生物GAN:通过生物知识增强转录基因数据生成
Francesca Pia Panaccione1, Sofia Mongardi1, Marco Masseroli1
1Department of Electronics, Information, and Bioengineering, Politecnico di Milano, 20133 Milan, Italy.
Bioengineering (Basel, Switzerland)
|June 26, 2025
概括
通过将生物网络集成到生成模型中,BioGAN产生了现实的合成转录基因数据. 这种方法提高了疾病预测和精准医学的数据实用性,克服了当前方法的局限性.
科学领域:
- 计算型基因组学计算型基因组学
- 生物信息学是一种生物信息学.
- 机器学习 机器学习
背景情况:
- 计算基因组学推动了数据驱动的疾病预测和精准医学.
- 挑战包括数据稀缺,隐私问题和固有的偏见.
- 合成数据生成是一个潜在的解决方案,但目前的AI方法缺乏生物基础.
研究的目的:
- 引入BioGAN,一种用于合成转录基因组数据的新型生成框架.
- 通过结合生物知识来解决现有方法的局限性.
- 提高生成的转录基因资料的现实性和实用性.
主要方法:
- 开发了BioGAN,将图形神经网络 (GNN) 集成到生成对抗网络 (GAN) 中.
- 利用基因调节和共同表达网络来指导数据生成.
- 通过使用无监督和监督指标对大肠杆菌和人类基因表达数据集进行验证.
主要成果:
- 在合成的转录基因数据中,BioGAN成功地保存了生物特性.
- 在人类数据上,BioGAN提高了精度4.3%,与真实数据的相关性高达2.6%.
- 来自BioGAN的合成数据将下游疾病和组织分类性能平均提高了5.7%.
结论:
- 将先验生物知识集成到生成模型中,有效地提高了合成数据的质量和效用.
- 生物GAN展示了稳健性和强大的预测效用,超过了最先进的模型.
- 该框架为基因组学研究中的数据稀缺性和偏见问题提供了一个有希望的解决方案.
相关概念视频
03:36Genome Annotation and Assembly
19.4K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
19.4K
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
02:24Ribosome Profiling
3.6K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
3.6K
02:02Genomics
37.5K
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...
37.5K
03:21RNA-seq
10.4K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
10.4K