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🧬🔮 Single cell foundation models have been a recent hot topic in bio-ML! A few of the recent methods and some thoughts 🧬🔮
1) Geneformer
2) scGPT
3) scFoundation
4) Exceiver
1) Geneformer
2) scGPT
3) scFoundation
4) Exceiver
Latest posts 5
🤌🏼🤌🏼
1/ Most genes and variants matter somewhere but look silent in any one cell model. Can we build conditions that reveal phenotypes? With @kanishkadey, we engineer cell states to expose hidden disease biology and trace how genetic risk reaches disease genes. biorxiv.org/content/10.648…View quoted post on X
If the goal is to simulate a cell’s gene regulatory logic I think a strong test is predicting held out time pts on a dataset of densely time-sampled targeted perts
Or a dataset of dense dose-sampled perts
We’re desperately missing measured changes over close cont intervals
Or a dataset of dense dose-sampled perts
We’re desperately missing measured changes over close cont intervals
Good time to ponder what we might actually need to get closer to useful “virtual cells” eventually. Laundry list:View quoted post on X
Measurements:
- non-destructive sampling of the same cell at <30 min intervals, high-quality measurements
- protein measurements, localization, TF-DNA binding 1/
My scoped takeaway is that LLMs can do similarity search "by eye," matching patterns in a way that's independent of statistical methods.
IMO this is more interesting. And this idea generalizes, we formalized it as LLM Kernel: openreview.net/forum?id=Rq5wD…
IMO this is more interesting. And this idea generalizes, we formalized it as LLM Kernel: openreview.net/forum?id=Rq5wD…
Claude has discovered a previously unknown enzyme system hidden in the DNA of bacteriophages. Beside the enzyme’s gene sits a long array of repeating DNA—a structure that looks somewhat similar to CRISPR.View quoted post on X
We don’t yet understand what this system does, but only a handful of known systems share its features, and all of them are able to cut, copy, and paste DNA. Historically, the discovery of such programmable systems has helped revolutionize medicine. CRISPR, for instance, is now the foundation of genetic medicines. But it will take much more work to learn what this system does, and whether it can be put to similar use.
Read more: anthropic.com/news/claude-di…
Imagine culling the tree of knowledge to reproducible conclusions.
IMO one of the first steps to accelerating science‼️
Eliminate entire hypothesis nodes that have misallocated scientific search for decades due to foundations of fraud, weak evidence, poor interpretation.
IMO one of the first steps to accelerating science‼️
Eliminate entire hypothesis nodes that have misallocated scientific search for decades due to foundations of fraud, weak evidence, poor interpretation.
BixBench3 is out! Our latest eval for biology capabilities in language models. Essentially requires agents to reproduce all work needed to write a paper from raw data. OpenAI is in the lead with 5.6-Sol at 48%, Anthropic is in 4th with Opus 4.8, after Kimi and GLM. Opus 5 has weird instruction following problems that severely degrade its performance. I’m sure Fable is great but can't be evalled on this. Read more below.
Also lest we miss the forest for the trees, we’re in a position now where the models can essentially reproduce entire papers ~50% of the time. Crazy time to be alive.View quoted post on X
