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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

#151
post #17

this is such an interesting problem. Imagine expanding the input size to 3.2Gbp, the size of human genome. I wonder if previously unimaginable interactions would occur. Also interesting how everything revolves around U-nets and transformers these days.

Even just modeling 3D genome organization or ultra-long-range enhancers more realistically could open up new insights

Re: AlphaGenome: AI for better understanding the genome

#152
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…

It's easy to forget how early some of these ideas were being pushed internally

Re: AlphaGenome: AI for better understanding the genome

#154
post #122

I wish there's some breakthrough in cell simulation that would allow us to create simulations that are similarly useful to molecular dynamics but feasible on modern supercomputers. Not being able to see what's happening inside cells seems like the main blocker to biological research.

You may enjoy this, from a top-down experimental perspective ( https://www.nikonsmallworld.com/galleries/small-world-in-mot... ). Only a few entries so far show intracellular dynamics (like this one: https://www.nikonsmallworld.com/galleries/2024-small-world-i... ), but I always enjoy the wide variety of dynamics some groups have been able to capture, like nervous system development ( https://www.nikonsmallworld.com/…

Very interesting, thanks.

Re: AlphaGenome: AI for better understanding the genome

#156
post #81
post #32

Earlier quoted context omitted.

Since we're on the topic of Microsoft, I'm sure you'd agree that Satya has done a phenomenal job. If you look objectively, what is Satya's accomplishments? One word - Azure. Azure is #2, behind AWS because Satya's effective and strategic decisions. But that's it. The "vibes" for Microsoft has changed, but MS hasnt innovated at all. Satya looked like a genius last year with OpenAI partnership, but it is becoming incre…

People now days don't understand how genius MS was in the 90s. Their strategy and execution was insanely good, and I doubt we'll ever see anything so comprehensive ever again. 1. Clear mission statement: A PC in very house. 2. A nationwide training + certification program for software engineers and system admins across all of Microsoft's tooling 3. Programming lessons in schools and community centers across the count…

There was some innovation - and some good products ( MS office stands out for me ) - however what MS did relentlessly well, as you mentioned, was sales, distribution and developers.

They also leveraged their relationship with Intel to the max - Wintel was a phrase for a reason. Companies like Apple faltered, in part, in the 90's because of hardware disadvantages.

Often their competitors had superior products - but MS still won through - in part helped by their ruthlessly leveraging of synergies across their platforms. ( though as new platforms emerged the desire to maximise synergies across platforms eventually held them back).

That aggressive, Windows everywhere behaviour, is what united it's competitors around things like Java, then Linux and open source in general which stopped MS's march into the data centre, and got regulators involved when they tried to strangle the web.

Re: AlphaGenome: AI for better understanding the genome

#157
post #52

Earlier quoted context omitted.

Microsoft has become a lot more friendly to open source under Satya. VSCode, GitHub, and WSL happened during his tenure, and probably wouldn't have happened under Ballmer. Turning the ship from a focus on protecting platform lock-in to meeting developers where they are is a huge accomplishment IMO.

> Microsoft has become a lot more friendly to open source under Satya. True, but that's just few open source projects, albeit influential ones. There are soo many other companies doing influential open source projects. I dont disagree with anything you said because turning a ship around is hard. But hand-to-heart, what big tech company is truly innovating to the future. Lets look at each company. Apple - bets are on…

Apple - have you used a Macbook recently - their ARM based product line is a big step forward - sure it's not self driving cars - but it's been the biggest jump in standard PC's for quite a while and has required innovation up and down the stack.

Microsoft - No new bets. Really? Their OpenAI deal and integrating that tech into core products?

Amazon - No new bets? It's still trying drone delivery, and it's also got project Kuiper - moving beyond data centres to providing the network

Re: AlphaGenome: AI for better understanding the genome

#158

I wish there's some breakthrough in cell simulation that would allow us to create simulations that are similarly useful to molecular dynamics but feasible on modern supercomputers. Not being able to see what's happening inside cells seems like the main blocker to biological research.

Simulating the real world at increasingly accurate scales is not that useful, because in biology - more than any other field - our assumptions are incorrect/flawed most of the time. The most useful thing simulations allow us to do is directly test those assumptions and in these cases, the simpler the model the better. Jeremy Gunawardena wrote a great piece on this: https://bmcbiol.biomedcentral.com/articles/10.1186/1741-7007...

Re: AlphaGenome: AI for better understanding the genome

#159
post #125

I wish there's some breakthrough in cell simulation that would allow us to create simulations that are similarly useful to molecular dynamics but feasible on modern supercomputers. Not being able to see what's happening inside cells seems like the main blocker to biological research.

Why simulate? We can already do it experimentally

You can't see what's going on in most cases.

Re: AlphaGenome: AI for better understanding the genome

#160

I wish there's some breakthrough in cell simulation that would allow us to create simulations that are similarly useful to molecular dynamics but feasible on modern supercomputers. Not being able to see what's happening inside cells seems like the main blocker to biological research.

It's a main aim at DeepMind. I hope they succeed as it could be very useful.
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