[HTML][HTML] Attractor detection and enumeration algorithms for Boolean networks

T Mori, T Akutsu - Computational and Structural Biotechnology Journal, 2022 - Elsevier
The Boolean network (BN) is a mathematical model used to represent various biological
processes such as gene regulatory networks. The state of a BN is determined from the …

AEON. py: Python library for attractor analysis in asynchronous Boolean networks

N Beneš, L Brim, O Huvar, S Pastva, D Šafránek… - …, 2022 - academic.oup.com
AEON. py is a Python library for the analysis of the long-term behaviour in very large
asynchronous Boolean networks. It provides significant computational improvements over …

Computing attractors of large-scale asynchronous Boolean networks using minimal trap spaces

VG Trinh, K Hiraishi, B Benhamou - Proceedings of the 13th ACM …, 2022 - dl.acm.org
Boolean Networks (BNs) play a crucial role in modeling, analyzing, and controlling
biological systems. One of the most important problems on BNs is to compute all the …

A Framework of Pinning Control for Non-periodical Stable Behaviors of Large-scale Asynchronous Boolean Networks

J Zhong, Q Pan, W Xu, B Chen - IEEE Transactions on …, 2024 - ieeexplore.ieee.org
In this paper, two pinning control (PC) schemes are proposed to achieve non-periodical
stable behaviors for asynchronous Boolean networks (BNs), from the aspects of state …

Design of reduced-order and pinning controllers for probabilistic Boolean networks using reinforcement learning

M Takizawa, K Kobayashi, Y Yamashita - Applied Mathematics and …, 2023 - Elsevier
In this paper, we study a stabilization method for probabilistic Boolean networks (PBNs)
using Q-learning, which is one of the typical methods in reinforcement learning. A PBN is a …

An improved method for finding attractors of large-scale asynchronous Boolean networks

T Van Giang, K Hiraishi - 2021 IEEE Conference on …, 2021 - ieeexplore.ieee.org
Attractor detection in Asynchronous Boolean Networks (ABNs) is very challenging due to the
high complexity of the state transition graph of an ABN. Recently, an efficient method (called …

A BDD-Based Approach to Model Reduction of Boolean Networks

F Motoyama, K Kobayashi… - IEEE Transactions on …, 2024 - ieeexplore.ieee.org
A Boolean network (BN) is well known as a discrete model for analysis and control of
complex networks such as gene regulatory networks. Since complex networks are large …

Efficient Enumeration of Fixed Points in Complex Boolean Networks Using Answer Set Programming

VG Trinh, B Benhamou, S Soliman - … International Conference on …, 2023 - drops.dagstuhl.de
Abstract Boolean Networks (BNs) are an efficient modeling formalism with applications in
various research fields such as mathematics, computer science, and more recently systems …

On attractor detection and optimal control of deterministic generalized asynchronous random Boolean networks

T Van Giang, K Hiraishi - IEEE/ACM Transactions on …, 2020 - ieeexplore.ieee.org
Deterministic asynchronous Boolean networks play a crucial role in modeling and analysis
of gene regulatory networks. In this paper, we focus on a typical type of deterministic …

A BDD-Based Approach to Finite-Time Control of Boolean Networks

F Motoyama, K Kobayashi… - IEICE Transactions on …, 2024 - search.ieice.org
Control of complex networks such as gene regulatory networks is one of the fundamental
problems in control theory. A Boolean network (BN) is one of the mathematical models in …