开源框架ChemReservoir支持化学启发的神经网络计算,提升可复现性。
ChemReservoir -- An Open-Source Framework for Chemically-Inspired Reservoir Computing
- 基于化学反应网络构建通用型动态储备池
- 在多种拓扑结构下内存容量表现稳定
- 适合计算化学与神经网络交叉研究者使用
储备池计算是一种递归神经网络,通过固定且非线性的动力系统(称为储备池)将输入映射到高维空间。现有研究中,储备池类型包括模拟与实验两种。在化学生物信息学领域,已有工作基于模拟化学反应网络开发了化学启发的模拟储备池模型。例如,Yahiro采用基于DNA的化学反应网络作为储备池,Nguyen则基于吉尔伯特算法开发了DNA化学启发工具。然而,这些软件主要聚焦于DNA化学,且维护状况不佳,限制了当前可用性。因此亟需一个可靠的开源工具。本研究提出ChemReservoir,一个面向化学启发储备池计算的开源框架。与以往专注DNA化学的研究不同,ChemReservoir是一个通用框架,支持化学启发储备池的构建与分析,并通过增强测试、评估与可复现性解决了前述局限。该工具在多种循环型储备池拓扑结构上进行了评估,在记忆容量任务中表现出稳定的性能。
原文摘要 · Abstract (English)
Reservoir computing is a type of a recurrent neural network, mapping the inputs into higher dimensional space using fixed and nonlinear dynamical systems, called reservoirs. In the literature, there are various types of reservoirs ranging from in-silico to in-vitro. In cheminformatics, previous studies contributed to the field by developing simulation-based chemically inspired in-silico reservoir models. Yahiro used a DNA-based chemical reaction network as its reservoir and Nguyen developed a DNA chemistry-inspired tool based on Gillespie algorithm. However, these software tools were designed mainly with the focus on DNA chemistry and their maintenance status has limited their current usability. Due to these limitations, there was a need for a proper open-source tool. This study introduces ChemReservoir, an open-source framework for chemically-inspired reservoir computing. In contrast to the former studies focused on DNA-chemistry, ChemReservoir is a general framework for the construction and analysis of chemically-inspired reservoirs, which also addresses the limitations in these previous studies by ensuring enhanced testing, evaluation, and reproducibility. The tool was evaluated using various cycle-based reservoir topologies and demonstrated stable performance across a range of configurations in memory capacity tasks.
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