用模块化结构先验,让神经网络更少数据就能学懂生物电路功能。
Learning Genetic Circuit Modules with Neural Networks: Full Version
- 基于系统组成结构先验,设计可识别模块函数的神经网络框架。
- 仅需少量数据即可准确恢复模块输入输出关系,且能外推未见输入。
- 适合合成生物学与多模块系统设计者,降低实验数据依赖。
在合成生物学等应用中,系统由多个未知功能的模块构成,尽管模块的输入输出关系和信号不明确,但若知晓其组合结构,可显著减少学习系统输入输出映射所需的训练数据。学习模块的输入输出函数对于从不同结构设计新系统至关重要。本文提出一种模块化学习框架,结合系统组成结构先验知识,从系统输入输出数据中识别各模块的输入输出函数,并通过减少所需数据量实现高效学习。为此,我们引入模块可辨识性概念,证明在特定遗传回路类系统中,可从子集输入输出数据中恢复模块函数,并提供理论保证。计算实验表明,考虑结构的神经网络能准确学习模块函数并预测训练分布外的输出;而忽略结构的网络则无法外推。该框架减少了实验数据需求,支持模块识别,有助于简化合成生物电路及多模块系统的构建。
原文摘要 · Abstract (English)
In several applications, including in synthetic biology, one often has input/output data on a system composed of many modules, and although the modules' input/output functions and signals may be unknown, knowledge of the composition architecture can significantly reduce the amount of training data required to learn the system's input/output mapping. Learning the modules' input/output functions is also necessary for designing new systems from different composition architectures. Here, we propose a modular learning framework, which incorporates prior knowledge of the system's compositional structure to (a) identify the composing modules' input/output functions from the system's input/output data and (b) achieve this by using a reduced amount of data compared to what would be required without knowledge of the compositional structure. To achieve this, we introduce the notion of modular identifiability, which allows recovery of modules' input/output functions from a subset of the system's input/output data, and provide theoretical guarantees on a class of systems motivated by genetic circuits. We demonstrate the theory on computational studies showing that a neural network (NNET) that accounts for the compositional structure can learn the composing modules' input/output functions and predict the system's output on inputs outside of the training set distribution. By contrast, a neural network that is agnostic of the structure is unable to predict on inputs that fall outside of the training set distribution. By reducing the need for experimental data and allowing module identification, this framework offers the potential to ease the design of synthetic biological circuits and of multi-module systems more generally.
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