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 …

A comprehensive survey of foundation models in medicine

W Khan, S Leem, KB See, JK Wong… - IEEE Reviews in …, 2025 - ieeexplore.ieee.org
Foundation models (FMs) are large-scale deeplearning models that are developed using
large datasets and self-supervised learning methods. These models serve as a base for …

Foundation Models for Translational Cancer Biology

KK Tsang, S Kivelson… - Annual Review of …, 2025 - annualreviews.org
Cancer remains a leading cause of death globally. The complexity and diversity of cancer-
related datasets across different specialties pose challenges in refining precision medicine …

Reply to: Deeper evaluation of a single-cell foundation model

F Yang, F Wang, L Huang, L Liu, J Huang… - Nature Machine …, 2024 - nature.com
At the beginning, we would like to discuss the performance on cell type annotation task with
few-shot learning. First, the so-called few-shot learning experiment conducted in the …

Cell-ontology guided transcriptome foundation model

X Yuan, Z Zhan, Z Zhang, M Zhou, J Zhao… - arxiv preprint arxiv …, 2024 - arxiv.org
Transcriptome foundation models TFMs hold great promises of deciphering the
transcriptomic language that dictate diverse cell functions by self-supervised learning on …

[PDF][PDF] From Transformers to the Future: An In-Depth Exploration of Modern Language Model Architectures

H Xu, Z Bi, H Tseng, X Song, P Feng - osf.io
The Transformer is a neural network architecture that was introduced in the paper Attention
is All You Need by Vaswani et al. in 2017 [294]. It fundamentally changed the way natural …