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Computational models of biological processes provide one of the most powerful methods for a detailed analysis of the mechanisms that drive the behavior of complex systems. Logic-based modeling has enhanced our understanding and…

Normalizing flows have emerged as an important family of deep neural networks for modelling complex probability distributions. In this note, we revisit their coupling and autoregressive transformation layers as probabilistic graphical…

The past decade has seen great advances in our understanding of the role of noise in gene regulation and the physical limits to signaling in biological networks. Here we introduce the spectral method for computation of the joint probability…

Computational properties of networks that can undergo cascades are examined. It is shown that universal Boolean logic circuits can be computed by a global cascade having antagonistic interactions. Determinism and cascade frequency of this…

Biological processes, including cell differentiation, organism development, and disease progression, can be interpreted as attractors (fixed points or limit cycles) of an underlying networked dynamical system. In this paper, we study the…

Empirical evidence has revealed that biological regulatory systems are controlled by high-level coordination between topology and Boolean rules. In this study, we study the joint effects of degree and Boolean functions on the stability of…

A Boolean network is a discrete dynamical system operating on vectors of Boolean variables. The action of a Boolean network can be conveniently expressed as a system of Boolean update functions, computing the new values for each component…

We propose doubly nested network(DNNet) where all neurons represent their own sub-models that solve the same task. Every sub-model is nested both layer-wise and channel-wise. While nesting sub-models layer-wise is straight-forward with…

Gene expression-based heterogeneity analysis has been extensively conducted. In recent studies, it has been shown that network-based analysis, which takes a system perspective and accommodates the interconnections among genes, can be more…

Boolean networks have been used in a variety of settings, as models for general complex systems as well as models of specific systems in diverse fields, such as biology, engineering, and computer science. Traditionally, their properties as…

Generative Flow Networks (GFlowNets), a new family of probabilistic samplers, have recently emerged as a promising framework for learning stochastic policies that generate high-quality and diverse objects proportionally to their rewards.…

Random Boolean networks have been used widely to explore aspects of gene regulatory networks. A modified form of the model through which to systematically explore the effects of increasing the number of gene states has previously been…

When analyzing complex networks a key target is to uncover their modular structure, which means searching for a family of modules, namely node subsets spanning each a subnetwork more densely connected than the average. This work proposes a…

We investigated the properties of Boolean networks that follow a given reliable trajectory in state space. A reliable trajectory is defined as a sequence of states which is independent of the order in which the nodes are updated. We…

Building on recent development by Padakandla and Pradhan, and by Lim, Feng, Pastore, Nazer, and Gastpar, this paper studies the potential of structured nested coset coding as a complete replacement for random coding in network information…

It has been shown that unclocked, recurrent networks of Boolean gates in FPGAs can be used for low-SWaP reservoir computing. In such systems, topology and node functionality of the network are randomly initialized. To create a network that…

Discrete modelling frameworks of Biological networks can be divided in two distinct categories: Boolean and Multi-valued. Although Multi-valued networks are more expressive for qualifying the regulatory behaviours modelled by more than two…

We show (almost) separation between certain important classes of Boolean functions. The technique that we use is to show that the total influence of functions in one class is less than the total influence of functions in the other class. In…

The effects of the finite size of the network on the evolutionary dynamics of a Boolean network are analyzed. In the model considered, Boolean networks evolve via a competition between nodes that punishes those in the majority. It is found…

Learning representations of nodes in a low dimensional space is a crucial task with numerous interesting applications in network analysis, including link prediction, node classification, and visualization. Two popular approaches for this…