相关实验视频

Updated: Jul 7, 2025

Analyzing Mitochondrial Morphology Through Simulation Supervised Learning

Analyzing Mitochondrial Morphology Through Simulation Supervised Learning

Published on: March 3, 2023

通过在生物过程中转移学习来推断差异化轨迹的推断

Gaurav Jumde¹, Bastiaan Spanjaard², Jan Philipp Junker²

¹Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, 10115 Berlin, Germany; Humboldt Universität zu Berlin, Faculty of Life Sciences, Department of Biology, 10115 Berlin, Germany.

|December 21, 2023

概括

本研究介绍了一种计算框架,使用转移学习来预测细胞分化轨迹. 该模型在胚胎发育中显示出高准确度,但由于不同的转录一致性,在成年人血液形成中显示出较低的一致性.

科学领域:

计算生物学是一种计算生物学.
发育生物学是发展生物学.
干细胞生物学干细胞生物学

背景情况:

细胞分化涉及通过转录状态的过渡.
从单细胞转录组学预测分化轨迹是一个持续的挑战.
当前的计算方法在跨过程可预测性方面存在局限性.

研究的目的:

使用转移学习推断差异化过程并量化生物背景中的可预测性.
为了比较线性与非线性计算方法的预测精度.
研究不同生物系统之间预测准确度差异的原因.

主要方法:

应用转移学习技术到单细胞转录组学数据.
开发并使用一个定制的变化自编码器 (VAE) 模型.
在VAE内显式建模了转录变异的变化.
分析了早期胚胎发育和成人血液形成的分化轨迹.

主要成果:

非线性计算方法比线性方法表现出更高的性能.
定制的VAE实现了最高的预测准确度.
对于胚胎发育轨迹,观察到高预测准确度.
对于成年人血液形成,发现与真实数据的一致性略低.
与成人恒温相比,差异归因于胚胎发育中的更高的转录过程一致性.

结论:

建立了一个新的框架来量化和利用细胞分化的可预测性.
强调了非线性模型的有效性,特别是VAE,用于轨迹推断.
确定了影响不同差异化环境中的预测准确性的生物因素 (转录一致性).
提供了关于发育和恒常细胞过程之间的基本差异的见解.

关键词:

差异化轨迹的差异化轨迹可以预测的可预测性.单细胞转录组学单细胞转录组学转移学习转移学习

更多相关视频

Author Spotlight: Enhancing PSC-to-Functional Cell Differentiation Using ML Models Based on Live-Cell Bright-Field Imaging

Author Spotlight: Enhancing PSC-to-Functional Cell Differentiation Using ML Models Based on Live-Cell Bright-Field Imaging

Published on: October 4, 2024

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Published on: December 7, 2021

相关概念视频

Forced Transdifferentiation

Forced Transdifferentiation

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...

Cellular Differentiation

Cellular Differentiation

How does a complex organism such as a human develop from a single cell? It all starts from a single fertilized egg which gives rise to a vast array of cell types, such as nerve cells, muscle cells, and epithelial cells that characterize the adult? Throughout development and adulthood, cellular differentiation leads cells to assume their final morphology and physiology. Differentiation is the process by which unspecialized cells become specialized to carry out distinct functions.
A zygote is a...

Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...