Nicheformer (spatial single-cell)
Nicheformer is a model trained on both dissociated and spatial data so it learns how a cell's neighbourhood shapes it.
Nicheformer (2024, Helmholtz Munich) pretrained on 110M cells (57M dissociated, 53M spatial) for niche and spatial-context tasks in tumours.
How it works
Nicheformer is a transformer with spatial context tokens.
- Spatial-aware
- Spatial data still sparse
Latest papers
topQuery for this technology: (TITLE:"Nicheformer" OR ABSTRACT:"Nicheformer" OR TITLE:"spatial single-cell" OR ABSTRACT:"spatial single-cell") AND (cancer OR tumor OR tumour OR oncology OR carcinoma OR lymphoma OR leukemia OR leukaemia OR myeloma OR sarcoma OR melanoma OR glioma). Results are unfiltered search hits about Nicheformer (spatial single-cell), not a curated reading list.
Pages like this
not linked directly; found by shared links- TechnologyGeneformer
Shares Virtual cell roadmap: from bulk omics to a predictive model of a cancer cell, Single-cell & spatial profiling and the tags foundation-model, virtual-cell.
- TechnologyscGPT
Shares Virtual cell roadmap: from bulk omics to a predictive model of a cancer cell, Single-cell & spatial profiling and the tags foundation-model, virtual-cell.
- TechnologyscFoundation (BioMap)
Shares Virtual cell roadmap: from bulk omics to a predictive model of a cancer cell and the tags foundation-model, virtual-cell.
- TechnologyState (Arc Institute perturbation model)
Shares Virtual cell roadmap: from bulk omics to a predictive model of a cancer cell, Single-cell & spatial profiling and the tags foundation-model, virtual-cell.
- TechnologyTranscriptFormer and rBio (CZI virtual cell models)
Shares Virtual cell roadmap: from bulk omics to a predictive model of a cancer cell and the tags foundation-model, virtual-cell.
- TechnologyUniversal Cell Embedding (UCE)
Shares Virtual cell roadmap: from bulk omics to a predictive model of a cancer cell and the tags foundation-model, virtual-cell.
- TechnologyCell2Sentence / C2S-Scale (Yale, Google)
Shares Virtual cell roadmap: from bulk omics to a predictive model of a cancer cell and the tags foundation-model, virtual-cell.
- TechnologyCellFM
Shares the tags foundation-model, virtual-cell.