转移学习和变-不变性 提高预测全基因组,细胞特异性和定向干预 复杂系统的影响
Boyang Wang1, Boyu Pan2, Tingyu Zhang1
1Institute for TCM-X, Department of Automation, Tsinghua University, Beijing, 100084, China.
Advanced science (Weinheim, Baden-Wurttemberg, Germany)
|September 19, 2025
概括
本研究介绍了SETComp,这是一种使用转移学习来预测复杂系统干预效应的深度学习模型. SETComp准确地预测了新型天然产品的结果,推进了精密医学.
科学领域:
- 计算生物学 计算生物学
- 药理学 药理学是指药理学的学科.
- 系统生物学 系统生物学
背景情况:
- 精准医学需要预测超出单一药物的复杂系统干预.
- 有广泛的单组合数据和深度学习模型.
- 转移学习为复杂系统利用现有数据提供了一个有希望的方法.
研究的目的:
- 使用转移学习开发复杂系统干预效应的预测模型.
- 为了对像自然产品这样的复杂系统的单个化合物数据进行预先训练的深度模型进行微调.
- 评估模型的准确性和对未见复杂系统的概括性.
主要方法:
- 作为核心,利用了一种变量不变的深度学习模型.
- 预先训练了模型在细胞系的大规模单一化合物干预数据上.
- 微调了在细胞系中有限的复杂系统干预数据上的模型,创建了SETComp (复杂系统的集嵌入和转移学习模型).
主要成果:
- 在复杂的系统-细胞-基因关联测试中,SETComp取得了高精度 (93.86%和92.70%),表现比基线高5.82%27.59%.
- 与基线相比,新型复杂系统的预测精度提高了高达24.83%.
- 在体外验证证了高达88.65%的预测,显示了与现实世界折叠变化有显著的正相关性.
结论:
- SETComp有效地预测了复杂的系统干预效应,证明了转移学习的力量.
- 该模型显示出在机制发现和药物重新定位方面的应用有很大的潜力.
- 在生物医学研究中,SETComp推动了深度学习与复杂的生物系统的整合.
相关概念视频
01:24Methods of Nuclear Reprogramming
2.1K
Nuclear reprogramming is a process of transforming one cell type into an unrelated cell type by epigenetic changes that alter the cell’s original gene expression pattern. Such epigenetic changes force cells to express a different set of genes, which play a significant role in inducing transformation into other cell types. Nuclear reprogramming offers applications in reproductive cloning for livestock propagation and regenerative medicine — developing patient-specific cells for...
2.1K
01:29Somatic to iPS Cell Reprogramming
2.6K
Reprogramming alters the gene expression in somatic cells, transforming them into induced pluripotent stem (iPS) cells over several generations. Scientists can reprogram cells by introducing genes for four transcription factors—Oct4, Sox2, Klf4, and c-Myc (OSKM) by viral or non-viral methods. These factors are also known as Yamanaka factors after Shinya Yamanaka, who first generated iPS cells using mouse skin cells. Yamanaka was awarded the Nobel Prize in Physiology or Medicine in 2012...
2.6K
01:28Forced Transdifferentiation
2.3K
Transdifferentiation, also known as lineage reprogramming, was first discovered by Selman and Kafatos in 1974 in silkmoths. They observed that the moths’ cuticle-producing cells transformed into salt-producing cells. Many such cases of natural transdifferentiation occur in organisms. In humans, pancreatic alpha cells can become beta cells. In newts, the loss of the eye’s lens causes the pigmented epithelial cells to transdifferentiate into the lens cells.
Artificial...
Artificial...
2.3K
02:13Overview of Transposition and Recombination
18.8K
Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...
18.8K