Ensemble deep learning in bioinformatics

Y Cao, TA Geddes, JYH Yang, P Yang - Nature Machine Intelligence, 2020 - nature.com
The remarkable flexibility and adaptability of ensemble methods and deep learning models
have led to the proliferation of their application in bioinformatics research. Traditionally …

Patch-seq: Past, present, and future

M Lipovsek, C Bardy, CR Cadwell… - Journal of …, 2021 - Soc Neuroscience
Single-cell transcriptomic approaches are revolutionizing neuroscience. Integrating this
wealth of data with morphology and physiology, for the comprehensive study of neuronal …

BABEL enables cross-modality translation between multiomic profiles at single-cell resolution

KE Wu, KE Yost, HY Chang… - Proceedings of the …, 2021 - National Acad Sciences
Simultaneous profiling of multiomic modalities within a single cell is a grand challenge for
single-cell biology. While there have been impressive technical innovations demonstrating …

Explainable multi-task learning for multi-modality biological data analysis

X Tang, J Zhang, Y He, X Zhang, Z Lin… - Nature …, 2023 - nature.com
Current biotechnologies can simultaneously measure multiple high-dimensional modalities
(eg, RNA, DNA accessibility, and protein) from the same cells. A combination of different …

Cross-linked unified embedding for cross-modality representation learning

X Tu, ZJ Cao, S Mostafavi… - Advances in Neural …, 2022 - proceedings.neurips.cc
Multi-modal learning is essential for understanding information in the real world. Jointly
learning from multi-modal data enables global integration of both shared and modality …

Common cell type nomenclature for the mammalian brain

JA Miller, NW Gouwens, B Tasic, F Collman… - Elife, 2020 - elifesciences.org
The advancement of single-cell RNA-sequencing technologies has led to an explosion of
cell type definitions across multiple organs and organisms. While standards for data and …

Multimodal deep learning approaches for single-cell multi-omics data integration

T Athaya, RC Ripan, X Li, H Hu - Briefings in Bioinformatics, 2023 - academic.oup.com
Integrating single-cell multi-omics data is a challenging task that has led to new insights into
complex cellular systems. Various computational methods have been proposed to effectively …

Joint variational autoencoders for multimodal imputation and embedding

N Cohen Kalafut, X Huang, D Wang - Nature Machine Intelligence, 2023 - nature.com
Single-cell multimodal datasets have measured various characteristics of individual cells,
enabling a deep understanding of cellular and molecular mechanisms. However …

Multimodal charting of molecular and functional cell states via in situ electro-sequencing

Q Li, Z Lin, R Liu, X Tang, J Huang, Y He, X Sui, W Tian… - Cell, 2023 - cell.com
Paired mapping of single-cell gene expression and electrophysiology is essential to
understand gene-to-function relationships in electrogenic tissues. Here, we developed in …

Consistent cross-modal identification of cortical neurons with coupled autoencoders

R Gala, A Budzillo, F Baftizadeh, J Miller… - Nature computational …, 2021 - nature.com
Consistent identification of neurons in different experimental modalities is a key problem in
neuroscience. Although methods to perform multimodal measurements in the same set of …