL
  Example 91(): NEGATIVE proven to be NIL
  Example 92(): NEGATIVE proven to be NIL
  Example 93(): NEGATIVE proven to be NIL
  Example 94(): NEGATIVE proven to be NIL
  Example 95(): NEGATIVE proven to be NIL
  Example 96(): NEGATIVE proven to be NIL
  Example 97(): NEGATIVE proven to be NIL
  Example 98(): NEGATIVE proven to be NIL
  Example 99(): NEGATIVE proven to be NIL
  Example 100(): NEGATIVE proven to be NIL
  Example 101(): NEGATIVE proven to be NIL
  Example 102(): NEGATIVE proven to be NIL
  Example 103(): NEGATIVE proven to be NIL
  Example 104(): NEGATIVE proven to be NIL
  Example 105(): NEGATIVE proven to be NIL

Percent correct: 100% of total=106
Number failing positives: 0
Number failing negatives: 0
100
0
0
 

;;***** looking at the output theory *****


> (decompile-theory result)
(0 PROMOTER <- (32914 . CONTACT) (32899 . CONFORMATION))
(0 CONTACT <- (32914 . MINUS_35) (32906 . MINUS_10))
(3 MINUS_35 <- (0 P-36 T) (0 P-35 T) (0 P-34 G) (0 P-32 C) (0 P-31 A))
(0 MINUS_35 <- (0 P-36 T) (0 P-35 T) (0 P-34 G) (0 P-33 A) (0 P-32 C))
(2 MINUS_10 <- (0 P-12 T) (0 P-11 A) (0 P-7 T))
(2 MINUS_10 <- (0 P-13 T) (0 P-12 A) (0 P-10 A) (0 P-8 T))
(0 MINUS_10 <- (0 P-14 T) (0 P-13 A) (0 P-12 T) (0 P-11 A) (0 P-10 A) (0 P-9 T))
(2 MINUS_10 <- (0 P-13 T) (0 P-12 A) (0 P-10 A) (0 P-49 A))
(0 CONFORMATION <- (0 P-45 A) (0 P-41 A) (0 P-28 T) (0 P-27 T) (0 P-23 T) (0 P-21 A) (0 P-20 A) (0 P-17 T) (0 P-15 T) (0 P-4 T))
(0 CONFORMATION <- (0 P-49 A) (0 P-27 T) (0 P-15 G))
(2 CONFORMATION <- (0 P-45 A) (0 P-44 A) (0 P-41 A))
(3 CONFORMATION <- (0 P-47 C) (0 P-46 A) (0 P-45 A) (0 P-43 T) (0 P-42 T) (0 P-40 A) (0 P-39 C) (0 P-22 G) (0 P-18 T) (0 P-16 C) (0 P-8 G) (0 P-7 C) (0 P-6 G) (0 P-5 C) (0 P-4 C) (0 P-2 C) (0 P-1 C))
(0 CONFORMATION <- (0 P-48 C))
(0 CONFORMATION <- (0 P-42 T))
NIL


;;***** resetting neither's internal data structures to the original theory *****


> (set-theory *theory*)
Theory in *neither-theory* has been updated.
NIL


;;***** printing out the default internal theory just loaded (for comparison) *****


> (decompile-theory)
(0 PROMOTER <- CONTACT CONFORMATION)
(0 CONTACT <- MINUS_35 MINUS_10)
(0 MINUS_35 <- (P-36 T) (P-35 T) (P-34 G) (P-32 C) (P-31 A))
(0 MINUS_35 <- (P-36 T) (P-35 T) (P-34 G) (P-33 A) (P-32 C))
(0 MINUS_10 <- (P-12 T) (P-11 A) (P-7 T))
(0 MINUS_10 <- (P-13 T) (P-12 A) (P-10 A) (P-8 T))
(0 MINUS_10 <- (P-14 T) (P-13 A) (P-12 T) (P-11 A) (P-10 A) (P-9 T))
(0 CONFORMATION <- (P-45 A) (P-41 A) (P-28 T) (P-27 T) (P-23 T) (P-21 A) (P-20 A) (P-17 T) (P-15 T) (P-4 T))
(0 CONFORMATION <- (P-49 A) (P-44 T) (P-27 T) (P-22 A) (P-18 T) (P-16 T) (P-15 G) (P-1 A))
(0 CONFORMATION <- (P-45 A) (P-44 A) (P-41 A))
(0 CONFORMATION <- (P-47 C) (P-46 A) (P-45 A) (P-43 T) (P-42 T) (P-40 A) (P-39 C) (P-22 G) (P-18 T) (P-16 C) (P-8 G) (P-7 C) (P-6 G) (P-5 C) (P-4 C) (P-2 C) (P-1 C))
NIL
> 
