How can you determine if a pathway link is missing? I mean, if you created
the AndLink, then its necessarily present/true, unless you are changing the
truth value to 0.0 under some cases.
what I'm trying to say is that determining if a biological pathway is
present/active is very similar to parsing an english-language sentence. For
a sentence to be valid, the words have to be present, and have to be
connected in the right order.
That is, a "path" in English is a "sentence", and for various reasons, we
never try to make a list of all possible sentences; instead opting to make
a list of sentence-parts, and then seeing how they can hook together
("parsing")
Perhaps, in biology, it is possible to make an exhaustive list of all
possible biological pathways. Maybe. But again: not that AndLink is
unordered: (AndLink A B) is exactly the same atom as (AndLink B A) ...
perhaps you want SequentialAndLink ??
--linas
On Mon, Aug 7, 2017 at 2:53 PM, mjsduncan <[email protected]> wrote:
> if any pathway link is missing/false, the whole pathway is false. all the
> links have to be present/true for the pathway to be in effect/true
>
>
> -------- Original message --------
> From: Ben Goertzel
> Date:07/08/2017 11:21 (GMT-08:00)
> To: Linas Vepstas
> Cc: opencog ,Michael Duncan
> Subject: Re: [opencog-dev] PartitionLink, biological pathways, human
> bodies, etc.
>
> 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
> >> >>>
> >> >>> 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
> >> >>>
> >> > --
> >> > You received this message because you are subscribed to the Google
> >> > Groups
> >> > "opencog" group.
> >> > To unsubscribe from this group and stop receiving emails from it, send
> >> > an
> >> > email to [email protected].
> >> > To post to this group, send email to [email protected].
> >> > Visit this group at https://groups.google.com/group/opencog.
> >> > To view this discussion on the web visit
> >> >
> >> > https://groups.google.com/d/msgid/opencog/e1df7273-da14-
> 45f5-8d0d-5ebad0d31217%40googlegroups.com.
> >> >
> >> > For more options, visit 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
>
--
You received this message because you are subscribed to the Google Groups
"opencog" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to [email protected].
To post to this group, send email to [email protected].
Visit this group at https://groups.google.com/group/opencog.
To view this discussion on the web visit
https://groups.google.com/d/msgid/opencog/CAHrUA36SS7ciVTWkUR859-bffUZ38cKV4e6AdLitL2mB_wBY1w%40mail.gmail.com.
For more options, visit https://groups.google.com/d/optout.
