RT Journal Article
SR Electronic
T1 DANCE: A Deep Learning Library and Benchmark for Single-Cell Analysis
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2022.10.19.512741
DO 10.1101/2022.10.19.512741
A1 Jiayuan Ding
A1 Hongzhi Wen
A1 Wenzhuo Tang
A1 Renming Liu
A1 Zhaoheng Li
A1 Julian Venegas
A1 Runze Su
A1 Dylan Molho
A1 Wei Jin
A1 Wangyang Zuo
A1 Yixin Wang
A1 Robert Yang
A1 Yuying Xie
A1 Jiliang Tang
YR 2022
UL http://biorxiv.org/content/early/2022/10/24/2022.10.19.512741.abstract
AB In the realm of single-cell analysis, computational approaches have brought an increasing number of fantastic prospects for innovation and invention. Meanwhile, it also presents enormous hurdles to reproducing the results of these models due to their diversity and complexity. In addition, the lack of gold-standard benchmark datasets, metrics, and implementations prevents systematic evaluations and fair comparisons of available methods. Thus, we introduce the DANCE platform, the first standard, generic, and extensible benchmark platform for accessing and evaluating computational methods across the spectrum of benchmark datasets for numerous single-cell analysis tasks. Currently, DANCE supports 3 modules and 8 popular tasks with 32 state-of-art methods on 21 benchmark datasets. People can easily reproduce the results of supported algorithms across major benchmark datasets via minimal efforts (e.g., only one command line). In addition, DANCE provides an ecosystem of deep learning architectures and tools for researchers to develop their own models conveniently. The goal of DANCE is to accelerate the development of deep learning models with complete validation and facilitate the overall advancement of single-cell analysis research. DANCE is an open-source python package that welcomes all kinds of contributions. All resources are integrated and available at https://omicsml.ai/.Competing Interest StatementThe authors have declared no competing interest.