I - Content
-----------

This package contains files related to inference on the set of middles, as 
presented in the paper From C.H. Bryant and D. Fredouille "A Parser for the 
Efficient Induction of Biological Grammars". More precisely, this files 
concern Section 3 of this paper.

This package contains:
- A README file (this file)
- example files for the inference process: middle.f middle.n
- background knowledge files for the inference process
    middle_dftd.b
    middle_dftd_cost.b
    middle_yap.b
    middle_yap_cost.b    
- Prolog instruction files to start inference
    middle_dftd.pl
    middle_dftd_cost.pl
    middle_yap.pl
    middle_yap_cost.pl
- csh scripts to start the inference processes
    middle_dftd.csh
    middle_dftd_cost.csh
    middle_yap.csh
    middle_yap_cost.csh


I - Use of the package
----------------------

You need installed:
- The Yap Prolog interpreter (http://www.ncc.up.pt/~vsc/Yap/yap.html)
- The Aleph ILP system (http://web.comlab.ox.ac.uk/oucl/research/areas/machlearn/Aleph/aleph_toc.html)
- The software presented in the paper "A Parser for the 
Efficient Induction of Biological Grammars". This software can be found at:
http://www.comp.rgu.ac.uk/staff/chb/research/data_sets/ilp05/

Section 3 of the paper considers four variants on the inference process:
- i-yap        corresponding to files middle_yap.*
- i-yap-cost   corresponding to files middle_yap_cost.*
- i-dftd       corresponding to files middle_dftd.*
- i-dftd-cost  corresponding to files middle_dftd_cost.*

To run one of these inference process:
1) Except for i-dftd, edit the corresponding .pl file and modify
   the first line to reflect the location of Aleph code on your machine.
2) For experiments using the dftd parser (middle_dftd and middle_dftd_cost), 
   edit the corresponding .pl file and modify the lines downloading the DFTD 
   parser to reflect the location of this parser on your machine: You have 
   three lines to change:
     :- load_foreign_files(['../dftdp_in_Yap/c/grammar_parser'],[],
	     download_cfgp_predicates).
     :- ['../dftdp_in_Yap/pl/grammar_parser_clause_to_grammar_rule.pl'].
     :- ['../dftdp_in_Yap/pl/grammar_parser_BK_to_C_structures.pl'].
3) Experiments of the paper considered different values for the "nodes"
   parameter of Aleph. To choose the value you want, edit the file .b 
   corresponding to the algorithm you are interested in, and modify the 
   set(nodes,value) line according to your wishes.
4) Run the script .csh corresponding to the inference process you are 
   considering.
   Outputs: - a file xxx.rules, where xxx is either middle_yap, 
              middle_yap_cost, middle_dftd or middle_dftd_cost depending on the
              inference process you consider. This file contains the set of 
              inferred rules (which should be the same for all algorithms)
            - the screen where, after execution, the running time will be 
              displayed. In case of errors during execution, they also should 
              appear on the screen.