Dave Burke (CTO at Arc Institute) evaluates the current benchmark state of virtual cell models predicting differentially expressed genes post-perturbation.
“The reality is today the best models are very poor at this.
like the predictive ability of the DEGs as we call them is, is in the order of 10%.”
quote is from the automated transcript, cleaned for reading:
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More from Dave Burke
Opinion
Burke: Virtual cell accuracy is limited by data quality, not architecture
“One of our conjectures is that one of the reasons the models aren't doing well is not just simply model structure. We have a lot of rich structures that we understand in the ML space and machine learning space that the issue is the Data quality.”
Dave BurkeFeb 25, 2025▶ 33:38No Priors Ep. 103 | With Vevo Therapeutics and the Arc Institute
Disclosure
Burke: Arc Institute built SC Basecamp with 230M single cells
“We've created something called SC Basecamp and you can almost think of it like the Google crawler and index, so we've built this agent that goes onto the internet, And basically mines public single cell sequenced RNA data, and then curates it in a very sort of…”
Dave BurkeFeb 25, 2025▶ 27:51No Priors Ep. 103 | With Vevo Therapeutics and the Arc Institute
Insight
Burke: Transcriptomic level is the right abstraction for cell modeling
“And so I think our belief around the room is the right level of abstraction is at the sort of transcriptomic level because you have these very complex gene pathways. And so whenever a cell is changing to its environment reacting, that it will be reflected and …”
Dave BurkeFeb 25, 2025▶ 41:59No Priors Ep. 103 | With Vevo Therapeutics and the Arc Institute
AssertionSupported
Burke: Evo 2 trained on 9.3 trillion nucleotides predicts BRCA1 pathogenicity
“Like, if you look at the EVO II model, we trained it on 9.3 trillion
nucleotides, but we didn't tell it anything about DNA.
We just like, here's a lot of DNA on the planet across, you know, every single piece of DNA we could get a hold of.
And then what di…”
Dave BurkeFeb 25, 2025▶ 54:27No Priors Ep. 103 | With Vevo Therapeutics and the Arc Institute
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