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Evo 2, our fully open-source biological foundation model trained on trillions of DNA tokens spanning the entire tree of life, is out in nature today We & the scientific community have done a lot with this Arc Institute NVIDIA model in the last year! 🧵👇

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Evo 2, the largest fully open biological AI model to date, is now published in nature.

Evo 2, the largest fully open biological AI model to date, is now published in nature.

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1/n: We are excited to share that our paper on Chroma, a general purpose diffusion model for proteins, is out today in nature! A couple of my favorite highlights in the 🧵below 👇

1/n: We are excited to share that our paper on Chroma, a general purpose diffusion model for proteins, is out today in nature! A couple of my favorite highlights in the 🧵below 👇

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We are releasing Carbon: a crazy fast DNA model Carbon is 275x faster than the next best model. So fast you can process the whole human genome on a single GPU in <2 days. Here are the tricks we used: When modelling DNA sequences a lot of the performance comes down to tokenizing the sequences in a smart way. BPE tokenizer struggle because there are no whitespaces and character (called base in DNA) level tokenizers waste a lot of compute on too many tokens. Carbon is built with a unique tokenizer: we split sequences in chunks of 6 bases, but during both training and inference we can work with single base resolution. That's similar to having word tokens but resolving them at the character level. All possible thanks to the DNA tokens unique structure. The architecture combined with the tokenizer makes the model 275x faster than the previous SoTA (Evo2) at this size. We built an interactive demo so you can explore how the model can generate DNA sequences, investigate the structure of genes, predict the effect of mutations, generate and fold proteins and even reconstruct parts of the tree of life.

We are releasing Carbon: a crazy fast DNA model Carbon is 275x faster than the next best model. So fast you can process the whole human genome on a single GPU in <2 days. Here are the tricks we used: When modelling DNA sequences a lot of the performance comes down to tokenizing the sequences in a smart way. BPE tokenizer struggle because there are no whitespaces and character (called base in DNA) level tokenizers waste a lot of compute on too many tokens. Carbon is built with a unique tokenizer: we split sequences in chunks of 6 bases, but during both training and inference we can work with single base resolution. That's similar to having word tokens but resolving them at the character level. All possible thanks to the DNA tokens unique structure. The architecture combined with the tokenizer makes the model 275x faster than the previous SoTA (Evo2) at this size. We built an interactive demo so you can explore how the model can generate DNA sequences, investigate the structure of genes, predict the effect of mutations, generate and fold proteins and even reconstruct parts of the tree of life.

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Earlier this week at GTC, we announced our partnership with Nvidia. We will work with Nvidia to build strong, American open-source models that are at the frontier of scientific reasoning. These models will be essential for the US to compete with China on science in the coming decades. Jensen is committing to spend tens of billions of dollars developing open-source models, and we are excited to be a partner with them in figuring out how to benchmark, train and use those agents to accelerate scientific research. We have already open-sourced some of the work we have done with them, and are looking forward to open-sourcing more. There are few things today that are more important. See our blog post below, and watch the video to learn more, narrated by the man himself.

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Today in nature, we report MouseMapper: foundation-model AI to map disease perturbations across the entire mouse body cell-by-cell. In obesity, it revealed body-wide inflammation & unexpected facial nerve damage. 🧵👇🔉 led by Doris Kaltenecker & Ying Chen

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🚨David Friedberg: AI is starting to identify and solve problems on its own “I'll give you a science corner example: there's this Evo 2 model that they publish at the Arc Institute, which Patrick Collison, you know, is the main funder and chairman.” “So that Evo 2 model, they just ingested all the DNA data they could find in the world.” “Trillions and trillions of base paired data that they ingested and then they looked at patterns in DNA. And that's it.” “They had no context for what the DNA represented, they had no context for the concept of genes, none of the structured understanding of what that DNA does, what it is, and you know what it did?” “They fed in the BRCA gene variant and the thing output a warning saying, ‘I think that this is a pathogenic variant to DNA,’ without having any context.” “This is the breast cancer allele.” “And it didn't have any knowledge and it wasn't trained on that at all.” “It had no knowledge that there are pathogenic variants for cancer, and it identified that this was a genetic variant that can cause some sort of pathogenic outcome in the organism.” “That's a great example where there's a lack of understanding at the human level on what really drives some of the patterns in nature, the patterns in society, the patterns in behavior that are kind of emergent phenomena perhaps, that these AI models are starting to identify.”

🚨David Friedberg: AI is starting to identify and solve problems on its own “I'll give you a science corner example: there's this Evo 2 model that they publish at the Arc Institute, which Patrick Collison, you know, is the main funder and chairman.” “So that Evo 2 model, they just ingested all the DNA data they could find in the world.” “Trillions and trillions of base paired data that they ingested and then they looked at patterns in DNA. And that's it.” “They had no context for what the DNA represented, they had no context for the concept of genes, none of the structured understanding of what that DNA does, what it is, and you know what it did?” “They fed in the BRCA gene variant and the thing output a warning saying, ‘I think that this is a pathogenic variant to DNA,’ without having any context.” “This is the breast cancer allele.” “And it didn't have any knowledge and it wasn't trained on that at all.” “It had no knowledge that there are pathogenic variants for cancer, and it identified that this was a genetic variant that can cause some sort of pathogenic outcome in the organism.” “That's a great example where there's a lack of understanding at the human level on what really drives some of the patterns in nature, the patterns in society, the patterns in behavior that are kind of emergent phenomena perhaps, that these AI models are starting to identify.”

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