Scientific discovery in the age of artificial intelligence

H Wang, T Fu, Y Du, W Gao, K Huang, Z Liu… - Nature, 2023 - nature.com
Artificial intelligence (AI) is being increasingly integrated into scientific discovery to augment
and accelerate research, helping scientists to generate hypotheses, design experiments …

AI in health and medicine

P Rajpurkar, E Chen, O Banerjee, EJ Topol - Nature medicine, 2022 - nature.com
Artificial intelligence (AI) is poised to broadly reshape medicine, potentially improving the
experiences of both clinicians and patients. We discuss key findings from a 2-year weekly …

Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly

H Li, J Janssens, M De Waegeneer, SS Kolluru… - Science, 2022 - science.org
For more than 100 years, the fruit fly Drosophila melanogaster has been one of the most
studied model organisms. Here, we present a single-cell atlas of the adult fly, Tabula …

Vicreg: Variance-invariance-covariance regularization for self-supervised learning

A Bardes, J Ponce, Y LeCun - arXiv preprint arXiv:2105.04906, 2021 - arxiv.org
Recent self-supervised methods for image representation learning are based on maximizing
the agreement between embedding vectors from different views of the same image. A trivial …

Interpretation of T cell states from single-cell transcriptomics data using reference atlases

M Andreatta, J Corria-Osorio, S Müller, R Cubas… - Nature …, 2021 - nature.com
Single-cell RNA sequencing (scRNA-seq) has revealed an unprecedented degree of
immune cell diversity. However, consistent definition of cell subtypes and cell states across …

A comprehensive survey on deep clustering: Taxonomy, challenges, and future directions

S Zhou, H Xu, Z Zheng, J Chen, Z Li, J Bu, J Wu… - ACM Computing …, 2024 - dl.acm.org
Clustering is a fundamental machine learning task, which aim at assigning instances into
groups so that similar samples belong to the same cluster while dissimilar samples belong …

Pan-peptide meta learning for T-cell receptor–antigen binding recognition

Y Gao, Y Gao, Y Fan, C Zhu, Z Wei, C Zhou… - Nature Machine …, 2023 - nature.com
The identification of the mechanisms by which T-cell receptors (TCRs) interact with human
antigens provides a crucial opportunity to develop new vaccines, diagnostics and …

Learning interpretable cellular and gene signature embeddings from single-cell transcriptomic data

Y Zhao, H Cai, Z Zhang, J Tang, Y Li - Nature communications, 2021 - nature.com
The advent of single-cell RNA sequencing (scRNA-seq) technologies has revolutionized
transcriptomic studies. However, large-scale integrative analysis of scRNA-seq data remains …

Computational immunogenomic approaches to predict response to cancer immunotherapies

V Addala, F Newell, JV Pearson, A Redwood… - Nature Reviews …, 2024 - nature.com
Cancer immunogenomics is an emerging field that bridges genomics and immunology. The
establishment of large-scale genomic collaborative efforts along with the development of …

Population-level integration of single-cell datasets enables multi-scale analysis across samples

C De Donno, S Hediyeh-Zadeh, AA Moinfar… - Nature …, 2023 - nature.com
The increasing generation of population-level single-cell atlases has the potential to link
sample metadata with cellular data. Constructing such references requires integration of …