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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
This is a major reason I joined @transcriptabio We've proved our platform in rare disease – an area that uniquely allows you to: 1) realize the mission of helping people, immediately 2) receive the gold-standard of clinical feedback, immediately 📄: researchsquare.com/article/rs-629…
I will not stop tweeting this until every drug discovery company gets human evidence in 3 years or less
Most current drug discovery efforts is structure-based eg. create small molecules or antibodies that best binds X. However, a drug may not drive its efficacy from its strongest binder. Taking a step away from structure-paradigm, we reason that if a CRISPR knockout of a gene…
“this discussion on the challenges of evaluating a Foundation model is more interesting than the challenge itself.” Agreed!
My second post on the Arc Virtual Cell Challenge. The challenge’s Discord forums are in turmoil. Some participants have discovered a trick to get to the top of the leaderboard. gmdbioinformatics.substack.com/p/arc-virtual-… #arc_virtual_cell_challenge #foundation_models
We're excited to present LeaVS, a method to scale up learning for protein function models. It is based on the co-design of wet lab experiments and in silico training.
Arc is hiring a unique role to lead the Virtual Cell Challenge. In its first year the Challenge has already attracted participation from thousands of top bio AI researchers and support from sponsors like NVIDIA. We need someone to help us make this annual competition historically…
Massive, clean Pertub-seq dataset. 8M cells, 2 cell types, deeply sequenced. 🧬🪩 👏
Virtual Cell community - this one's for you! X-Atlas/Orion is now live on Hugging Face. Train your own models with streamlined workflows built into the Hugging Face API. 🔗 HuggingFace: huggingface.co/datasets/Xaira… 📜 License: cc-by-nc-sa-4.0
Awesome 👏🏼👏🏼
Welcome to the age of generative genome design! In 1977, Sanger et al. sequenced the first genome—of phage ΦX174. Today, led by @samuelhking, we report the first AI-generated genomes. Using ΦX174 as a template, we made novel, high-fitness phages with genome language models. 🧵
*using the ctrl pop as a ref biases perturbation effects to be poorly distinguishable* a new study by @mariabrbic's lab reaches the same conclusion as the @ShiftBioscience study I highlighted recently 👏 ...with an nice fwd comment on model "utility" 😎 x.com/mariabrbic/sta…
What is the state of research on the emerging grand challenge of virtual cell modeling? 1/n open.substack.com/pub/behindbiom…
The biggest challenge for AI in biology isn't just models, it's the data used to train them. Standard biological data isn't built for AI. To unlock generative AI for drug discovery, we must rethink how we generate and capture data. 1/
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