Machine learning for lung cancer diagnosis, treatment, and prognosis

Y Li, X Wu, P Yang, G Jiang… - Genomics, Proteomics and …, 2022 - academic.oup.com
The recent development of imaging and sequencing technologies enables systematic
advances in the clinical study of lung cancer. Meanwhile, the human mind is limited in …

A single-cell analysis reveals tumor heterogeneity and immune environment of acral melanoma

C Zhang, H Shen, T Yang, T Li, X Liu, J Wang… - Nature …, 2022 - nature.com
Acral melanoma is a dismal subtype of melanoma occurring in glabrous acral skin, and has
a higher incidence in East Asians. We perform single-cell RNA sequencing for 63,394 cells …

Delineating the effective use of self-supervised learning in single-cell genomics

T Richter, M Bahrami, Y Xia, DS Fischer… - Nature Machine …, 2024 - nature.com
Self-supervised learning (SSL) has emerged as a powerful method for extracting meaningful
representations from vast, unlabelled datasets, transforming computer vision and natural …

Robust evaluation of deep learning-based representation methods for survival and gene essentiality prediction on bulk RNA-seq data

B Gross, A Dauvin, V Cabeli, V Kmetzsch… - Scientific Reports, 2024 - nature.com
Deep learning (DL) has shown potential to provide powerful representations of bulk RNA-
seq data in cancer research. However, there is no consensus regarding the impact of design …

Deep enhanced constraint clustering based on contrastive learning for scRNA-seq data

Y Gan, Y Chen, G Xu, W Guo, G Zou - Briefings in Bioinformatics, 2023 - academic.oup.com
Single-cell RNA sequencing (scRNA-seq) measures transcriptome-wide gene expression at
single-cell resolution. Clustering analysis of scRNA-seq data enables researchers to …

Cellular data extraction from multiplexed brain imaging data using self-supervised Dual-loss Adaptive Masked Autoencoder

ST Ly, B Lin, HQ Vo, D Maric, B Roysam… - Artificial Intelligence in …, 2024 - Elsevier
Reliable large-scale cell detection and segmentation is the fundamental first step to
understanding biological processes in the brain. The ability to phenotype cells at scale can …

[HTML][HTML] Deep-learning methods for unveiling large-scale single-cell transcriptomes

X Shen, X Li - Cancer Biology & Medicine, 2023 - ncbi.nlm.nih.gov
The rapidly evolving realm of single-cell transcriptomics offers vital new perspectives into the
understanding of intra-and inter-cellular molecular dynamics governing development …

Scalable batch-correction approach for integrating large-scale single-cell transcriptomes

X Shen, H Shen, D Wu, M Feng, J Hu… - Briefings in …, 2022 - academic.oup.com
Integration of accumulative large-scale single-cell transcriptomes requires scalable batch-
correction approaches. Here we propose Fugue, a simple and efficient batch-correction …

Multiplexed Immunofluorescence Brain Image Analysis Using Self-Supervised Dual-Loss Adaptive Masked Autoencoder

ST Ly, B Lin, HQ Vo, D Maric, B Roysam… - arXiv preprint arXiv …, 2022 - arxiv.org
Reliable large-scale cell detection and segmentation is the fundamental first step to
understanding biological processes in the brain. The ability to phenotype cells at scale can …