ok maybe that was a typo on linus' part, then his responses would make more
sense to me.
defining a pathway as:
MemberLink
ConceptNode "GO pathway term name"
Predicate "protein relationship 1"
ProteinNode "x"
ProteinNode "y"
MemberLink
ConceptNode "GO pathway term name"
Predicate "protein relationship 2"
ProteinNode "y"
ProteinNode "z"
....
would follow from his comments.
On Wednesday, September 20, 2017 at 6:59:38 PM UTC+8, Nil wrote:
>
> Hi Mike,
>
> > 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"
> > ....
>
> just a little remark, these look wrong. A MemberLink link elements
> concepts, not predicates.
>
> Nil
>
> >
> > 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
> > <[email protected]> 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"
> > <[email protected]> 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
> > <[email protected]> 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 <[email protected]> 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 <[email protected]> wrote:
> > >>
> > >> I don't understand the proposed
> > semantics of AndMemberLink, could you
> > >> explain?
> > >>
> > >>
> > >>
> > >> On Sat, Aug 5, 2017 at 1:07 AM,
> > Michael Duncan <[email protected]>
> > >> 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 <[email protected]>
> > >> >> 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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> > >> > To view this discussion on the web
> > visit
> > >> >
> > >> >
> >
> https://groups.google.com/d/msgid/opencog/e1df7273-da14-45f5-8d0d-5ebad0d31217%40googlegroups.com
>
> > <
> https://groups.google.com/d/msgid/opencog/e1df7273-da14-45f5-8d0d-5ebad0d31217%40googlegroups.com>.
>
>
> > >> >
> > >> > For more options, visit
> > https://groups.google.com/d/optout
> > <https://groups.google.com/d/optout>.
> > >>
> > >>
> > >>
> > >> --
> > >> 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
> >
> >
> >
> >
> >
> >
> > --
> > /"The problem is not that artificial intelligence will get too smart
> > and take over the world," computer scientist Pedro Domingos writes,
> > "the problem is that it's too stupid and already has." /
> >
> > --
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