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. 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CMakeCache.txt
Description: application/embl
