Benchmarking Transcriptomics Foundation Models for Perturbation Analysis : one PCA still rules them all — mentioned by donovanr

Fri, 20 Jun 2025 08:01:10 GMT

Yes, this. A lot of work in this field is missing from that timeline. Just circa 2010-2020, Les Loew's VCell 3D PDE approaches, Faeder et al.'s BioNetGen / ODE work, Luthey-Schulten Shulten's grid based cell models, the Pittsburgh supercomputing center's 3D monte-carlo MCell, the image-based deep learning models at the Allen Institute for Cell Science... It's nice to see the idea of virtual cells make a comeback now, though the meaning seems to have shifted to transciptomics-based transformer / gpu-powered models (which have issues[0]), it's a fun field / problem, but I think it will make…

Paper and discussion history. A mention is not an endorsement.

Benchmarking Transcriptomics Foundation Models for Perturbation Analysis : one PCA still rules them all · HackerPapers discussions

Benchmarking Transcriptomics Foundation Models for Perturbation Analysis : one PCA still rules them all — mentioned by donovanr