Transformers in single-cell omics: a review and new perspectives

A Szałata, K Hrovatin, S Becker, A Tejada-Lapuerta… - Nature …, 2024 - nature.com
Recent efforts to construct reference maps of cellular phenotypes have expanded the
volume and diversity of single-cell omics data, providing an unprecedented resource for …

Discrete representation learning for modeling imaging-based spatial transcriptomics data

DVK Yarlagadda, J Massagué… - Proceedings of the …, 2023 - openaccess.thecvf.com
Imaging-based spatial transcriptomics (ST) provides single-transcript-level spatial resolution
for hundreds of genes, unlike sequencing-based ST technologies whose resolution is …

CellPLM: pre-training of cell language model beyond single cells

H Wen, W Tang, X Dai, J Ding, W Jin, Y Xie, J Tang - bioRxiv, 2023 - biorxiv.org
The current state-of-the-art single-cell pre-trained models are greatly inspired by the success
of large language models. They trained transformers by treating genes as tokens and cells …

stMCDI: Masked Conditional Diffusion Model with Graph Neural Network for Spatial Transcriptomics Data Imputation

X Li, W Min, S Wang, C Wang, T Xu - arXiv preprint arXiv:2403.10863, 2024 - arxiv.org
Spatially resolved transcriptomics represents a significant advancement in single-cell
analysis by offering both gene expression data and their corresponding physical locations …

Single Cells Are Biological Tokens: Towards Cell Language Models

H Wen - 2024 - search.proquest.com
The rapid advancement of single-cell technologies allows for simultaneous measurement of
multiple molecular features within individual cells, providing unprecedented multimodal data …

Integrating Spatial Transcriptomics Data for Cross-Species Molecular Region Comparison

B Li - 2024 - dspace.mit.edu
Comparative analysis of brain patterns across species can advance understanding of
different biological processes and functions. Spatially resolved transcriptomics (SRT) …