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These are transformer models pretrained on expression profiles: UCE and GeneCompass on tens of millions of single cells, BulkFormer and BulkRNABert on bulk tumour and tissue transcriptomes.
Universal Cell Embeddings (Rosen and colleagues) is a 650-million-parameter cell model that represents genes by their ESM2 protein embeddings so it works across species; GeneCompass (Yang and colleagues) is a knowledge-informed model trained on over a hundred million human and mouse cells. Bulk-native models are fewer: BulkFormer (Kang and colleagues, Cell Systems 2026) is a 147-million-parameter model trained on about half a million bulk profiles and released with code and weights; BulkRNABert (Gélard and colleagues, InstaDeep) is a language model for bulk RNA-seq cancer prognosis under a research-only licence. Frozen bulk embeddings have not consistently beaten a genome-wide linear baseline on TCGA survival, so their value is still being established.
Showing the technology this term belongs to: scFoundation (BioMap).
Shares Fine-tuning versus frozen features, and LoRA, Foundation model, Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares Single-cell RNA sequencing (scRNA-seq, 10x Chromium), CZ CELLxGENE / Human Cell Atlas, Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares Single-cell RNA sequencing (scRNA-seq, 10x Chromium), CZ CELLxGENE / Human Cell Atlas, Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares Tokenisation (genes, tiles and sequence as tokens), Foundation model, Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares Tokenisation (genes, tiles and sequence as tokens), Fine-tuning versus frozen features, and LoRA, Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares Single-cell RNA sequencing (scRNA-seq, 10x Chromium), Foundation model, Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares Fine-tuning versus frozen features, and LoRA, Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares Fine-tuning versus frozen features, and LoRA, Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.