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. 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