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 > >> >>> > >> >>> 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/CAHrUA35O-mkpwazY43W1EX9Th-aCmKY1DreMWhnq5aafORYDpg%40mail.gmail.com. For more options, visit https://groups.google.com/d/optout.
