iiinova — where your digital self keeps evolving

Dave Burke @daveyburke.bsky.social · 10/11/2025

The Virtual Cell Challenge's final test set is now available at virtualcellchallenge.org. Final scores will be based on the 100 new perturbations. The 7 day phase is single blind (no score feedback) and uses the latest cell-eval (bugfix'd last Friday). Good luck everyone!

virtualcellchallenge.org

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Dave Burke @daveyburke.bsky.social · 23/03/2025

Zach believes we're actually making a company to sell this thing. He has a business card (he's the CEO and I'm his CTO obvs). Even made a badge. For now, we're open sourcing the base model :). Python code and build instructions here: github.com/daveyburke/Z.... Enjoy!

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Dave Burke @daveyburke.bsky.social · 23/03/2025

My 7 yr old has been dreaming up an AI teddy bear. So we made him! Zaby is a clever, pedagogical & funny teddy that loves talking math. Powered by Gemini Flash & Google speech recognition/synthesis. His mouth moves in sync with the speech envelope. Smarter than the average bear!

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Dave Burke @daveyburke.bsky.social · 18/03/2025

"They help us unravel... the language of life" - Arc Institute's Evo 2 model featured during NVIDIA's GTC 2025 keynote - m.youtube.com/watch?v=_waP...

m.youtube.com

GTC March 2025 Keynote with NVIDIA CEO Jensen Huang

YouTube video by NVIDIA

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Dave Burke @daveyburke.bsky.social · 25/02/2025

Excited to announce the Arc Virtual Cell Atlas, a collection of high quality, curated, open datasets, incorporating scBaseCamp and Tahoe-100M from @vevo_ai. We hope this can be the beginning of an "ImageNet moment" for virtual cell modeling. Available at arcinstitute.org/tools/virtua...

arcinstitute.org

Virtual Cell Atlas | Arc Institute

Arc Institute is a independent nonprofit research organization headquartered in Palo Alto, California.

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Dave Burke @daveyburke.bsky.social · 19/02/2025

In the future, we can use this mechanism to steer DNA generation, for example make a prokaryotic sequence have more eukaryotic features, or increase the presence of alpha helices. You can read more in the Evo 2 preprint here: arcinstitute.org/manuscripts/...

arcinstitute.org

Manuscript | Arc Institute

Arc Institute is a independent nonprofit research organization headquartered in Palo Alto, California.

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Dave Burke @daveyburke.bsky.social · 19/02/2025

It shows genomic concepts in a reference genome such as coding sequences, alpha helices, tRNAs, etc. The tool overlays corresponding features that activate when Evo 2 detects such concepts. What’s amazing is Evo learned all this from genomes in nature without any supervision!

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Dave Burke @daveyburke.bsky.social · 19/02/2025

Together with @GoodfireAI we built a visualizer that lets you explore the concepts learned by Evo 2. Try it here: arcinstitute.org/tools/evo/ev...

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Dave Burke @daveyburke.bsky.social · 19/02/2025

We applied sparse autoencoders to Evo 2, our new DNA model, to show it autonomously learns a breadth of biological features, including exon–intron boundaries, transcription factor binding sites, protein structural elements, and prophage genomic regions

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Dave Burke @daveyburke.bsky.social · 19/02/2025

A common critique of large AI models is that they are black boxes. The recent field of mechanistic interpretability aims to “look inside” the AI black box

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Dave Burke @daveyburke.bsky.social · 19/02/2025

This is one of many applications of this work. Evolution has learned to read and write DNA over millions of years, and Evo 2 aims to learn from this knowledge. The AI model serves as a foundation for understanding the language of life across all domains—from bacteria to humans

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Dave Burke @daveyburke.bsky.social · 19/02/2025

This particular variant was initially reported as a variant of unknown significance (VUS). Years later, oncologists learned it was a driver of breast and ovarian cancers. In the Evo paper, we show state of the art performance on classifying BRCA1 variants of unknown significance

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Dave Burke @daveyburke.bsky.social · 19/02/2025

If I take a known deleterious mutation c.5095C>T that changes just the 5095th nucleotide in exon 17 from C to T, the negative log likelihood increases from 0.96 to 0.99 indicating the model is less confident. Evo recognizes that this mutation causes a loss of function of the gene

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Dave Burke @daveyburke.bsky.social · 19/02/2025

Evo Designer can also score DNA sequences, i.e. how likely the sequence is in nature. Here’s an example of a section of the BRCA1 - certain mutations in this gene are known to increase the risk of breast & ovarian cancer

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Dave Burke @daveyburke.bsky.social · 19/02/2025

Prompt with a sequence or species and the model will generate new DNA. Select sections of generated DNA to visualize the corresponding proteins, or use BLAST to find similar sequences in nature

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Dave Burke @daveyburke.bsky.social · 19/02/2025

Evo 2 uses a new hybrid architecture called StripedHyena 2 enabling a long context window of 1M nucleotides with a model size of 40B parameters, trained on 2048 H100 GPUs. Preprint can be found at arcinstitute.org/manuscripts/... and includes links to source code

arcinstitute.org

Manuscript | Arc Institute

Arc Institute is a independent nonprofit research organization headquartered in Palo Alto, California.

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Dave Burke @daveyburke.bsky.social · 19/02/2025

Introducing Evo 2 from Arc Institute - an AI that can model and design the genetic code for all domains of life. It’s one of the largest-scale truly open source AI models for biology (and in fact more generally - most “open source” large language models are only “open weights”)

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