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BioNTech-InstaDeep Early Warning System to Detect High-Risk SARS-CoV-2 Variants

investors.biontech.de

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Re: BioNTech-InstaDeep Early Warning System to Detect High-Risk SARS-CoV-2 Variants

#41

Post by hirenj »

orintorynchus wrote: post #37
hirenj wrote: post #28

Earlier quoted context omitted.

Dear Marcin - congratulations on the manuscript! Do you think the immune escape parameters would need to be retuned in a post Omicron world? Do you need the actual epitopes recognised by antibodies, or can you guess this from structure. Do you capture any aspects with respect to changes in spike glycosylation in your models? Finally, as with another reply, do you have a guess about the specificity of this system? Is…

The system is constantly learning, so it "retunes" itself. We can infer epitopes from structure, but we found that data derived from known complexes is sufficient for our purpose. Current version of EWS does not explicitly account for glycosylation. It is implicitly handled by the ML models, though. For specificity, it is difficult to estimate. We know that for each of the named Variants of Concern, the signal from E…

Thanks for the info! That ability to retune sounds excellent. I wonder if you could spin this out to have an EWS for influenzas too (although hopefully it’ll never get as severe!)

I guess for the glycosylation when you say it’s implicitly handled, there’s a N-linked sequon pattern somewhere in the language model, which I guess covers a good deal of info :)

Jury still out on effects of O-linked glyco on spike, but give me a shout if you’re interested in it!

Anyway, cool work, and all the best in where you’re taking the work next!

Re: BioNTech-InstaDeep Early Warning System to Detect High-Risk SARS-CoV-2 Variants

#42

Post by newsclues »

fasteddie31003 wrote: post #5

I'm all for stopping new variants of COVID. Why in the world do we have a treatment for COVID that intentionally creates mutations in COVID https://en.wikipedia.org/wiki/Molnupiravir ? I'm not a doctor but it seems pretty clear to me that Molnupiravir creates a great environment for new variants to arise (along with cancer, but that's another issue).

Because it’s possible to justify the risk with saving lives.

Because creating mutations and prolonged pandemics are more profitable.

Re: BioNTech-InstaDeep Early Warning System to Detect High-Risk SARS-CoV-2 Variants

#43

Post by orintorynchus »

axg11 wrote: post #31
orintorynchus wrote: post #23

Earlier quoted context omitted.

I am the second author of the paper. We have been putting our head on the line for the last half a year. We detected Lambda, Mu (with a caveat, that we did not consider it competitive) and Omicron - all blindly. We have been verifying all our predictions experimentally, post factum. And the method is purely data driven - with no fitting to the experiments or observations. The first author came up with the approach, p…

Thanks for adding this information. I was unfair to judge so harshly and be so sceptical. So the $1T question is ... what (if anything) is this model currently predicting about the next variant?

The method, in its current incarnation, is detecting dangerous variants and not foreseeing them. We can use the same approach to forecast plausible developments, but there are so many latent variables (intrapatient evolution, mobility, vaccination status, restriction compliance), that it is more of an informed "What If?" exercise, than a true prediction. Same as with many good stories on predicting the future, we can only see what is likely to happen, not what will necessarily happen... Out of many paths only a few will be explored in the end :-)

Re: BioNTech-InstaDeep Early Warning System to Detect High-Risk SARS-CoV-2 Variants

#44

Post by orintorynchus »

solididiot wrote: post #6

Regardless of the specifics here, I'm pleased and envious of being reminded that some people have meaningful jobs that actually make a difference.

We are actively looking for motivated colleagues. Feel free to look at the page above or drop us an email at hello[at]instadeep.com. We are also happy to make new friends and work together on exciting projects - same email as above works.

Re: BioNTech-InstaDeep Early Warning System to Detect High-Risk SARS-CoV-2 Variants

#45

Post by orintorynchus »

liuliu wrote: post #36

Is the idea to develop mRNA vaccines that can boost immunity against variants that haven't existed today?

The idea is to introduce a bit of sanity into the current world, to calm down overreactions to every new, scary looking variant. And on the flip side - to identify the truly scary ones early on, so that proper measures can be taken.

But the idea above directly follows from the work in the paper.

Re: BioNTech-InstaDeep Early Warning System to Detect High-Risk SARS-CoV-2 Variants

#47

Post by jdavis703 »

spuz wrote: post #18

> More than 10,000 novel variant sequences are currently discovered every week and human experts simply cannot cope with complex data at this scale This is interesting. I think the Greek alphabet naming system would lead some people to believe the virus only mutates once every few months. Of course, the reality is that every infected individual will produce hundreds of mutations within their body. I think there's a g…

This is the kind of education that needs to be done in high school during health and biology classes. We can’t hope the general public will become epidemiologically literate on 240 character tweets and 30-second television quotes. Heck, my old high school biology teacher remains a source of coronavirus FUD, so maybe that’s not even enough.

Re: BioNTech-InstaDeep Early Warning System to Detect High-Risk SARS-CoV-2 Variants

#48

Post by jdavis703 »

axg11 wrote: post #3

Impressive if true, although I am very sceptical of the results. The real test is to put their neck on the line and predict/warn of the next significant variant. If the authors are not willing to do this, I doubt that the algorithm is useful. As a side note, the first author on this paper is the CEO of InstaDeep. I see it as a red flag that the CEO of a 150+ person company would put themselves as first author on this…

Because of both founder effects and potentially people taking earlier containment actions, I’m unsure that’s a realistic measure.

It’s like how people said Y2K was just a conspiracy theory because most systems kept running — without realizing the early warnings and preparations is the reason Y2K wasn’t a civilizational disruption.

Re: BioNTech-InstaDeep Early Warning System to Detect High-Risk SARS-CoV-2 Variants

#49

Post by jdavis703 »

newsclues wrote: post #42
fasteddie31003 wrote: post #5

I'm all for stopping new variants of COVID. Why in the world do we have a treatment for COVID that intentionally creates mutations in COVID https://en.wikipedia.org/wiki/Molnupiravir ? I'm not a doctor but it seems pretty clear to me that Molnupiravir creates a great environment for new variants to arise (along with cancer, but that's another issue).

Because it’s possible to justify the risk with saving lives. Because creating mutations and prolonged pandemics are more profitable.

The government looses money from pandemics, so there’s no profit motive for FDA regulators to prolong the pandemic. There’s both direct costs of coronavirus response, and then there’s indirect costs (lower tax revenue from empty downtowns, less travel, more workers on taking from disability insurance instead of paying in to it, etc).

Re: BioNTech-InstaDeep Early Warning System to Detect High-Risk SARS-CoV-2 Variants

#50

Post by dfsegoat »

jdavis703 wrote: post #47
spuz wrote: post #18

> More than 10,000 novel variant sequences are currently discovered every week and human experts simply cannot cope with complex data at this scale This is interesting. I think the Greek alphabet naming system would lead some people to believe the virus only mutates once every few months. Of course, the reality is that every infected individual will produce hundreds of mutations within their body. I think there's a g…

This is the kind of education that needs to be done in high school during health and biology classes. We can’t hope the general public will become epidemiologically literate on 240 character tweets and 30-second television quotes. Heck, my old high school biology teacher remains a source of coronavirus FUD, so maybe that’s not even enough.

I think most high school (USA) biology courses probably touch on the concept of viruses? This level of detail was certainly taught in high school Advanced Placement (AP) Biology when I took it many years ago.
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