Alpha Fold has continued to impact the field of protein networks, but I do hear that not every one of the deep learning biology models from Google/Deep Mind and others have made equivalent impact or had as lasting relevance in their respective domains..some have performed more poorly than other available models. I'd love to learn more about this, but this has mostly come from little snips of conversations here and there, in person and online, but I haven't seen anything comprehensive in terms of evaluating their impacts overall
AlphaGenome Atlas: a high-resolution map of human DNA
101–110 of 133 posts
Re: AlphaGenome Atlas: a high-resolution map of human DNA
#102People are upvoting this because it has the “Alpha______” prefix. Meanwhile, everyone in the field of genomics knows that AlphaGenome provides essentially zero improvements over the previous SOTA, Borzoi…
Is it so bad to have another entrant, especially with the resources Google could bring to bear?
Imagine if the Apple EV had actually happened, you think the EV enthusiasts would roll their eyes like you are?
Re: AlphaGenome Atlas: a high-resolution map of human DNA
#103Earlier quoted context omitted.
Why would you be grateful? I don't think any of that should be under private control to begin with.
And which public enterprise has undertaken those projects? Looking at current hot problems, and exemplary of the situation: which public entities have endeavoured to backup the most important channels and videos from YouTube, the current historic video archive? Why would I be grateful?! Because somebody did create those resources and made them available! And they did to common good (if anybody refused the expression…
They said should be under public control, not is under public control.
Re: AlphaGenome Atlas: a high-resolution map of human DNA
#104People are upvoting this because it has the “Alpha______” prefix. Meanwhile, everyone in the field of genomics knows that AlphaGenome provides essentially zero improvements over the previous SOTA, Borzoi…
> Meanwhile, everyone in the field of genomics knows that AlphaGenome provides essentially zero improvements over the previous SOTA, Borzoi… Can you elaborate on this? I'm confused why Google would build something that provides zero improvements over SOTA, Borzoi... as you mention. I'm not familiar with this field, just curious.
Speaking as somebody who has worked within Google Research before: the researchers are under tremendous pressure to publish SOTA and sometimes they juice their results a bit to look competitive when they can't match. This is not uncommon in the field- it's remarkably easy to edit a paper to make yourself look good by omitting information.
Re: AlphaGenome Atlas: a high-resolution map of human DNA
#105Earlier quoted context omitted.
> Meanwhile, everyone in the field of genomics knows that AlphaGenome provides essentially zero improvements over the previous SOTA, Borzoi… Can you elaborate on this? I'm confused why Google would build something that provides zero improvements over SOTA, Borzoi... as you mention. I'm not familiar with this field, just curious.
Speaking as somebody who has worked within Google Research before: the researchers are under tremendous pressure to publish SOTA and sometimes they juice their results a bit to look competitive when they can't match. This is not uncommon in the field- it's remarkably easy to edit a paper to make yourself look good by omitting information.
One of the most egregious cases of this, in my opinion, is only publishing metrics that cover part of the confusion matrix. “The false-negative rate? That could not possibly matter for a variant effect prediction model; why would we include that in the paper?” Example: AlphaMissense.
Re: AlphaGenome Atlas: a high-resolution map of human DNA
#106Don't be put off by the box asking for your "affiliation". I wrote "None", clicked submit and it took me straight to the Atlas.
Re: AlphaGenome Atlas: a high-resolution map of human DNA
#107People are upvoting this because it has the “Alpha______” prefix. Meanwhile, everyone in the field of genomics knows that AlphaGenome provides essentially zero improvements over the previous SOTA, Borzoi…
> Meanwhile, everyone in the field of genomics knows that AlphaGenome provides essentially zero improvements over the previous SOTA, Borzoi… Can you elaborate on this? I'm confused why Google would build something that provides zero improvements over SOTA, Borzoi... as you mention. I'm not familiar with this field, just curious.
The use of an exact quote in an ungrammatical fashion is a bit of a language model smell. I can’t help but be reminded of the purely nonsensical AI interview answers. “It’s a pleasure to meet you, Chick Bongo”
Re: AlphaGenome Atlas: a high-resolution map of human DNA
#108Earlier quoted context omitted.
> Meanwhile, everyone in the field of genomics knows that AlphaGenome provides essentially zero improvements over the previous SOTA, Borzoi… Can you elaborate on this? I'm confused why Google would build something that provides zero improvements over SOTA, Borzoi... as you mention. I'm not familiar with this field, just curious.
The use of an exact quote in an ungrammatical fashion is a bit of a language model smell. I can’t help but be reminded of the purely nonsensical AI interview answers. “It’s a pleasure to meet you, Chick Bongo”
Creating an account 12 minutes ago (from the time of this posting) to comment on how another comment seems to you like a "language model smell" is itself, a language model smell, or a scammer.
Please stop accusing or hinting at others being a language model or bot. Not only is it a dumb waste of time, it's wrong in this instance and you are not only going to continue to be wrong but you have no way to prove or demonstrate that any single post comes from a bot nor the ability to do anything about it if you did in fact believe some comment to be attributed to a bot.
Re: AlphaGenome Atlas: a high-resolution map of human DNA
#109People are upvoting this because it has the “Alpha______” prefix. Meanwhile, everyone in the field of genomics knows that AlphaGenome provides essentially zero improvements over the previous SOTA, Borzoi…
> a database that predicts the effects of every possible single nucleotide variant in the human genome. We used the AlphaGenome AI model to pre-calculate the regulatory impact of all 9 billion single-letter genetic changes, resulting in a massive, 1-petabyte dataset. This is for a database, no? While Borzoi is a model? > Here, we introduce Borzoi, a model that learns to predict cell-type-specific and tissue-specific…
Any model can be expressed as a database.
Re: AlphaGenome Atlas: a high-resolution map of human DNA
#110Earlier quoted context omitted.
> a database that predicts the effects of every possible single nucleotide variant in the human genome. We used the AlphaGenome AI model to pre-calculate the regulatory impact of all 9 billion single-letter genetic changes, resulting in a massive, 1-petabyte dataset. This is for a database, no? While Borzoi is a model? > Here, we introduce Borzoi, a model that learns to predict cell-type-specific and tissue-specific…
Any model can be expressed as a database.
Kolmogorov looks at this with a ‘duh’ face