Re: [opencog-dev] PartitionLink, biological pathways, human bodies, etc.

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

Re: [opencog-dev] PartitionLink, biological pathways, human bodies, etc.

Once again: let me reiterate: I believe that using DefineLink for this kind of data prepresentation is an abuse, and it will only lead to trouble and heart-ache down the road. Please use EquivalenceLink instead. That link type was designed and intended for what you are trying to do here. The

Re: [opencog-dev] PartitionLink, biological pathways, human bodies, etc.

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"

Re: [opencog-dev] PartitionLink, biological pathways, human bodies, etc.

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

Re: [opencog-dev] PartitionLink, biological pathways, human bodies, etc.

Hi Mike, MemberLink DefinedPredicateNode "GO pathway term name" Predicate "protein relationship 1" ProteinNode "x" ProteinNode "y" MemberLink DefinedPredicateNode "GO pathway term name" Predicate "protein

Re: [opencog-dev] PartitionLink, biological pathways, human bodies, etc.

Quick comment, I did not review the Doc. On Tue, Aug 8, 2017 at 3:11 PM, Michael Duncan wrote: > the pathway links are predicates defined here > . > the pathways are > > DefineLink > I

Re: [opencog-dev] PartitionLink, biological pathways, human bodies, etc.

On Tue, Aug 8, 2017 at 2:37 AM, Nil Geisweiller wrote: > > However I don't think the more "atomic" representation should replace the > more "holistic" one, both should be allowed in parallel, right? Would that > be for backward compatibility at least. Then if it becomes

Re: [opencog-dev] PartitionLink, biological pathways, human bodies, etc.

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: ... ->

Re: [opencog-dev] PartitionLink, biological pathways, human bodies, etc.

On 08/06/2017 11:41 PM, Linas Vepstas wrote: Search becomes a problem. Say I want to find (using the pattern matcher) all sets that contain, as members, A B C. With set notation, I have to search for (Set X A B C) where X==(VariableNode "X") for 4-elelemnt sets, and then (Set X Y A B C) for

Re: [Link Grammar] Re: [opencog-dev] PartitionLink, biological pathways, human bodies, etc.

This representation makes sense to me for biological pathways Although, making PLN deal with these is another problem... On Mon, Aug 7, 2017 at 12:19 PM, Linas Vepstas wrote: > Nothing wrong with lots of arrows arranged into loops. If I were doing this, > this is what I

Re: [opencog-dev] PartitionLink, biological pathways, human bodies, etc.

> 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

Re: [opencog-dev] PartitionLink, biological pathways, human bodies, etc.

gmail.com> Cc: opencog <opencog@googlegroups.com>,Michael Duncan <mjsdun...@gmail.com> 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 a

Re: [opencog-dev] PartitionLink, biological pathways, human bodies, etc.

Nothing wrong with lots of arrows arranged into loops. If I were doing this, this is what I would propose: The single most important #1 special super-duper innovation I have recently discovered is to represent biological pathways like so: SectionLink CatalystNode "alpha-ketoglutarate

Re: [opencog-dev] PartitionLink, biological pathways, human bodies, etc.

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" wrote: > no clue why its appropriate for

Re: [opencog-dev] PartitionLink, biological pathways, human bodies, etc.

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

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 wrote: > First, lets review SetLink: > > SetLink > ConceptNode "x" > ConceptNode "y" > ConceptNode "z" > > > EquivalenceLink >

Re: [opencog-dev] PartitionLink, biological pathways, human bodies, etc.

First, lets review SetLink: SetLink ConceptNode "x" ConceptNode "y" ConceptNode "z" EquivalenceLink ConceptNode "last three letters of the alphabet" SetLink ConceptNode "x"

Re: [opencog-dev] PartitionLink, biological pathways, human bodies, etc.

I mean, if a pathway is just viewed as a semi-arbitrary set of relationships, then why not just make the pathway a ConceptNode, with MemberLinks to the relationships contained in the pathway? MemberLInks can then have fuzzy weights as needed. I am unsure why we want conjunction semantics here...

Re: [opencog-dev] PartitionLink, biological pathways, human bodies, etc.

I don't understand the proposed semantics of AndMemberLink, could you explain? On Sat, Aug 5, 2017 at 1:07 AM, Michael Duncan wrote: > i actually think an AndLink-like semantics better fits biochemical pathways > at a computationally tractable level than partitions in that

Re: [opencog-dev] PartitionLink, biological pathways, human bodies, etc.

On Fri, Aug 4, 2017 at 3:07 AM, Nil Geisweiller wrote: > On 08/03/2017 10:06 AM, Linas Vepstas wrote: > >> There's also a problem of editing: what if, half-way through, you want to >> change the partition? Can you? should you? should users instead be told >> that a

Re: [opencog-dev] PartitionLink, biological pathways, human bodies, etc.

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

Re: [opencog-dev] PartitionLink, biological pathways, human bodies, etc.

On 08/03/2017 10:06 AM, Linas Vepstas wrote: There's also a problem of editing: what if, half-way through, you want to change the partition? Can you? should you? should users instead be told that a partition, once-created, is immutable, so you can only create and destroy them? But isn't the

Re: [opencog-dev] PartitionLink, biological pathways, human bodies, etc.

On Tue, Aug 1, 2017 at 1:24 AM, Ben Goertzel wrote: > Hi Linas, > > The difference between PartitionLink and MemberLink is pretty obvious, > right? Not to me ... I realize now that perhaps you mean "SubSetLink" and I thought we had one of those, but perhaps it has different

Re: [opencog-dev] PartitionLink, biological pathways, human bodies, etc.

Hi Linas, The difference between PartitionLink and MemberLink is pretty obvious, right? A PartitionNode defines a partition of the set denoted by a ConceptNode. The partition elements that are linked to the PartitionNode by a PartitionLink can of course also be linked via a MemberLink to the