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. For more options, visit https://groups.google.com/d/optout.
