thanks, nil; i just replied to just you because you replied to me twice personally ;) according to linus the 330 atom limit on outgoing sets is hard wired in the sql code. the MemberLink formulation was meant to get around that. more generally what i'm trying to do with the pathway representation is to have a graph model of the protein interactions that can be compared to experimental data to infer which subsets of the interaction graph are likely to be active in the experimental sample.
On Thu, Sep 21, 2017 at 12:25 AM, Nil Geisweiller <[email protected]> wrote: > Hi Mike (sending back to opencog list, I think you forgot to reply all), > > On 09/20/2017 06:24 PM, Michael Duncan wrote: > >> ok i have the list order wrong and i'm trying to use shorthand "sugar" to >> write down the h-graph. >> i'm trying to say: >> >> MemberLink >> Predicate "protein relationship 1" >> ProteinNode "x" >> ProteinNode "y" >> ConceptNode "GO pathway term name" >> >> MemberLink >> ConceptNode "GO pathway term name" >> Predicate "protein relationship 2" >> ProteinNode "y" >> ProteinNode "z" >> .... >> > > OK, that looks correct. > > >> where >> >> Predicate "protein relationship 1" >> ProteinNode "x" >> ProteinNode "y" >> >> is shorthand for one of the fully spelled out h-graphs defined for >> specific protein concepts "x" and "y" here <https://docs.google.com/docum >> ent/d/1R_AiCCRuWKI92JUCYXJRnKeYw-MiwKLR3kr9fJyYZfs/edit>. >> >> my original formulation was >> >> DefineLink >> DefinedPredicateNode "GO pathway term name" >> AndLink >> Predicate "protein relationship 1" >> ProteinNode "x" >> ProteinNode "y" >> Predicate "protein relationship 2" >> ProteinNode "y" >> ProteinNode "z" >> .... >> which was originally problematic because of the sql storage limit on the >> size of incoming sets. >> > > You say "originally problematic", you mean it no longer is problematic? > > Do you mean outgoing set? I think it's unfortunate that the SQL encoding > has such limit, there must be a way to alleviate that, I hope. > > Nil > > >> >> >> On Wed, Sep 20, 2017 at 9:36 PM, Nil Geisweiller <[email protected] >> <mailto:[email protected]>> wrote: >> >> On 09/20/2017 03:20 PM, Michael Duncan wrote: >> >> 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" >> >> >> Also, it's not clear what >> >> > Predicate "protein relationship 1" >> > ProteinNode "x" >> > ProteinNode "y" >> >> is. >> >> Usually we write >> >> Evaluation >> Predicate "P" >> List >> <arg1> >> ... >> <argn> >> >> Nil >> >> >> >> 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] >> <mailto:[email protected]>> wrote: >> > >> > the pathway links are predicates defined >> here >> > <https://docs.google.com/docu >> ment/d/1R_AiCCRuWKI92JUCYXJRnKeYw-MiwKLR3kr9fJyYZfs/edit >> <https://docs.google.com/document/d/1R_AiCCRuWKI92JUCYXJRnKe >> Yw-MiwKLR3kr9fJyYZfs/edit> >> <https://docs.google.com/docum >> ent/d/1R_AiCCRuWKI92JUCYXJRnKeYw-MiwKLR3kr9fJyYZfs/edit >> <https://docs.google.com/document/d/1R_AiCCRuWKI92JUCYXJRnKe >> Yw-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] >> <mailto:[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] >> <mailto:[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] <mailto:[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] <mailto:[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] <mailto:[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] <mailto:[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> >> <https://www.academia.edu/1016959/Fuzzy_mereology >> <https://www.academia.edu/1016959/Fuzzy_mereology>> >> > < >> https://www.academia.edu/1016959/Fuzzy_mereology >> <https://www.academia.edu/1016959/Fuzzy_mereology> >> <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 > > -- 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/CAOoNsN8yU%3DSZ67jTkiMHkHDBMOSNDgRnL95xrzDBs-4T%3Da1AWQ%40mail.gmail.com. For more options, visit https://groups.google.com/d/optout.
