Graph representation learning in biomedicine and healthcare

MM Li, K Huang, M Zitnik - Nature Biomedical Engineering, 2022 - nature.com
Networks—or graphs—are universal descriptors of systems of interacting elements. In
biomedicine and healthcare, they can represent, for example, molecular interactions …

Application of deep learning on single-cell RNA sequencing data analysis: a review

M Brendel, C Su, Z Bai, H Zhang… - Genomics …, 2022 - academic.oup.com
Single-cell RNA sequencing (scRNA-seq) has become a routinely used technique to
quantify the gene expression profile of thousands of single cells simultaneously. Analysis of …

Single-cell spatial metabolomics with cell-type specific protein profiling for tissue systems biology

T Hu, M Allam, S Cai, W Henderson, B Yueh… - Nature …, 2023 - nature.com
Metabolic reprogramming in cancer and immune cells occurs to support their increasing
energy needs in biological tissues. Here we propose Single Cell Spatially resolved …

Single cell RNA‐sequencing: A powerful yet still challenging technology to study cellular heterogeneity

M Ke, B Elshenawy, H Sheldon, A Arora, FM Buffa - Bioessays, 2022 - Wiley Online Library
Almost all biomedical research to date has relied upon mean measurements from cell
populations, however it is well established that what it is observed at this macroscopic level …

Topological identification and interpretation for single-cell gene regulation elucidation across multiple platforms using scMGCA

Z Yu, Y Su, Y Lu, Y Yang, F Wang, S Zhang… - Nature …, 2023 - nature.com
Single-cell RNA sequencing provides high-throughput gene expression information to
explore cellular heterogeneity at the individual cell level. A major challenge in characterizing …

Zinb-based graph embedding autoencoder for single-cell rna-seq interpretations

Z Yu, Y Lu, Y Wang, F Tang, KC Wong… - Proceedings of the AAAI …, 2022 - ojs.aaai.org
Single-cell RNA sequencing (scRNA-seq) provides high-throughput information about the
genome-wide gene expression levels at the single-cell resolution, bringing a precise …

Machine learning boosts the design and discovery of nanomaterials

Y Jia, X Hou, Z Wang, X Hu - ACS Sustainable Chemistry & …, 2021 - ACS Publications
Nanomaterials (NMs) have developed quickly and cover various fields, but research on
nanotechnology and NMs largely relies on costly experiments or complex calculations (eg …

A non‐linear non‐intrusive reduced order model of fluid flow by auto‐encoder and self‐attention deep learning methods

R Fu, D **ao, IM Navon, F Fang, L Yang… - International Journal …, 2023 - Wiley Online Library
This paper presents a new nonlinear non‐intrusive reduced‐order model (NL‐NIROM) that
outperforms traditional proper orthogonal decomposition (POD)‐based reduced order model …

scDCCA: deep contrastive clustering for single-cell RNA-seq data based on auto-encoder network

J Wang, J **a, H Wang, Y Su… - Briefings in …, 2023 - academic.oup.com
The advances in single-cell ribonucleic acid sequencing (scRNA-seq) allow researchers to
explore cellular heterogeneity and human diseases at cell resolution. Cell clustering is a …

CIForm as a transformer-based model for cell-type annotation of large-scale single-cell RNA-seq data

J Xu, A Zhang, F Liu, L Chen… - Briefings in …, 2023 - academic.oup.com
Single-cell omics technologies have made it possible to analyze the individual cells within a
biological sample, providing a more detailed understanding of biological systems …