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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

#21

Post by maxerickson »

dopylitty wrote: post #13

Given that we still don’t know the mechanism by which variants achieve their increased fitness I’m a little suspicious of claims of using “AI” to identify new variants. Claims that spike affinity for ACE2 (or indeed changes to the spike protein at all) haven’t been conclusively proven to increase fitness as far as I know. It’s possible that this tool is simply overfit to the known variants and wouldn’t detect a new o…

Is the concern that this tool would be prioritized over other information?

Like what is the harm in doing the data collection and publishing about how it is going?

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

#22

Post by twofornone »

>More than 10,000 novel variant sequences are currently discovered every week and human experts simply cannot cope with complex data at this scale

I suspected something like this, given the frequency of viral mutation. Officials announce a dominant global strain but what proportion of positive cases are actually sequenced and evaluated for confirmation? How many undiscovered strains are actually in circulation at any given time, in geographically isolated areas? Could that explain variability in severity and/or long covid?

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

#23

Post by orintorynchus »

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…

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, participated in analysis and got his hands dirty as everyone else. While he is a CEO of a 160+ person company, this has been a labor of love for all of us, done to a large extent in the evenings, during weekends and holidays. It is indeed an unusual situation. But this was not a regular project and InstaDeep is not a regular company either.

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

#24

Post by orintorynchus »

gpm wrote: post #14
mlindner wrote: post #10

Earlier quoted context omitted.

> 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 paper. Perhaps I'm unfairly judging and the CEO really was the lead contributor to the study. Authors on scientific papers are ordered by name, so whoever's name is first is pure coincidence.

The order of authors varies by field. I believe in biology it usually starts with the person who did most of the work (or people, but if more than one it's explicitly noted), everyone who contributed in the middle, principal investigator (i.e. head of lab) last. In this case I notice that they first sorted all the instadeep people to the front, and biontech people to the end... not sure what I'm supposed to take away…

It is not random. InstaDeep has designed, developed, built, benchmarked the method. BioNTech performed experimental validation, provided expert insight into the problem domain. Hence, authors are segmented by contribution areas.

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

#25

Post by whycombagator »

orintorynchus wrote: post #23
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…

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…

Thank you for chiming in. It’s great that you detected them. I’m curious how many false positives you had during that same time? Did you detect many others that just didn’t pan out to be of significance?

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

#26

Post by adsodemelk »

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.

Another author of the paper here. We are recruiting in case you would like to contribute in further meaningful projects. https://www.instadeep.com/about-us/careers/

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

#27

Post by zxexz »

orintorynchus wrote: post #23
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…

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…

Wow, amazing to see you here. I have somewhat of a bioinformatics background, and this is the sort of work that I always found very interesting - do you think your team will produce some sort of high level architectural and process breakdown at some point?

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

#28

Post by hirenj »

orintorynchus wrote: post #23
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…

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…

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 it good enough to get production of vaccines going on variants that are flagged, just in case?

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

#29

Post by kerneloftruth »

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).

"I'm all for stopping new variants of COVID"

That's very likely not even possible[1]; and, it not being realistic, would be a waste of time, effort, and money. There are lots of corona viruses that we have never stopped, and we live with via herd immunity, hygiene, and therapeutics[2].

[1] https://www.acsh.org/news/2020/11/05/covid-why-we-will-never...

[2] https://www.cdc.gov/coronavirus/general-information.html

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

#30

Post by im3w1l »

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…

Well to be classified as a variant it would have to be phenotypically different right? And also viable enough to infect a number of people.
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