Hi Griffith, Looks like It is a problem from my side. Wondering why?
Kind regards, Abu On Tue, 14 Jan 2025 at 18:57, Griffith Mehaffey (Gemini47) < [email protected]> wrote: > Excellent 😎 > > That’ll work 👏 > > Sent from my iPhone > > On Jan 14, 2025, at 12:43 PM, Abu Naser <[email protected]> wrote: > > > Hi Griffith, > > Did you mean CMakeCache.txt file? I have attached the file with > this email. > > Kind regards, > Abu > > On Tue, 14 Jan 2025 at 14:56, Griffith Mehaffey (Gemini47) < > [email protected]> wrote: > >> Good morning, Abu. >> >> I’d sure be happy to try. If you’re able to send a txt file detailing >> everything you’re doing to try and achieve the Python bindings that might >> help to see where the bottleneck is. >> >> But 97% is pretty darn close so congrats 🎊🍾 to you there. >> >> Certainly would be a lot of advantages to using the AtomSpace once those >> Python bindings become fully integrated. >> >> And let me know about the txt file option. If we’re able, I’d like to >> start there to try and find a solution. >> >> Cheers 🍻 >> >> Sent from my iPhone >> >> On Jan 14, 2025, at 7:45 AM, Abu Naser <[email protected]> wrote: >> >> >> Hi Griffith, >> >> I am reading from the Opencog wiki. Are there any better materials >> available? >> >> While I was trying to compile atomspace with python bindings, I have got >> the following error: >> [ 97%] Built target utilities_cython >> make[2]: *** No rule to make target >> '../opencog/persist/api/cython/../../storage/storage_types.pyx', needed by >> 'opencog/persist/api/cython/storage.cpp'. Stop. >> >> Would you be able to help me with this? >> >> Kind regards, >> Abu >> >> >> >> On Tue, 14 Jan 2025 at 03:04, Griffith Mehaffey (Gemini47) < >> [email protected]> wrote: >> >>> You’re most welcome Abu. >>> >>> Quick question: What sources are you using to read up on AtomSpace? Just >>> curious :) >>> >>> Keep us all posted on how it’s going. >>> >>> Cheers 🍻 >>> >>> -Griffith >>> >>> Sent from my iPhone >>> >>> On Jan 13, 2025, at 4:52 PM, Abu Naser <[email protected]> wrote: >>> >>> >>> Responding to Griffith >>> >>> Thank you very much for your email and suggestions. My immediate plan is >>> to work with viral genomes, which are much simpler and smaller, and I guess >>> it is possible to put those genomes in a MongoDB. >>> At the moment I am still in the dark about what to do and how to >>> implement some ideas using atomspace. Currently, I am doing some reading on >>> atomspace. I will keep you posted about my progress and seek help if I may. >>> >>> Responding to Linas >>> >>> I am planning to read about atomspace and to execute some of >>> the examples that came with the package. Python would be an easier choice >>> for me. >>> While I was trying to compile atomspace with python bindings, I have got >>> the following error: >>> >>> [ 97%] Built target utilities_cython >>> make[2]: *** No rule to make target >>> '../opencog/persist/api/cython/../../storage/storage_types.pyx', needed by >>> 'opencog/persist/api/cython/storage.cpp'. Stop. >>> >>> Please let me know the potential solutions for this error. >>> >>> Kind regards, >>> >>> Abu >>> >>> >>> On Sat, 11 Jan 2025 at 05:26, Linas Vepstas <[email protected]> >>> wrote: >>> >>>> Replying to Abu. >>>> >>>> On Wed, Jan 8, 2025 at 12:34 PM Abu Naser <[email protected]> wrote: >>>> > >>>> > Good to hear from you. >>>> > I have done some googling about the LLM, I have found many people are >>>> using LLM for analysing genomic data. >>>> >>>> I'd be amazed if there weren't. Pharma is a $1.6 trillion-dollar >>>> business in the US alone. >>>> https://www.statista.com/topics/1764/global-pharmaceutical-industry/ >>>> If some of that money *wasn't* going into LLM's, I would conclude that >>>> I had died and been reanimated in a crappy universe simulation. >>>> >>>> > (https://github.com/MAGICS-LAB/DNABERT_2?tab=readme-ov-file that can >>>> easily be used via https://huggingface.co/docs/transformers/en/index) >>>> > Their approach is usual, 1st train a model and then use it to >>>> predict. In our case, where do we get the knowledge to store on atomspace? >>>> >>>> That's a great question. (If I understand you correctly) I assume you >>>> already know how to get, have access to oodles and poodles of genomic >>>> data. There are open, public databases of genomic data, in all shapes >>>> and sizes. No doubt there's even more that's proprietary, say, the >>>> 23+me dataset. >>>> >>>> I think the issue is "how do I hook up an LLM to the AtomSpace?" and >>>> the short answer is "I don't know". Well, I do know, but I am unhappy >>>> with all the ways I know how. So I've recently and with some urgency >>>> started to think about "what is the *best* way to hook up LLMs to the >>>> atomspace?" and I don't have an answer to that, yet. Might take a >>>> while >>>> >>>> > I can certainly to do some reading on their work and figure out how >>>> they do it. >>>> >>>> Yes, please! If you can then explain it to me, in email, that would >>>> be excellent. If you can't explain it, then some paper references... >>>> >>>> > Do you have the pattern matching tool set in github? >>>> >>>> Yes. https://github.com/opencog/learn >>>> >>>> Terminology: in comp-sci, "pattern matching" usually refers to a very >>>> simple kind of matching, called "regular expressions" (regex), with >>>> theory developed in 1960's and a standard part of Unix by the 1980's >>>> see e.g. "perl regex". >>>> >>>> Besides regex, many programming languages have a similar but different >>>> idea: scheme has "hygenic macros". as do other functional languages. >>>> Python does not javascript does not. I think some of the latest and >>>> weirdest c++ standards track is trying to go that way. C++ templates >>>> are kind-of pattern-matcher-like-ish, but they're simple, and 30-35 >>>> years old, now. >>>> >>>> In atomese, I made the mistake of calling it's graph rewriting system >>>> "pattern matching". Bad mistake, because it makes people think of the >>>> above rather simple systems. In fact, Atomese has 2 or 3 or 4 distinct >>>> systems that, uhh, "process patterns" >>>> >>>> At the bottom end, its the "query engine", which is a sophisticated >>>> and fast graph rewrite engine. Tutorials here: >>>> >>>> https://github.com/opencog/atomspace/tree/master/examples/pattern-matcher >>>> you might find these to be .. mind-bendingly complicated. A theory >>>> paper is here: >>>> https://github.com/opencog/atomspace/raw/master/opencog/sheaf/docs/ram-cpu.pdf >>>> >>>> At the mid-range, there's a rule system and a unifier. The unifier >>>> works. The rule system needs to be torched and rewritten. >>>> >>>> At the "high-end", there's https://github.com/opencog/learn In many >>>> ways, it kind-of-ish resembles transformers. Except that it works with >>>> structures, rather than linear strings of data. And that kind-of >>>> changes everything. It gets kind-of-ish similar results, but since its >>>> also kind-of-ish completely different (because instead of working with >>>> strings, it works with trees) its ... well, its a weird-ass >>>> half-finished prototype. I love/hate it because I know why its great >>>> and why it's utterly mis-designed. Its a steep hill to climb. >>>> >>>> > I am a command line person. I would not mind even if it is a bit >>>> messy. I am a biologist by training but >>>> > professionally I don't do biology. It would be fun for me to do some >>>> biology on the sideline of my profession. >>>> >>>> Ah! Well, let's start small. Look at and plan what is doable and >>>> interesting and fun. >>>> >>>> > My shortcoming is that I am not a good coder. >>>> >>>> Heh. I'm a *very good coder*, and so when I say "this shit is >>>> difficult", trust me. This shit is difficult. >>>> >>>> (yes, that's an "appeal to authority", but .. hey.) >>>> >>>> --linas >>>> >>>> -- >>>> 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 view this discussion visit >>>> https://groups.google.com/d/msgid/opencog/CAHrUA37Be-ak%3DvBrc7%2B4QXB6zYWOfGCB1BuSkxb0VFfh6N%2BNKw%40mail.gmail.com >>>> . >>>> >>> -- >>> 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 view this discussion visit >>> https://groups.google.com/d/msgid/opencog/CAMw3wdi2YGioOgDSiNf75pm5HY3pyUfuoFqX4pSSSEMzuj9mKQ%40mail.gmail.com >>> <https://groups.google.com/d/msgid/opencog/CAMw3wdi2YGioOgDSiNf75pm5HY3pyUfuoFqX4pSSSEMzuj9mKQ%40mail.gmail.com?utm_medium=email&utm_source=footer> >>> . >>> >>> -- >>> 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 view this discussion visit >>> https://groups.google.com/d/msgid/opencog/90A19806-4280-4A33-81CC-0A567EB0297B%40gmail.com >>> <https://groups.google.com/d/msgid/opencog/90A19806-4280-4A33-81CC-0A567EB0297B%40gmail.com?utm_medium=email&utm_source=footer> >>> . >>> >> -- >> 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 view this discussion visit >> https://groups.google.com/d/msgid/opencog/CAMw3wdgXcj4mzc5zbn8orJL4MV6X5zGt2p0YJMExDhFLoTiVEA%40mail.gmail.com >> <https://groups.google.com/d/msgid/opencog/CAMw3wdgXcj4mzc5zbn8orJL4MV6X5zGt2p0YJMExDhFLoTiVEA%40mail.gmail.com?utm_medium=email&utm_source=footer> >> . >> >> -- >> 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 view this discussion visit >> https://groups.google.com/d/msgid/opencog/4A666237-00A9-4D6D-8BE3-E482B09A2304%40gmail.com >> <https://groups.google.com/d/msgid/opencog/4A666237-00A9-4D6D-8BE3-E482B09A2304%40gmail.com?utm_medium=email&utm_source=footer> >> . >> > -- > 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 view this discussion visit > https://groups.google.com/d/msgid/opencog/CAMw3wdhDE6KkEQs0xtLtNbid1vjQQtMZxbguWYX9TobHp6GogQ%40mail.gmail.com > <https://groups.google.com/d/msgid/opencog/CAMw3wdhDE6KkEQs0xtLtNbid1vjQQtMZxbguWYX9TobHp6GogQ%40mail.gmail.com?utm_medium=email&utm_source=footer> > . > <CMakeCache.txt> > > -- > 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 view this discussion visit > https://groups.google.com/d/msgid/opencog/EC579F10-0BA9-4D17-89A4-8A0BD996F992%40gmail.com > <https://groups.google.com/d/msgid/opencog/EC579F10-0BA9-4D17-89A4-8A0BD996F992%40gmail.com?utm_medium=email&utm_source=footer> > . > -- You received this message because you are subscribed to the Google Groups "opencog" group. 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