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 >> >> >>> >> >> >>> 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/CACYTDBdPxXgCwCVaFVVb26GprHjELZVJOmDa_4D5%3DXqnCM5cbQ%40mail.gmail.com. For more options, visit https://groups.google.com/d/optout.
