Hi LInas, Thank you very much for your very informative email. Among topics you mentioned, following two sounds interesting:
1) Pattern discovery 2) Hooking up an LLM-based chatbot to a large genomics data. What tools do you have for pattern discovery? Regarding LLM-based chatbot, is it expected to implement LLM chatbot from the scratch? Kind regards, Abu On Tue, 7 Jan 2025 at 17:47, Linas Vepstas <[email protected]> wrote: > On Tue, Jan 7, 2025 at 3:46 AM Abu Naser <[email protected]> wrote: > > > > I am interested in applying agi in genomics. Is there any tutorial on > how to build models, etc. ? > > OpenCog is not AGI, since that doesn't exist. Although everyone says > they are working on it. OpenCog is a system for implementing various > aspects of AGI: exploring, experimenting, tinkering. > > OpenCog has a set of components, ranging from rock-solid, stable, > high-performance, to buggy, incomplete, abandoned. > > At the stable end is the AtomSpace, which is a way for storing > anything in any way: vectors, dense networks, sparse networks, graphs, > things that flow or change in time, whatever. It has been used for > storing genomic and proteomic data, and the reactomes connecting them. > I did look at that code: the core storage idea seemed fine. Some of > the processing algorithms were poorly designed. I was called in for > emergency repairs on one: after a month's worth of work, I got it to > run 200x faster. That's right, two-hundred times. Unfortunately, by > then, the client lost interest. The moral of the story is that > software engineering matters: just cause its whiz-bang AI doesn't mean > you can ignore basic design principles. So it goes. > > That project was mining for small reactome networks: for example, > given one gene and one protein, find one other gene, two up/down > regulators, and one other (I don't know, I'm not a geneticist) that > formed a loop, or a star-shape, or something. The issue was that these > sometimes could be found in a second or two, and sometimes it would > take an hour of data-mining, which was annoying for the geneticists > who just wanted the answer but didn't want to wait an hour. Of course, > as the reaction network moved from 4 or 5 interactions, to 6 or 8, > there was a combinatorial explosion. > > The reason for this was that that system performed an exhaustive > search: it literally tried every possible combination, so that even > obscure, opaque and thus "novel" combinations would be found. The > deep-learning neural nets provide an alternative to exhaustive search. > However, no one has hooked up a deep learning net for genomics into > opencog, so you will not get lucky, there. > > MOSES (that you had trouble building) is a system for discovering > pattern correlations in datasets. One project applied it to find a > list of about 100 or 200 genes that correlated with long lifespans. > The code, the adapter that did that was either proprietary, or was > lost to the sands of time. > > I've been working on a tool for pattern discovery. In principle ("in > theory") it could be used for genomics data. In practice, this would > require adapters, shims and rejiggering. > > And so what? You use it, you can find some patterns, some > correlations, and so what? There must be a zillion patterns and > correlations in genomic data, so you have to be more focused than > that. > > Some parts of the AI world talk about building "virtual scientists" > that can "create hypotheses and test them". OpenCog does not do this. > > Creating an AI scientist that automatically makes discoveries sounds > really cool! An exciting and new shiny future of AI machine > scientists! But for one thing: the mathematicians have already tried > this. > > Math is crisp enough that it is very easy to "create hypotheses and > test them". They're called "theorems", > and you test them with "theorem provers". Turns out that 99.999% of > all theorems are boring (to humans). Yes, it might be true that X+Y=Z, > but who cares? So what? > > I suspect a similar problem applies to genomics. Yes, someday, we > might have AI scientists making "profound" discoveries, but the "so > what?" question lingers. Unless that discovery is very specific: "take > these pills, eat these foods and exercise regularly, you will become > smarter and have a longer healthspan", that discovery is useless, in > and of itself. > > There is a way out. In science, it turns out that making discoveries > is hard, but once you have them, you can remember them, so you don't > have to re-discover from scratch. You write them down in textbooks, > teach the next generation, who then takes those discoveries and > recombines them to make new discoveries. In mathematics, these are > called "oracles": you have a question, the oracle can answer them > instantly. Now, you can't actually build the pure mathematical > definition of an oracle, but if you pretend you can, you can make > deductions that are otherwise hard. > > If you can collect all the hard-to-find interrelations in genetics, so > that the next time around it's instant and easy, then .. ? > > Let amble down that path. The various LLM's -- ChatGPT, and the OpenAI > stuff and the Gemini from google are question-oracle-like things. You > can ask questions, and get answers. OpenCog does NOT have one of > these, and certainly not one optimized for genomics questions. If > you want a natural language, chatbot interface to your genomics > oracle, OpenCog is not the thing. Because OpenCog does not have > chatbot natural language interfaces to its tools: the tools are all > old-style, "Dr. DOS Prompt", and not windows-n-mouse interfaces, and > certainly not LLM chatbots. Alas. > > Could you hook up an LLM-based chatbot to a large dataset of genomics > data (using, for example, the OpenCog AtomSpace to hold it, and > various tools to data-mine it?) I guess you could. But no one has done > this, and this would be a large project. Not something you'd > accomplish in a week or two of tinkering. > > -- linas > > > > > Kind regards, > > > > Abu > > > > > > > > On Tue, 7 Jan 2025 at 03:55, Linas Vepstas <[email protected]> > wrote: > >> > >> Hi Abu, > >> > >> I just merged a fix into as-moses which I think will solve the build > >> problem you had. Try `git pull` on as-moses and with luck, the problem > >> will be gone. > >> > >> --linas > >> > >> On Mon, Jan 6, 2025 at 5:56 PM Linas Vepstas <[email protected]> > wrote: > >> > > >> > I can't reproduce this problem, so I will need your help. Try changing > >> > bind to std::bind and changing _2 to std::placeholders::_2 > >> > > >> > If that doesn't fix it, try try changing the two std's to boost, so, > >> > boost::bind and boost::placeholders > >> > > >> > Boost has been the source of ongoing breakage, and the decision to use > >> > it was a mistake. So it goes. > >> > > >> > --linas > >> > > >> > On Mon, Jan 6, 2025 at 3:49 PM Abu Naser <[email protected]> wrote: > >> > > > >> > > Hi Linas, > >> > > > >> > > I have another error while I was installing asmoses: > >> > > /asmoses/opencog/asmoses/reduct/reduct/flat_normal_form.cc:34:36: > error: call of overloaded ‘bind(std::negate<int>, const boost::arg<2>&)’ is > ambiguous > >> > > 34 | bind(std::negate<int>(), _2))) != c.end()); > >> > > > >> > > Please let me know if you have any solution for this issue. > >> > > > >> > > Kind regards, > >> > > Abu > >> > > > >> > > On Mon, 6 Jan 2025 at 20:06, Abu Naser <[email protected]> wrote: > >> > >> > >> > >> Thank you Linas. It works now. > >> > >> > >> > >> Kind regards, > >> > >> > >> > >> Abu > >> > >> > >> > >> On Mon, 6 Jan 2025 at 19:41, Linas Vepstas <[email protected]> > wrote: > >> > >>> > >> > >>> Hi Abu, > >> > >>> > >> > >>> class concurrent_set is provided by cogutils -- the solution > would be to got to > >> > >>> cd cogutils, git pull, rebuild and reinstall. Then the atomspace > >> > >>> should build. See here: > >> > >>> > >> > >>> > https://github.com/opencog/cogutil/blob/be54bfcadaf8439f324cf525781b254c87fa0722/opencog/util/concurrent_set.h#L162-L168 > >> > >>> > >> > >>> --linas > >> > >>> > >> > >>> On Sat, Jan 4, 2025 at 6:11 AM Abu Naser <[email protected]> > wrote: > >> > >>> > > >> > >>> > Hi Everyone, > >> > >>> > > >> > >>> > The following error is thrown while I was compiling atomspace > on Ubuntu: > >> > >>> > > >> > >>> > > opencog_repos/atomspace/opencog/persist/proxy/WriteBufferProxy.cc:85:14: > error: ‘class concurrent_set<opencog::Handle>’ has no member named ‘clear’ > >> > >>> > 85 | _atom_queue.clear(); > >> > >>> > > >> > >>> > > >> > >>> > Is there any solution for this error? > >> > >>> > > >> > >>> > > >> > >>> > Kind 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 [email protected]. > >> > >>> > To view this discussion visit > https://groups.google.com/d/msgid/opencog/CAMw3wdg6zMZgwF0hwk_ibqHuMyc9EC30qsJQPbRwmqEnexXLNg%40mail.gmail.com > . > >> > >>> > >> > >>> > >> > >>> > >> > >>> -- > >> > >>> Patrick: Are they laughing at us? > >> > >>> Sponge Bob: No, Patrick, they are laughing next to us. > >> > >>> > >> > >>> -- > >> > >>> 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/CAHrUA35N%2BhqA8CKtMBU4wJhmUQ8xKDivQHpx7%3DbdrZ9K_txg6Q%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/CAMw3wdjKdP7tfgxReFeXJ8z7sEt9x53pP0VMUzttL8xxE9%3Djag%40mail.gmail.com > . > >> > > >> > > >> > > >> > -- > >> > Patrick: Are they laughing at us? > >> > Sponge Bob: No, Patrick, they are laughing next to us. > >> > >> > >> > >> -- > >> Patrick: Are they laughing at us? > >> Sponge Bob: No, Patrick, they are laughing next to us. > >> > >> -- > >> 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/CAHrUA36fMLjzP%3D2%2Bzjr5BLf3qPdCOUfBv2-D7pttzCb1sjnodw%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/CAMw3wdgntkGmEFpZrs8wspfv8vFanEAT-6W-tbCQAt25-NQVyw%40mail.gmail.com > . > > > > -- > Patrick: Are they laughing at us? > Sponge Bob: No, Patrick, they are laughing next to us. > > -- > 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/CAHrUA36XK%3DtaeydW5WT4KtqCNa8eJ%2BzsFVWZJBTYv_3%2Bws3rDg%40mail.gmail.com > . > -- You received this message because you are subscribed to the Google Groups "opencog" group. 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