Some interesting representational issues have come up in the context
of Atomspace representation of pathways, which appear to have more
general implications…
It seems the semantics we want for a biological pathway is sort of
like “the pathway P is a set of relationships R1, R2, …, R20” in kinda
the same sense that “the human body is a set of organs: brain, heart,
lungs, legs, etc.”
First of all it seems what we have here is a part of relationship… maybe we want
PartLink
ConceptNode “heart”
ConceptNode “human-body”
and
PartLink
>relationship<
>pathway<
PartLink and PartOfLink have come and gone in
OpenCog/Novamente/Webmind history...
An argument that PartLink should have fundamental status and a
well-defined fuzzy truth value is given in this paper:
https://www.academia.edu/1016959/Fuzzy_mereology
However what we need for biological pathways and human bodies seems
like a bit more. We want to say that a human body consists of a
certain set of parts... not just that each of them is a part... We're
doing a decomposition.
One way to do this would be
PartitionLink
ConceptNode “human-body”
ListLink
ConceptNode “legs”
ConceptNode “arms”
ConceptNode “brain”
etc.
Relatedly, we could also have
OverlappingPartitionLink
C
L
if we want to encompass cases where the partition elements in L can overlap; or
CoveringLink
C
L
if we want to encompass cases where the partition elements in L can
overlap, AND the elements in L may encompass some stuff that’s not in
C
For the pathway case, we could then say
PartitionLink
ConceptNode “Krebs cycle”
ListLink
>relationship 1<
>relationship 2<
etc.
Now this solves the semantics problem but doesn’t solve the problem of
having a long ListLink…. A biological pathway might have 100s or
1000s of relationships in it, and we don't usually want to make lists
that big in the Atomspace...
To solve this we could do something like (for the human body case)
PartitionLink
ConceptNode “human-body”
PartitionNode “body-partition-1”
PartitionElementLink
PartitionNode “body-partition-1"
ConceptNode “legs”
PartitionElementLink
PartitionNode “body-partition-1"
ConceptNode “arms”
etc.
and similarly (for the biological pathway case)
PartitionLink
ConceptNode “Krebs cycle”
PartitionNode “krebs-partition-1”
PartitionElementLink
PartitionNode “krebs-partition-1"
>relationship 1<
PartitionElementLink
PartitionNode “krebs-partition-1”
>relationship 2<
...
There could be some nice truth value math regarding these, e.g. we
could introduce Ellerman's "logical entropy" which is really a
partition entropy. There are also connections with some recent
theoretical work I've been doing on "graphtropy" (using "distinction
graphs" that generalize partitions), which I'll post a paper on
sometime in the next week or two.... But that will be another email
for another day...
-- Ben
--
Ben Goertzel, PhD
http://goertzel.org
"I am God! I am nothing, I'm play, I am freedom, I am life. I am the
boundary, I am the peak." -- Alexander Scriabin
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