[jashephe]

I'm a little disappointed that their linked preprint doesn't appear to include any molecular biology; i.e. they don't actually try to synthesize any of their predicted sequences and test function. It wouldn't be an outrageous synthesis task to make some of the CRISPR-Cas sequences they generated.

Also interesting that AlphaMisense is omitted from Figure 2B; it substantially outperforms the ESM-based ESM1b in our hands. But I guess the idea is that this is a general-purpose DNA language model whereas AlphaMissense is domain-specific for variant effect prediction?

[bnprks]

Strong second for wishing they tried physically testing some model output. The importance of "model that makes outputs AlphaFold thinks look like Cas" is very different from "model that makes functional Cas variants".

For design tasks like in this paper, I think computational models have a big hill to climb in order to compete with physical high-throughput screening. Most of the time the goal is to get a small number of hits (<10) out of a pool of millions of candidates. At those levels, you need to work in the >99.9% precision regime to have any hope of finding significant hits after multiple-hypothesis correction. I don't think they showed anything near that accurate in the paper.

Maybe we'll get there eventually, but the high-throughput techniques in molecular biology are also getting better at the same time.

[theGnuMe]

You are correct that it is dangerous to rely on the results of a model being an oracle for another model, extremely good models (say F=ma) are used all the time.

[ackbar03]

This should really be a requirement for bio type related generative methods rather than a nice-to-have. A very high percentage of compounds generated by genai type methods have been shown not to work as intended. Anything without wetlab validation should really be taken with a large grain of salt

[rdmirza]

My immediate thought. Big Claims without backing.

Your model makes predictions. Prove they’re worth salt.