what i mean by "invoke" is just how do i access the members of the
pathway DPN to apply them to ProteinNodes and their interaction
predicates in a particular context?
mike
On Wednesday, August 9, 2017 at 1:54:16 PM UTC-7, linas wrote:
Quick comment, I did not review the Doc.
On Tue, Aug 8, 2017 at 3:11 PM, Michael Duncan
<mjsd...@gmail.com> wrote:
the pathway links are predicates defined here
<https://docs.google.com/document/d/1R_AiCCRuWKI92JUCYXJRnKeYw-MiwKLR3kr9fJyYZfs/edit>.
the pathways are
DefineLink
I strongly urge that EquivalenceLink be used here, and not
DefineLink. DefineLink is meant for something else.
DefinedPredicateNode "GO pathway term name"
Isn't an ordinary Predicatenode enough??
AndLink
Again: the anlink is completely unordered, so in this case,
would be exactly the same thing as a SetLink: its just a
collection of "stuff" (a collection of protein
relationships, it seems) Because its not ordered, its not a
"path" per se, its just a set.
You keep saying that you use AndLink because its "true" when
everything is in it, but that is also the case for SetLink.
When I say "x and y are in set A", that always true that x
is in A and Y is in A, and you don't need an AndLink to say
this. The SetLink is enough. The SetLink is effectively an
AndLink, from the truthiness of it.
Predicate "protein relationship 1"
ProteinNode "x"
ProteinNode "y"
Predicate "protein relationship 2"
ProteinNode "y"
ProteinNode "z"
....
I'm proposing this:
MemberLink
DefinedPredicateNode "GO pathway term name"
Predicate "protein relationship 1"
ProteinNode "x"
ProteinNode "y"
MemberLink
DefinedPredicateNode "GO pathway term name"
Predicate "protein relationship 2"
ProteinNode "y"
ProteinNode "z"
....
--linas
On Tuesday, August 8, 2017 at 11:00:54 AM UTC-7, Michael
Duncan wrote:
the AndLink semantics are for the simplified pathway
representation for the current demo/toy
bio-atomspace which only has binary links between
proteins and abstracts out small molecules. so the
pathway for the krebs cycle for instance is just
directed links between the enzymes: ... ->
isocitrate dehydrogenase -> alpha-ketoglutarate
dehydrogenase -> Succinyl-CoA synthetase -> ...
linus semantics look good for when the complete
biopax pathway representation is translated into
atomese.
even then my intuition is that the AndLink semantics
should be useful in pln inference about say the
likelihood of a pathway being involved in
distinguishing a case-control phenotype based on
moses models of relative gene expression levels.
On Monday, August 7, 2017 at 11:31:59 AM UTC-7, Ben
Goertzel wrote:
a pathway in biology is actually a network with
directed arrows and generally lots of loops....
there are even some hyperlinks e.g. for
catalysis... a pathway is a subhypergraph...
On Aug 7, 2017 11:25, "Linas Vepstas"
<linasv...@gmail.com> wrote:
no clue why its appropriate for biological
pathways. Mike is designing that, not me.
Anyway, a "pathway" is an ordered sequence
where the ordering matters. Neither SetLink,
nor AndLink are ordered. So if you actually
want to have a path, i.e. a sequence of
directed arrows, well .. you need to find a
representation of biological pathways as
directed arrows. But this is familiar
ground, for opencog...
--linas
On Mon, Aug 7, 2017 at 1:21 PM, Ben Goertzel
<b...@goertzel.org> wrote:
OK I get that... but I don't see why it
is appropriate for biological
pathways...
On Tue, Aug 8, 2017 at 2:19 AM, Linas
Vepstas <linasv...@gmail.com> wrote:
> First, lets review SetLink:
>
> SetLink
> ConceptNode "x"
> ConceptNode "y"
> ConceptNode "z"
>
>
> EquivalenceLink
> ConceptNode "last three letters
of the alphabet"
> SetLink
> ConceptNode "x"
> ConceptNode "y"
> ConceptNode "z"
>
>
> MemberLink
> ConceptNode "x"
> ConceptNode "last three letters
of the alphabet"
> MemberLink
> ConceptNode "y"
> ConceptNode "last three letters
of the alphabet"
> MemberLink
> ConceptNode "z"
> ConceptNode "last three letters
of the alphabet"
>
> Again, with TV's:
>
> MemberLink <1.0>
> ConceptNode "z"
> ConceptNode "last letters of the
alphabet"
> MemberLink <0.9>
> ConceptNode "w"
> ConceptNode "last letters of the
alphabet"
> MemberLink <0.8>
> ConceptNode "s"
> ConceptNode "last letters of the
alphabet"
> MemberLink <0.2>
> ConceptNode "m"
> ConceptNode "last letters of the
alphabet"
>
>
>
> Sooo .. AndMemberLink would be just
like the above, except that whereever
> you see SetLink above, you would have
AndLink, and wherever you see
> MmeberLink above, you would have
AndMemeberLink.
>
> --linas
>
>
>
>
> On Mon, Aug 7, 2017 at 1:11 PM, Ben
Goertzel <b...@goertzel.org> wrote:
>>
>> I don't understand the proposed
semantics of AndMemberLink, could you
>> explain?
>>
>>
>>
>> On Sat, Aug 5, 2017 at 1:07 AM,
Michael Duncan <mjsd...@gmail.com>
>> wrote:
>> > i actually think an AndLink-like
semantics better fits biochemical
>> > pathways
>> > at a computationally tractable
level than partitions in that below the
>> > level
>> > of a whole organism, where one
pathway ends and another begins is
>> > largely
>> > arbitrary. also, if one link is
missing then the whole thing doesn't
>> > work
>> > but the last bit of a dead end
might be the start of another path that
>> > goes
>> > to the same place, more like words
and phrases that can be rearranged
>> > and
>> > swapped in different ways to say
the same thing. linus idea of
>> > AndMemberLinks and OrMemeberLinks
would get around the size limitation
>> > and
>> > also seem like they would be
useful for reasoning on moses models.
>> >
>> > On Monday, July 31, 2017 at
5:55:16 PM UTC-4, linas wrote:
>> >>
>> >> Hi Ben, Mike,
>> >>
>> >>
>> >> On Fri, Jul 21, 2017 at 9:41 PM,
Ben Goertzel <b...@goertzel.org>
>> >> wrote:
>> >>>
>> >>> 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
<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
>> >>
>> >>
>> >> As mentioned earlier, there are
several problems with this format. One
>> >> is
>> >> the "oops I forgot to mention xyz
in the list" or "gosh I should have
>> >> left
>> >> out pqr" and this becomes a big
problem: you have to delete the
>> >> PartitionLink, delete the
ListLink, create a new list and partition.
>> >> In the
>> >> meanwhile, some other subsystem
might be holding a handle to the old,
>> >> now-wrong PartitionLink, and
there is no effective way of announcing
>> >> "hey
>> >> stop using that old thing, get my
new thing now".
>> >>
>> >> A second problem is that the
above doesn't have anywhere to hang
>> >> addtional
>> >> data: e.g. "legs are a big part
of the human body, having a mas of
>> >> nearly
>> >> half of the body." You can't just
slap that on as a (truth)value, cause
>> >> there's no where to put that value.
>> >>
>> >> Third problem is that large
list-links are hard to handle in the
>> >> pattern
>> >> matcher. Its much much harder to
write a query of the form "find me
>> >> all
>> >> values of $X where
>> >>
>> >> PartitionLink
>> >> ConceptNode “human-body”
>> >> ListLink
>> >> ConceptNode “legs”
>> >> VariableNode “$X”
>> >> ConceptNode “brain”
>> >>
>> >> because, ... well the ListLink is
an ordrerd link, not an unordered
>> >> link.
>> >> If you forget to include the pqr
(added above) then the search will
>> >> fail.
>> >> You could try to use unordered
links and globnodes, but these lead to
>> >> other
>> >> difficulties, including the n!
possible permutations of an unordered
>> >> link
>> >> become large n-factorial large
when the unordered link has n items in
>> >> it.
>> >> Recall that old factorial-70
trick used to make calculators overflow.
>> >>
>> >> In general, any link with more
than 3 or 4 or 5 items in it is bad
>> >> news.
>> >> This is a generic statement about
knowledge representation in opencog.
>> >>
>> >>
>> >>> 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<
>> >>
>> >>
>> >>
>> >> Yeah, sure. Not sure why the
existing MemberLink is not sufficient for
>> >> your purposes. The MemberLink has
reasonably-well-defined semantics,
>> >> there
>> >> are already rules for handling it
in PLN (or there will be rules -- I
>> >> think
>> >> its something Nil has thought
about) I'm not clear on why you'd want
>> >> to
>> >> invent something that is just
like MemberLink but is different.
>> >>
>> >>>
>> >>>
>> >>> ...
>> >>>
>> >>> 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...
>> >>
>> >>
>> >> Yeah graphical-entropy is
something that I keep trying to work on,
>> >> except
>> >> that every new urgent disaster of
the day distracts me from it.
>> >>
>> >> --linas
>> >>>
>> >>>
>> >>> -- Ben
>> >>>
>> > --
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>>
>> --
>> 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
>
>
--
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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