On Sat, Mar 2, 2019 at 2:21 PM Abu Naser <[email protected]> wrote:
> Hi Linas, > > It is probably easier for your to change for me. > OK. > > Thanks for letting me know the performance limitation of as-moses. > There might not be one. I'm just not sure. OpenCog is all about "how do you represent knowledge?" and "how do you move it around frictionlessly between different processing systems?" A meta-goal is to avoid brittle stove-pipe constructions, AKA spaghetti-code of data moving from here to there. Moses does a very specific kind of machine learning. The way it represents data is "almost like" how the atomspace does. The AtomSpace provides a foundation for reasoning and inference and other kinds of knowledge processing; (e.g. adding appropriate neural-net support is a work-in-progress). So far, we don't have seamless, friction-free access between different algorithms, and the different kinds of data people use. But we're making small steps. In the meanwhile, you are welcome to create stove-pipe constructions that are just good enough for what you need to do... -- Linas > > With regards. > > Abu > > On Sat, 2 Mar 2019 at 18:32, Linas Vepstas <[email protected]> wrote: > >> Hi Abu, >> >> The changes you propose are completely reasonable. >> >> If you really want to participate in the formal coding process, you >> should create a github pull request with these changes in them. .. or I >> could make them for you. Let me know. >> >> 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. >> >> ----- >> 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. >> >> 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]> 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]> 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]> 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]> 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]> >>>> 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]> >>>> 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]. >>>> >> >> 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/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]. >>>> >> > 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/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]. >>>> >> 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/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]. >>>> > 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/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]. >>>> 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/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]. >>> 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/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/CAHrUA35L-f0_VkcPfXzTK%2BhwVtVKzD78NCo1MnCH2ep%3Dhc%3DodQ%40mail.gmail.com >> <https://groups.google.com/d/msgid/opencog/CAHrUA35L-f0_VkcPfXzTK%2BhwVtVKzD78NCo1MnCH2ep%3Dhc%3DodQ%40mail.gmail.com?utm_medium=email&utm_source=footer> >> . >> 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]. > 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/CAMw3wdiYO8dQoc9uLgy4x37aBonf8%2BCU7ypOS5%3DkcV6S2UNkxQ%40mail.gmail.com > <https://groups.google.com/d/msgid/opencog/CAMw3wdiYO8dQoc9uLgy4x37aBonf8%2BCU7ypOS5%3DkcV6S2UNkxQ%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/CAHrUA346w_c0w1F_c_jUONu3zj-MPa5VJq1tozz8Dkt0NRp0RQ%40mail.gmail.com. For more options, visit https://groups.google.com/d/optout.
