CellMemory: hierarchical interpretation of out-of-distribution cells using bottlenecked transformer

• Published in: Genome Biology Vol. 26; no. 1; pp. 178 - 37
• Main Authors: Wang, Qifei, Zhu, He, Hu, Yiwen, Chen, Yanjie, Wang, Yuwei, Li, Guochao, Li, Yun, Chen, Jinfeng, Zhang, Xuegong, Zou, James, Kellis, Manolis, Li, Yue, Liu, Dianbo, Jiang, Lan
• Format: Journal Article
• Language: English
• Published: England BioMed Central 23.06.2025; BMC
• Subjects: Accuracy; Annotations; Cell culture; Cells; Consciousness; Datasets; Genes; Humans; Information dissemination; Lung cancer; Machine Learning; Memory; Methodology; Neurosciences; Single-Cell Analysis - methods; Transcriptome; Transcriptomics

Machine learning methods, especially Transformer architectures, have been widely employed in single-cell omics studies. However, interpretability and accurate representation of out-of-distribution (OOD) cells remains challenging. Inspired by the global workspace theory in cognitive neuroscience, we...