[Biojava-dev] reasoning

[Schreiber, Mark]

Matthew -
 
Would this kind of thing be useful for text (natural language) processing? If so would it be possible for you to make a toy example to serve as a starting point for lesser mortals?
 
- Mark

	-----Original Message----- 
	From: Matthew Pocock [mailto:matthew_pocock at yahoo.co.uk] 
	Sent: Fri 10/10/2003 7:44 a.m. 
	To: BioJava Dev List 
	Cc: 
	Subject: [Biojava-dev] reasoning
	
	

	Hi,
	
	I have checked in new ontology code. It doesn't crash, but doesn't
	entirly work yet. Please add sablecc 3.* to your ant/lib directory to
	enable the new ontology parser code to be generated.
	
	Good points:
	
	* much more sane core ontology with a workable type-system - strictly
	typed higher-order predicate logic!
	
	* a fairly nice text format for writing things down - I have yet to find
	anything that can't be represented
	
	* the reasoner can execute proofs that require variable substitution e.g.
	
	  axiom: instance_of(_x, ANY)
	  proposition: instance_of(dog, ANY)
	  proof: instance_of(_x, ANY)[_x = dog]
	
	  proposition: sub_type_of(_x, mammal)
	  proof: sub_type_of(_x, mammal)[_x = dog] ; axiom(dog, mammal)
	
	Bad points:
	
	* I haven't been able to get it to find proofs for things that require
	an inference step without manually pruning the search space e.g.
	
	  axiom: sub_type_of(dog, mammal)
	  axiom: sub_type_of(mammal, animal)
	  axiom: implies( and(sub_type_of(_x, _y), sub_type_of(_y, _z)),
	                             sub_type_of(_x, _z))
	
	  proposition: sub_type_of(dog, animal)
	
	Well, it can do this, but it gets stuck in an infinite recursion before
	it gets arround to using the right variable substitutions.
	
	* It runs slowly - there is loads of scope for naive performance tuning,
	and once inference works propperly, it should be generating it's own
	interpreter in bytecode, but not today.
	
	The code is in CVS, so if you are interested in any of this then please
	get involved. I am wondering which bits will survive - certainly, some
	of the code needs gutting for functional and aesthetic reasons. However,
	I'm not even sure if this is the correct approach.
	
	Matthew
	
	
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