ranzispa
@ranzispa@mander.xyz
- Comment on 1 day ago:
It Is true! Now you just have to convince them to have dinner together and spend the night together.
- Comment on Protein folding is not solved yet 6 days ago:
Hello, thank you for the lead. I tried replying the other day but I had just woken up drunk in the campment of a homeless guy and I was not in the best conditions to go through the math.
I took a look at this worked example: dojo.qulacs.org/…/7.1_quantum_phase_estimation_de…
As far as I understand they use the iterative approach because it requires less qbits and are able to decompose the eigenvalues of a Hamiltonian in more or less a single step.
If it is as I understand it this would be quite huge, since you’d be able to directly apply this to the Hartree-Fock equation or Density Functional Theory without having to come up with new ways to represent molecules.
One thing which appears quite critical is:
Prepare an initial state with sufficient overlap with the ground state
What does sufficient overlap mean? Could we take an AlphaFold model and that’s sufficient to then determine the ground state?
I guess this is easy with helium when you have 2 atoms, but when you have hundred of thousands it becomes a difficult task even to get to that point.
Moreover, I’m not exactly sure what they’re calculating: they plot an error; but it appears to be an error over the computed energy and not atom positions.
We already have reliable ways, and moderately fast, to compute the energy of a system. What we’re missing is a quick way to explore different spatial conformations of atoms to identify the one which leads to the lowest energy.
Another problem which I could not determine is whether the amount of required qbits scales with the dimensions of the molecular system. I suppose it does. In that case, could we estimate how many qbits would be required for a protein or at least a peptide?
- Comment on Protein folding is not solved yet 6 days ago:
As far as I understand it a billion qbit computer is not possible because the time to setup the system would be too long to retain coherence.
But maybe new techniques will be developed, who knows.
- Comment on Protein folding is not solved yet 1 week ago:
I did not yet see a single quantum algorithm able to tackle the protein folding problem.
Sure, quantum computers could be faster at solving graph related problems, but I did not see an approach able to reduce protein folding to a graph problem.
On the other hand neural networks have been successfully applied to the protein folding problem, and they do that quite quickly.
Not a perfect solution indeed, quantum computers may be much better at that; but I still do not see a theoretical framework which justifies claims as to the applicability of quantum computers to the protein folding problem.
- Comment on Protein folding is not solved yet 1 week ago:
Agreed, I still do hope they can maintain some of their promises. However until now, I have not really seen any real advances towards making something useful.
I do not have a deep knowledge of quantum computers, but I know plenty people working on them and often get to talk about it.
I know people working on chemical problems who are basically approximating atoms to point charges. And either way those calculations are slower than on a CPU. For the uninformed, in chemistry the interactions between electronic orbitals is fundamental; this is in no way an approximation useful to obtain any kind of information.
This is fine, I understand methodologies take time to develop; however as far as I understand it those techniques they’re using are mathematically limited to using point charges: no matter how much they improve them that’ll be the highest level of accuracy.
I hope someone finds a way to handle such things better: as much as you can make a great machine learning model you’re always depending on available data.
- Comment on Protein folding is not solved yet 1 week ago:
Yes, X-ray is the gold standard. Technology has advanced in the sense that the protein crystallization is now more standardized and automated, as well as the analysis of the results.
It is not the only technique, for example there are cheaper ones based on mass spectrometry which do not resolve the full structure but allow to understand which amino acids are spatially near; such information is useful when developing a protein model and to validate whether a model is plausible.
The other two major techniques for structure resolution are NMR spectra analysis and the fairly novel technique of cryo electro microscopy.
These in general do not resolve the protein structure to the same resolution as X-ray but have other advantages: they allow you to observe the protein structure when in solution, which may be significantly different from the crystallized structure.
- Comment on Protein folding is not solved yet 1 week ago:
I doubt there is a comparable correctness metric between LLMs and protein structure prediction models.
You can measure how many times they correctly predict a thing, but results will greatly change according to what your objective is. Those are only comparable when you’re trying to predict the same thing.
As such my reply would be: sometimes more incorrect sometimes more correct. However, in general, a mishandled incorrect protein structure prediction is way more expensive than an LLM hallucination.
- Comment on Protein folding is not solved yet 1 week ago:
The interesting part would be to a reliable and computationally accessible way to handle disordered proteins. Seeing how they can move could be quite revolutionary.
I had to work on some disordered proteins and you’re pretty much just guessing, plausibly you’re better off going to a casino blindfolded and play blackjack.
- Comment on Protein folding is not solved yet 1 week ago:
AlphaFold is incorrect in plenty occasions.
- Comment on Protein folding is not solved yet 1 week ago:
Not solved, no. Definitely much much better than before. The difference AlphaFold made is significant: we’re talking about getting a decent model in a couple minutes using a PC compared to several months of calculations before.
However we still need experimental data: in many occasions AlphaFold gives an incorrect model. With some experimental data that model can be improved, but we still have no reliable way to know what the structure of a protein is starting from the amino acidic sequence without extensive experimentation.
That’s the big promise of quantum computers, there are however two major problems in my opinion:
- There’s still no theoretical framework which explains how once we have a quantum computer we may tackle protein folding
- Plenty quantum computing companies closed shortly after AlphaFold was published since they lost all funding because protein folding was “solved”
- Submitted 1 week ago to science_memes@mander.xyz | 38 comments
- Comment on Ecosystem services 1 week ago:
~100x it’s a logarithmic scale
- Comment on Its all about bonding 3 weeks ago:
Just prepare the sauce before you cook the pasta, that way you’re sure.
It’s better to cook the pasta together with the sauce for a minute or two.
- Comment on Its all about bonding 3 weeks ago:
Just add an appropriate amount of water to you pot.
- Comment on Its all about bonding 3 weeks ago:
Use plenty water. If they stick together with the advised amount, use more water. Doing that won’t change the taste.
Regarding the boiling of water, it is not required. I believe pasta needs about 80°C to cook. If you have enough water and cover the pot with a lid you can turn off the fire and it will cook.
- Comment on Its all about bonding 3 weeks ago:
You have at most 15 seconds to thoroughly mix your pasta with the sauce.
Nobody in their right mind would ever let pasta sit without sauce.
Once I had to watch while some people strained the pasta, let it there and then started chatting about something else. They were wondering about why I was going crazy and then they complained the pasta stuck together…
Please, don’t let your pasta sit unattended. Also, Barilla is not a particularly good brand of pasta.
- Comment on Calibration Nobel 4 weeks ago:
So much unpublished work. They should have published it and retracted it the following day, just to prove they did the work.
- Comment on Roses 5 weeks ago:
Greater than the cumulative speed achieved by 20,000 horses fed with 3 canisters of barley.
- Comment on Walls within walls 5 weeks ago:
I have seen that, but did not understand how to sign up.
- Comment on Walls within walls 1 month ago:
Yes, much better than the alternative system. Look, I found a cool article about a topic. Let’s open it on the publisher website. Oh I need access for this, let’s login. After login I still have no access and get redirected to institutional login. Get back to publisher, now I have institutional credentials, but need to login again. Finally done!
Your institution does not have access to this paper.
- Comment on Whoops! 1 month ago:
I don’t want to be guy who needs to read the NMR spectra of this stuff.
- Comment on Walls within walls 1 month ago:
This is talking about scientific papers. Stripping JavaScript does not work, you need authenticated and paid access to read those.
- Comment on Walls within walls 1 month ago:
I know people who get 12,000€ for a year long research project which includes employing other part time people. I doubt they can pay for open access.
However, the submitted version is yours to do whatever you want; please host it on your website or wherever it may be simple for you.
- Comment on Walls within walls 1 month ago:
Happens often to me. I know nobody in research who would care about it. Most people will likely congratulate you for not paying for access. Nobody likes the way journals do business.
Fuck you Elsevier.
- Comment on Walls within walls 1 month ago:
Papers in Anna’s archive are mostly from sci-hub. There’s something not available on sci-hub, but not much.
Real problem is that sci-hub was the organization doing the archival on large scale and it is now dead.
- Comment on Walls within walls 1 month ago:
I like to keep the submitted version after review but without editing on my public repositories. Even when I publish open access.
- Comment on Walls within walls 1 month ago:
I’d rather use sci-hub than institutional access when the article is available. Fuck publishers.
Really hope someone comes up, recognizes how much public research money is wasted on this bullshit and sets up a public publisher directly funded by research funds which allows people to publish and read freely.
- Comment on Seafood!!! 1 month ago:
Did they have dedicated cat food before WWII? until recently I was convinced people were just giving their dogs and cats their scraps. With cats possibly not even giving them the scraps and just letting them go hunt.
- Comment on There is a heat wave going hard, please stay hydrated 1 month ago:
Sorry, this is not about you; just a reflection. I’ve been in the US a couple times and I got my positive and negative impressions. The more I learn about life in the US, the less it feels like a desirable country to live in. Not talking about the current political situation, just how life works and quality of life.
- Comment on There is a heat wave going hard, please stay hydrated 1 month ago:
Sorry you live in a place where tap water is not good. Wherever I lived, except china and India, tap water was always better than bottled water.
