Hi,
On 3/2/19 8:32 PM, Linas Vepstas wrote:
A word of caution about as-moses: it may have some unintended
performance profile. The original moses got very optimized to run fast;
but the atomspace is an in RAM graph database which means it has indexes
which means index insertion has a real cost. Exactly how the two get
stapled together is an open work item.
For now as-moses is fully backward compatible with moses. That is it
should behave identically as long as you don't use new options like
--atomspace-port, etc.
However if stability is a primary concern it's better to use moses,
just to be cautious.
-----
BTW -- if Nil or Kasim or other as-moses people are listening -- perhaps
it makes more sense to have make combo-trees be Value-trees during the
computation -- Values are NOT indexed, they're meant to be fast, provide
fast access. Then after computation is done, the best trees, the
results can be copied into the atomspace.
as-combo actually has its own interpreter, that indeed outputs
values. It is planned to eventually merge this interpreter to
atomspace's but for now we feel it's easier if they are separated,
especially since it is still highly experimental at this stage.
Nil
Another possibility might be to have either a tree-Value, (i.e. a new
kind of Value that is a combo-tree) or something that converts
LinkValues into combo trees (or vice-versa). All of this might
alleviate issues related to performance and mapping & etc. I don't know
where you guys have these design discussions, but if any of this sounds
appealing, let me know; I can clarify details.
--linas
On Sat, Mar 2, 2019 at 10:56 AM Abu Naser <[email protected]
<mailto:[email protected]>> wrote:
Thank you Ben for your suggestions. I have installed AS-MOSES (the
version works on atomspace). However, I had to make following
changes during installation:
3) In bscores.cc, I had to insert #include <set>
2) in build_knobs.cc, at line 237, I had to change distance(from,
to) to std::distance(from, to)
1) In table.cc, at line 259, I had to change return
distance(labels.begin(), pos) to return
std::distance(labels.begin(), pos)
Hope these changes will not raise other issues down the line.
Thank you again Ben, I have now something to play around with.
With regards,
Abu
On Fri, 1 Mar 2019 at 23:59, Ben Goertzel <[email protected]
<mailto:[email protected]>> wrote:
The MOSES-for-supervised-learning stuff is a bit specialized, and
doesn't use the main OpenCog codebase, MOSES is a standalone system
However Nil wrote code for importing learned MOSES models into the
Atomspace, and once you've done that you can play with PLN inference
or other tools for combining MOSES models w/ other knowledge
A great project for a brave soul right now would be
-- run MOSES on some categorial SNP or gene expression data to get a
big diverse model ensemble
-- load these models into Atomspace
-- use Nil's new Pattern Miner to find surprising patterns among the
MOSES models
Then one could bring PLN into the story to integrate, say, Gene
Ontology into the surprisingness assessment...
ben
On Sat, Mar 2, 2019 at 7:41 AM Abu Naser <[email protected]
<mailto:[email protected]>> wrote:
>
> Hi Ben,
>
> Thank your for responding my queries. I will try to find the
papers and guessing you are one of the authors of the papers. It
would be very useful for me if I could get Bioinfromatics
related toy examples to play around, which will help me to get
to know the opencog code. Hope Mike will point me to one of
those example code.
>
> With kind regards,
>
> Abu
>
> On Fri, 1 Mar 2019 at 23:14, Ben Goertzel <[email protected]
<mailto:[email protected]>> wrote:
>>
>> There are two pieces to what we've been doing w/ OpenCog for
bioinformatics
>>
>> 1) supervised classification of genomics datasets (e.g.
SNPs, gene
>> expression) using MOSES
>>
>> 2) integration of various ontologies into the Atomspace,
import of
>> MOSES classification models into the Atomspace, and use of PLN
>> reasoning (currently on a pretty ad hoc, human guided basis)
to do
>> inference based on this combined data
>>
>> There are publications on both of these things, though I
don't have
>> time to dig up the URL right now, and Mike can point you to the
>> code...
>>
>> ben
>>
>> On Sat, Mar 2, 2019 at 5:51 AM Linas Vepstas
<[email protected] <mailto:[email protected]>> wrote:
>> >
>> > Hi,
>> >
>> > Opencog has many parts to it.There is an agi-bio part for
bioinformatics but it seems slim, and I think the main part of
that system is somewhere else. I'm hoping Mike Duncan can
respond in more detail.
>> >
>> > --linas
>> >
>> > On Fri, Mar 1, 2019 at 1:15 PM Abu Naser
<[email protected] <mailto:[email protected]>> wrote:
>> >>
>> >> Hello Everyone,
>> >>
>> >> I have just installed opencog on Ubuntu. I am a biologist
and wish to use opencog for solving biological problems. I have
been wondering whether there is any tutorial related to
Bioinformatics. Please let me know.
>> >>
>> >> With best regards,
>> >>
>> >> Abu
>> >>
>> >> --
>> >> 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]
<mailto:opencog%[email protected]>.
>> >> To post to this group, send email to
[email protected] <mailto:[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/b91a8dda-25db-48ea-80ed-776fed30dea6%40googlegroups.com.
>> >> For more options, visit https://groups.google.com/d/optout.
>> >
>> >
>> >
>> > --
>> > cassette tapes - analog TV - film cameras - you
>> >
>> > --
>> > 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]
<mailto:opencog%[email protected]>.
>> > To post to this group, send email to
[email protected] <mailto:[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/CAHrUA34wuXH1z%3DiDwE9_HX7%2BN04SPyTHjzSp8hKPR6%2Bgih1rXA%40mail.gmail.com.
>> > For more options, visit https://groups.google.com/d/optout.
>>
>>
>>
>> --
>> Ben Goertzel, PhD
>> http://goertzel.org
>>
>> "Listen: This world is the lunatic's sphere, / Don't
always agree
>> it's real. / Even with my feet upon it / And the postman
knowing my
>> door / My address is somewhere else." -- Hafiz
>>
>> --
>> 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]
<mailto:opencog%[email protected]>.
>> To post to this group, send email to
[email protected] <mailto:[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/CACYTDBe4hX_MK2x2wXRmZ6ZiVqGO5Q48FC%3DJoyPYWAUYOv3VBQ%40mail.gmail.com.
>> For more options, visit https://groups.google.com/d/optout.
>
> --
> 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]
<mailto:opencog%[email protected]>.
> To post to this group, send email to [email protected]
<mailto:[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/CAMw3wdhhdkdNMGLGPxf0aRZOG9VkaU05sNdc87%2B7TOYYiZi0tg%40mail.gmail.com.
> For more options, visit https://groups.google.com/d/optout.
--
Ben Goertzel, PhD
http://goertzel.org
"Listen: This world is the lunatic's sphere, / Don't always agree
it's real. / Even with my feet upon it / And the postman
knowing my
door / My address is somewhere else." -- Hafiz
--
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]
<mailto:opencog%[email protected]>.
To post to this group, send email to [email protected]
<mailto:[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/CACYTDBf4tv8-sJ9FV%3DFbGwb9ny3GbZ%3DYRZWSS%2BbpKCjOYnBKpw%40mail.gmail.com.
For more options, visit https://groups.google.com/d/optout.
--
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]
<mailto:[email protected]>.
To post to this group, send email to [email protected]
<mailto:[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/CAMw3wdgRL0UtUxbMY2%2BfmYH0aNO5CoY67dRyUVdb4NLd%3D7vo-Q%40mail.gmail.com
<https://groups.google.com/d/msgid/opencog/CAMw3wdgRL0UtUxbMY2%2BfmYH0aNO5CoY67dRyUVdb4NLd%3D7vo-Q%40mail.gmail.com?utm_medium=email&utm_source=footer>.
For more options, visit https://groups.google.com/d/optout.
--
cassette tapes - analog TV - film cameras - you
--
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/9b260c93-5ab0-140c-0897-f48fde4c7ce4%40gmail.com.
For more options, visit https://groups.google.com/d/optout.
