Hi Linas, It is probably easier for your to change for me.
Thanks for letting me know the performance limitation of as-moses. With regards. Abu On Sat, 2 Mar 2019 at 18:32, Linas Vepstas <linasveps...@gmail.com> 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 <naser....@gmail.com> 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 <b...@goertzel.org> 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 <naser....@gmail.com> 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 <b...@goertzel.org> 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 <linasveps...@gmail.com> >>> 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 <naser....@gmail.com> >>> 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 opencog+unsubscr...@googlegroups.com. >>> >> >> To post to this group, send email to opencog@googlegroups.com. >>> >> >> 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 opencog+unsubscr...@googlegroups.com. >>> >> > To post to this group, send email to opencog@googlegroups.com. >>> >> > 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 opencog+unsubscr...@googlegroups.com. >>> >> To post to this group, send email to opencog@googlegroups.com. >>> >> 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 opencog+unsubscr...@googlegroups.com. >>> > To post to this group, send email to opencog@googlegroups.com. >>> > 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 opencog+unsubscr...@googlegroups.com. >>> To post to this group, send email to opencog@googlegroups.com. >>> 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 opencog+unsubscr...@googlegroups.com. >> To post to this group, send email to opencog@googlegroups.com. >> 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 opencog+unsubscr...@googlegroups.com. > To post to this group, send email to opencog@googlegroups.com. > 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. 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