GREmLN: A Cellular Regulatory Network-Aware Transcriptomics Foundation Model
https://www.biorxiv.org/content/10.1101/2025.07.03.663009v1?rss=1

Comments
* really brilliant work: LLM + neural transformer architecture
* a molecular biologist, I long-thought (no time to learn / program) flux-based analysis / ODE models
* this type of modeling is foundational to in silico modeling
* huge proponent of graphs - add LLM, attention heads - brilliant! 😀 👍️ kudos

#BiologicalModeling #FoundationModels #LLM #attention #GraphTheory #bioinformatics

https://pubs.acs.org/doi/10.1021/acscentsci.2c01473

"we demonstrate that conjugates triggered robust expression of hallmark GC markers, B cell receptor clustering, intracellular signaling, and somatic hypermutation. These responses depended on the relative immunogenicity of the conjugate and correlated with the humoral response in vivo... these findings highlight the potential of synthetic organoids for rapidly predicting conjugate vaccine efficacy"

#organoid #vaccine #biologicalModeling #medicalResearch