single-cell 5 scPRINT 4 python 3 rna-seq 3 gene regulatory networks 2 GRN 2 pytorch 2 non-negative-matrix-factorization 2 multi-omic-integration 2 niche covariation 2 nico 2 STARmap 2 seqFISH 2 MERFISH 2 scRNA-seq 2 single-cell RNA sequencing 2 spatial transcriptomics 2 niche 2 tissue niche 2 scverse 1 gene-regulatory-network 1 anndata 1 single-cell-sequencing 1 single-cell-omics 1 single-cell-genomics 1 single-cell-analysis 1 scrnaseq 1 scrna-seq-analysis 1 scrna-seq 1 utils 1 foundation model 1 gene regulatory network 1 large cell model 1 transformer 1 foundation 1 gene 1 network 1 regulatory 1 dataloader 1 lamindb 1 PLN 1 high dimension 1 ml 1 single-cell-rna-seq 1 count data 1 benchmark 1 comp bio 1 data 1 transcriptomics 1 atacseq 1 rnaseq 1 bioinformatics 1 life-sciences 1 computation-biology 1 data-science 1 system-biology 1 count 1