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AlphaGenome: AI for better understanding the genome

deepmind.google

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Re: AlphaGenome: AI for better understanding the genome

#11

Post by nextos »

ejstronge wrote: post #8
nextos wrote: post #7

Earlier quoted context omitted.

Yes, but it's not dramatically different from what is out there already. There is a concerning gap between prediction and causality. In problems, like this one, where lots of variables are highly correlated, prediction methods that only have an implicit notion of causality don't perform well. Right now, SOTA seems to use huge population data to infer causality within each linkage block of interest in the genome. Thes…

> SOTA seems to use huge population data to infer causality within each linkage block of interest in the genome. This has existed for at least a decade, maybe two. > There is a concerning gap between prediction and causality. Which can be bridged with protein prediction (alphafold) and non-coding regulatory predictions (alphagenome) amongst all the other tools that exist. What is it that does not exist that you "foun…

> This has existed for at least a decade, maybe two.

Methods have evolved a lot in a decade.

Note how AlphaGenome prediction at 1 bp resolution for CAGE is poor. Just Pearson r = 0.49. CAGE is very often used to pinpoint causal regulatory variants.

Re: AlphaGenome: AI for better understanding the genome

#12

Post by CGMthrowaway »

bitpush wrote: post #9
dekhn wrote: post #2

When I went to work at Google in 2008 I immediately advocated for spending significant resources on the biological sciences (this was well before DM started working on biology). I reasoned that Google had the data mangling and ML capabilities required to demonstrate world-leading results (and hopefully guide the way so other biologists could reproduce their techniques). We made some progress- we used exacycle to demo…

[flagged]

Yeah it comes off as braggy, but it’s only natural to be proud of your foresight

Re: AlphaGenome: AI for better understanding the genome

#14

Post by shadowgovt »

bitpush wrote: post #9
dekhn wrote: post #2

When I went to work at Google in 2008 I immediately advocated for spending significant resources on the biological sciences (this was well before DM started working on biology). I reasoned that Google had the data mangling and ML capabilities required to demonstrate world-leading results (and hopefully guide the way so other biologists could reproduce their techniques). We made some progress- we used exacycle to demo…

[flagged]

FWIW, I interpreted more as "This is something I wanted to see happen, and I'm glad to see it happening even if I'm not involved in it."

Re: AlphaGenome: AI for better understanding the genome

#15

Post by dvaun »

bitpush wrote: post #9
dekhn wrote: post #2

When I went to work at Google in 2008 I immediately advocated for spending significant resources on the biological sciences (this was well before DM started working on biology). I reasoned that Google had the data mangling and ML capabilities required to demonstrate world-leading results (and hopefully guide the way so other biologists could reproduce their techniques). We made some progress- we used exacycle to demo…

[flagged]

A charitable view is that they intended "ideas that I had germinating for decades" to be from their own perspective, and not necessarily spurred inside Google by their initiative. I think that what they stated prior to this conflated the two, so it may come across as bragging. I don't think they were trying to brag.

Re: AlphaGenome: AI for better understanding the genome

#16

Post by plemer »

shadowgovt wrote: post #14
bitpush wrote: post #9

Earlier quoted context omitted.

[flagged]

FWIW, I interpreted more as "This is something I wanted to see happen, and I'm glad to see it happening even if I'm not involved in it."

Could be either. Nevertheless, while tone is tricky in text, the writer is responsible for relieving ambiguity.

Re: AlphaGenome: AI for better understanding the genome

#18

Post by dekhn »

shadowgovt wrote: post #14
bitpush wrote: post #9

Earlier quoted context omitted.

[flagged]

FWIW, I interpreted more as "This is something I wanted to see happen, and I'm glad to see it happening even if I'm not involved in it."

That's correct. I can't even really take credit for any of the really nice work, as much as I wish I could!

Re: AlphaGenome: AI for better understanding the genome

#19

Post by deepdarkforest »

dekhn wrote: post #2

When I went to work at Google in 2008 I immediately advocated for spending significant resources on the biological sciences (this was well before DM started working on biology). I reasoned that Google had the data mangling and ML capabilities required to demonstrate world-leading results (and hopefully guide the way so other biologists could reproduce their techniques). We made some progress- we used exacycle to demo…

> Sundar is a really uninspiring leader

I understand, but he made google a cash machine. Last quarter BEFORE he was CEO in 2015, google made a quarterly profit of around 3B. Q1 2025 was 35B. a 10x profit growth at this scale well, its unprecedented, the numbers are inspiring themselves, that's his job. He made mistakes sure, but he stuck to google's big gun, ads, and it paid off. The transition to AI started late but gemini is super competitive overall. Deepmind has been doing great as well.

Sundar is not a hypeman like Sam or Cook, but he delivers. He is very underrated imo.

Re: AlphaGenome: AI for better understanding the genome

#20

Post by alfanick »

bitpush wrote: post #9
dekhn wrote: post #2

When I went to work at Google in 2008 I immediately advocated for spending significant resources on the biological sciences (this was well before DM started working on biology). I reasoned that Google had the data mangling and ML capabilities required to demonstrate world-leading results (and hopefully guide the way so other biologists could reproduce their techniques). We made some progress- we used exacycle to demo…

[flagged]

I don't find it rude or pretentious. Sometimes it's really hard to express yourself in hmm acceptable neutral way when you worked on truly cool stuff. It may look like bragging, but that's probably not the intention. I often face this myself, especially when talking to non-tech people - how the heck do I explain what I work on without giving a primer on computer science!? Often "whenever you visit any website, it eventually uses my code" is good enough answer (worked on aws ec2 hypervisor, and well, whenever you visit any website, some dependency of it eventually hits aws ec2)
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