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tomohelix

2,119 karma · joined February 12, 2023

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tomohelix··on Large language models generate functional protein sequences across families
Perhaps fine-tuning is a better word? I am unsure what is the process that let an LLM switch from just a next word prediction tool to a chatbox. Instruction tuning?

The author basically chose some of the output based on set criteria. I think this can eventually be automated and embedded into the protein language model the same way ChatGPT now has guardrails and specific ways to answer questions, instead of following up with the most likely sentence, e.g.: asking it what is the capital of france get an output of another question about what is the capital of germany.

tomohelix··on 47% of all internet traffic came from bots in 2022?
Anecdotally, I have drastically reduced my internet activity in recent years. So many of the websites are just noise with crappy information. The good answers are often found on reddit in one or two clicks or directly asked on discord so there is no need to spend hours with google anymore (the crappy algo doesn't help). I also refrained from posting or discussing anything on social media after some bad experience with the users there. It takes effort to make good quality posts, but it rarely goes anywhere in those massive social media sites and often it may even get punished if it is against the public opinion.

So I am tired and only make a few posts every few days now on HN. I am sure while my activity has dropped, the bots are getting more active so nothing is lost. Maybe some quality and how the traffic share look like, but I don't know.

tomohelix··on Large language models generate functional protein sequences across families
I think English is also just the rehash of the same 2000-3000 words. The ability to meaningfully arrange those words in new ways and in longer sentences are what make the current LLMs so powerful. In that way, these protein models can still learn more from the new data but they will definitely need some sort of reinforcement learning and grounding. That is where wetlab scientists will have to do. Verifying the generated protein is functional and stable, i.e. "making sense", is where we will need more data.

Only a miniscule amount of protein has verified structure and function. While an HMM can predict their functions pretty well based on homology, it can often be wrong. Having that kind of noise in the training data can degrade the performance of these protein models. Perhaps we need better curated dataset before we can scale these up.

tomohelix··on Large language models generate functional protein sequences across families
I consider all the manual curation effectively a form of RLHF that can be imposed automatically later on. We saw how much this can improve a raw LLM by looking at the output of ChatGPT. Otherwise, the criticism of LLMs being just glorified autocomplete machines isn't that far from reality. In other words, it is just an expected requirement for LLMs to be effective.

You are probably right that lysozyme is an easy target and may have large sequence variety between homologs so saying "very different" for 30-40% is not correct. But that is only in the context of biology and protein structure and function. This is an LLM trained on primary sequences only. It doesn't know anything about the folds or domains or functional sites (unless I am wrong and those are part of the metadata fed to it during training). Yet it did learn enough to generalize to the point that even with only 30-40% identity, it still produces soluble proteins with the same function. I am sure you know that at 40% differences, one protein can be in an entirely different superfamily from another. So it is still an impressively low identity score.

Also, I think it is more appropriate to compare the amino acids to things like the alphabets than vocabs. Domains would probably be an equivalent to LLaMa vocab.

tomohelix··on Large language models generate functional protein sequences across families
>Published: 26 January 2023

Well, technically it is out in 2023 but sure, you can argue it was probably in the prepub state since 2022...

tomohelix··on Large language models generate functional protein sequences across families
Some notable technical information: It is a 1.2bln param model, trained on raw sequences only, can generate full length functional proteins of about 150-200 residues (approx lysozyme size). The generated proteins are very different to native ones (30-40% similarity).

The interesting thing about this model is that it also exhibit emergent capabilities. It was trained only on raw sequences but somehow managed to capture information about functionality and solubility of the folded proteins, and then implemented that in the generated sequences.

Amino acid sequences are just a bunch of jumbled words if you compared them to English. It usually has to go through folding to form proper "sentences" with meanings. I guess you can compare this to "grammar". This is probably the model managed to learn protein grammar purely by brute force. Now if only we can get a model in the range of 100bln parameters...

tomohelix··on Singh proposes corporate tax hike tied to CEO-worker pay gap
Here come the contractors...

Or, CEOs receive 50k/yr compensation, but the company will approve a certain discretionary spending amount every year to cover living expenses for the CEO. This may or may not include dining at the most expensive restaurants around, free travel to anywhere with any arbitrary amount of number of people, house purchases, luxury spending like a yacht... No, these are not regular compensation. We are simply subsidizing the living expenses. There is no concrete amount involved. No sir.

Or pick any other number of convoluted schemes to mask "compensation". Best way to do this is the easiest way, raise the corporate tax directly.

tomohelix··on How AI knows things no one told it
Let for the sake of argument, assume that the LLM is truly sapience. Then this would be the first alien intelligence we have ever encountered. All life and intelligence we have seen before were organic, carbon-based life, including the most distant and unintuitive ones like the cephalopods, cetaceans, and primates. Even now we are still arguing whether these creatures are intelligent or they are just "not there" yet. We refuse to acknowledge their higher reasoning capacity regardless of evidences like rudimentary communication, social structure, tool use, etc. And these are things sharing >70% similarity to us.

An LLM is so different and alien we would literally incapable of imagining their thought process even if they are pummeling us with evidences of their intelligence. It is just how it is. So I think it is futile and even foolish to try to quantify or create criteria for "intelligence" when discussing AI. Let it be and accept it for what it is: something we humans have created that can do lots of stuff.

tomohelix··on OpenAI Sued for Fraud Allegations
Here is a quick summary:

They are calling fraud because OAI was mixing nonprofit and capped profit to avoid taxes and the likes. They also made claims about unfair representations coming from ChatGPT and the executive composition of OAI, which apparently looks like insider trading and information manipulation. They alleged that OAI participated in election interference during 2020. They also said OAI was recklessly making advances in disruptive tech faster than legislators can make laws for them.

Basically, a prime example of a vulture coming in to sue anything that looks like it can give them some money. This is part of the reason why every company need a team of lawyers to deal with this perversion of justice.

tomohelix··on EU ready to back immediate open access without author fees
So now we are hiding behind semantics? If 942M is 37% operating profit then with a tax rate of 22% the net profit is still 29% for the publishing arm. Still way higher than 19%.

You are confusing the parent company with the publishing part for that 19%, which is the main subject here. You are uninformed.

tomohelix··on EU ready to back immediate open access without author fees
https://www.relx.com/~/media/Files/R/RELX-Group/documents/pr...

Look under the Scientific, Technical & Medical financial review. That is their scientific publishing arm.

tomohelix··on EU ready to back immediate open access without author fees
Disingenuous comparison. We are talking about Elsevier the journal publisher, not the parent conglomerate that also deal with legal, analytics, software and a bunch of other businesses.
tomohelix··on EU ready to back immediate open access without author fees
A quick google search quickly shows you are either uninformed or lying. Elsevier margin is at least 37% in 2018 and its profit has increased in 2022.

https://www.relx.com/~/media/Files/R/RELX-Group/documents/pr...

Most journal reviewers and editors are academics who do the work as public service, i.e. free. Even top spots like editor in chief only get an honorarium of maybe 10k a year. Considering these people are the top of their field and can easily command 6-7 figures salary at minimum, that amount is nothing. Only very few journals have full time editors and even those end up relying on the volunteers to vet and review articles.

A full time professor is expected to be an editor for some journals. And these academics make up the bulk of "journal editors". But they would not list it as their jobs. I suspect that is why if you look for "editor jobs" you will get lobsided salary ranges that doesn't reflect reality.

tomohelix··on EU ready to back immediate open access without author fees
To this day, I still do not understand what can be a reasonable cause for a paper to cost >$50 just to read it. Besides greed of course. Editors review paper for free, authors pay to get paper published, taxpayers fund the research. What do the journal's staff actually do that worth that kind of money?

All those "publisher" middlemen can go eat dirt and I would be happy to shovel more dirt on them until they are 6 feet under. They do no work, take all the profit, and obstruct research and the spread of knowledge. Those are some of the worst scums of capitalism.

tomohelix··on UFOs exist in the low information zone
The same reason why petting zoos exist. The thrill and experience of getting so close to something exotic.
tomohelix··on We aren't close to creating a rapidly self-improving AI
I agree that it is unknown when such an AI will come around. But hardware limitation problem is more nuance than just GPU power. The brain is analog and in a way, the current LLMs and neural networks are an approximation of an analog computer. There are current research into making an AI dedicated chip or even an analog computer specifically for neural networks. Digital was easy to work with but when it comes to fuzzy stuff like AI, there are better ways.

We used to think 100mph was the fastest speed we could achieve even with machine (back when trains were the cutting edge). New tech will change things quickly, all we need is one breakthrough and things will fall into place.

tomohelix··on We aren't close to creating a rapidly self-improving AI
Our minds are optimal with respect to size and energy supply and birthing process. An AI has no such limitations. All the wrinkles in our brain gave us enough intelligence to outsmart everything else on earth. That amount of surface area increase with that mutation is nigh negligible if you start scaling things to the size of a room. And an AI can be the size of a warehouse.

Also, faster is understated. You are talking about the speed difference between chemical gradients and the speed of light.

tomohelix··on Europe to ChatGPT: disclose your sources
The EU is trying to rein in a completely new and different tech using old ideas about "control" and "regulation". Most likely it won't work and will just end up hamstring itself.

This would be like if internet social media came out and the laws tried to control it using rules similar to physical books and newspapers. They won't be effective and will just create a hostile environment for development of these techs where these laws are in effect. Meanwhile, those who don't care about doing these control freak things will develop the tech and dominate the new sector.

The EU need to sit down and really think about how to control AI tech properly instead of passing kneejerk and lazy regulations. It isn't easy to make a legislation framework for something entirely new. But it can be done instead of ruining the whole thing.

tomohelix··on Intel is expected to post its biggest loss on record
A lot of thing, China's economy and the country itself, might be numbered if they decide to invade Taiwan.

This isn't like Ukraine where there was an implicit agreement that nobody will send actual troops into Ukraine to fight its war. If Taiwan is invaded, the US will send its own troops. And if the US is involved, the EU is likely involved too. China is big but not enough to challenge the US militarily. Not yet.

It would take an absolute madman to make China go to war just for Taiwan.

tomohelix··on Scaling Transformer to 1M tokens and beyond with RMT
>the output is conditional on the input

Uh, isn't that how it should always be? If the output isn't conditional on the input, then it is basically noise or worthless. How the conditionals are setup are the key but not really sure how does this relate to the point you are making.

tomohelix··on Squawk bots: Can generative AI lead us to understanding animals?
This is potentially huge. LLMs have shown how they can encompass patterns unknown to its creators and effectively use it. If for some reason, we can actually start seeing something resembling higher thought patterns in animals, that can up end society.

But still, we already had lots of evidence how some animals like cetacean and primate are potentially sentient. Many people just don't want to admit it and we can't convince them that human isn't anything special. In the end this may just be another piece of proof on a pile that get ignored.

tomohelix··on Scaling Transformer to 1M tokens and beyond with RMT
An AI can theoretically ingest 1M token of data, analyze, summarize, indexing, and storing the condensed information in a hard drive. Then later on retrieve it based on the metadata for specific situations that needs it. At millions of token, it is basically a superhuman that can learn new things on the fly at the speed unimaginable to any organic based life.

We are so close to something amazing, and scary.

tomohelix··on Xiaomi 13 Ultra: “Real camera” phone makes Samsung, Apple shake nervously
You are free to use your real name and connect your real life to social media. I don't and have no need to. You are also free to check every post history of everyone you interact with. I don't have that amount of time. And I am free to call out a bad argument when I see one. If you had practiced the checking post history properly, you would have noticed that account age and karma rarely correlate to anything.

You are also free to respond to the other comment I made to your post and not jumping to another one. These remarks are not specifically for you. Go take a look at the account I replied to above yours to see why I said that.

tomohelix··on Xiaomi 13 Ultra: “Real camera” phone makes Samsung, Apple shake nervously
True. Perhaps I should have been more generous in interpreting intentions. Difficult change my habit though when there are accounts whose posts are completely dedicated to defending China's actions, even in egregious matters like Hong Kong and Tibet.

I tried giving them benefits of the doubt before, it never went anywhere. Maybe here it is different. I guess I can try again.

tomohelix··on Xiaomi 13 Ultra: “Real camera” phone makes Samsung, Apple shake nervously
>It's tit for tat anyway, China has banned order of magnitude more US products.

The context in this specific part is about the retaliations between countries. It has expanded beyond just one company when you start talking about entire economies fighting each other.

Besides, I already gave you the US hardware that China banned.

tomohelix··on Xiaomi 13 Ultra: “Real camera” phone makes Samsung, Apple shake nervously
Well, first, Cisco router, then TPM chips, then most of foreign hardware in government offices. I won't even mention Raytheon and Lockheed stuff.

Also, you are making a bad faith argument. The topic was in "product". You specifically tried to gate it to "hardware". China is the producer of most hardware in the world. They aren't going to ban stuff that was made by them. Software product on the other hand, aren't really their forte until recently and that they banned plenty.

tomohelix··on DinoV2: Meta’s Open Source State-of-the-art computer vision models
Well, can't believe I am saying this but I am glad we still have facebook to open sourcing their models.

We have cover texts, images, videos. I wonder what is going on with audio. Once all of these get merged into one combined model, I honestly don't see any differences between a random person on the net and an AI. The only ways we can interact with each other through the internet are those 4 things.

tomohelix··on Why do ships use “port” and “starboard” instead of “left” and “right?”
I actually don't know. Like I mentioned above, there have been a few theories about how life is so strongly asymmetrical but nothing concrete or proven yet. In fact, it is a bit counterintuitive because all natural chemical reactions produces racemic mixtures and only life produces specific stereoisomers. It also means life has evolved to give up nearly half of the natural resources available, a very strange thing in terms of evolution.

Not all enzymes are stereospecific though. Some of them can take any configuration of a chemical and convert them to other type of isomer. But these are rare and usually an exception, not the norm. Still, it makes it harder to figure out why chirality is so important in life and not so much in some other parts of life.

Maybe your explanation about handedness makes sense. But then it would fail at explaining ambidextrous people since they are definitely better and yet still so rare. Life is really difficult to figure out.

tomohelix··on Why do ships use “port” and “starboard” instead of “left” and “right?”
Haha no, I think you misunderstood. I meant the underlying reason for human to have a preferred "side" is probably the same reason that life has a preferred "side" for chemicals. Both humans and enzymes can be chiral, i.e. asymmetrical so I think they might be connected.

Don't worry, I am not an atom-ist or a chiral-ist. All sides are equal! (except the ambidextrous master race :D )

tomohelix··on Why do ships use “port” and “starboard” instead of “left” and “right?”
Probably the same reason why most biomolecules are chiral, i.e. having left and right side.

Last time I read about this, I think some physicist said something about the rotation of elementary particles and radiation stuff that are way over my head.

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