sCIN:用于单细胞多组数据集成的对比学习框架
Amir Ebrahimi1, Alireza Fotuhi Siahpirani2, Hesam Montazeri2
1Department of Biotechnology, College of Science, University of Tehran, Ghods 37, Tehran, 1417763135, Iran.
Briefings in bioinformatics
|August 26, 2025
概括
我们开发了一种名为sCIN的新方法, 这种框架有效地结合了不同类型的数据,克服了技术偏见,揭示了细胞异质性和调控机制.
科学领域:
- 单细胞多组合集成
- 计算生物学
- 基因组学和转录组学
背景情况:
- 像scRNA-seq和scATAC-seq这样的单细胞欧米技术已经进行了先进的细胞异质性研究.
- 由于分布差异和独特的特征空间,整合多种数据具有挑战性.
研究的目的:
- 提出一种新的框架,即单细胞对比集成 (sCIN),用于集成多种单细胞体质的模式.
- 能够将不同类型的数据组合到一个共享的隐藏空间中,克服技术偏差.
主要方法:
- 开发了sCIN,一个使用模式特定编码器和对比学习的框架.
- 确保在训练和测试组之间严格防止数据泄露.
- 在配对 (scRNA-ATAC,10X PBMC,CITE-seq) 和未配对 (基因表达,染色质可访问性) 数据集上进行评估.
主要成果:
- 与最先进的模型 (scGLUE,scBridge,sciCAN,Con-AAE,Harmony,MOFA+) 相比,sCIN在多重集成和集群指标方面表现出更好的表现.
- 包括模拟的未配对数据在内的配对和未配对数据集都显示出有效的整合.
- 在多式联通过程中,该框架成功地保留了生物意义.
结论:
- sCIN提供了一个强大的解决方案,用于整合单细胞的奥米克模式.
- 该框架有效地解决了技术偏差,并保留了对和未对的多组数据中的生物洞察力.
- 通过可靠的数据集成,sCIN促进了对细胞异质性和调控机制的理解.
相关概念视频
02:02Genomics
37.4K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
37.4K
02:16Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes
13.4K
The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
13.4K
02:55Synthetic Biology
5.0K
Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...
Golden rice
Golden rice is a genetically modified...
5.0K
02:51Multi-species Conserved Sequences
4.3K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
4.3K
01:22Multi-input and Multi-variable systems
149
Cruise control systems in cars are designed as multi-input systems to maintain a driver's desired speed while compensating for external disturbances such as changes in terrain. The block diagram for a cruise control system typically includes two main inputs: the desired speed set by the driver and any external disturbances, such as the incline of the road. By adjusting the engine throttle, the system maintains the vehicle's speed as close to the desired value as possible.
In the absence...
In the absence...
149
01:20Applications of Molecular Taxonomy
99
Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...
99