Related papers: Introduction to Random Boolean Networks

In cosmology, the analysis of observational evidence is very important to test theoretical models of the Universe. Artificial neural networks are powerful and versatile computational tools for data modelling and are recently being…

Boolean network models of molecular regulatory networks have been used successfully in computational systems biology. The Boolean functions that appear in published models tend to have special properties, in particular the property of being…

Neural networks leverage robust internal representations in order to generalise. Learning them is difficult, and often requires a large training set that covers the data distribution densely. We study a common setting where our task is not…

Artificial and natural neural network models are a new toolkit which could be potentially have been used for clarifying of complex brain functions. To attend this goal, such models need to be neurobiologically realistic. However, although…

Convolutional networks are ubiquitous in deep learning. They are particularly useful for images, as they reduce the number of parameters, reduce training time, and increase accuracy. However, as a model of the brain they are seriously…

This paper investigates the stabilization of probabilistic Boolean networks (PBNs) via a novel pinning control strategy based on network structure. In a PBN, the evolution equation of each gene switches among a collection of candidate…

This tutorial introduces a new and powerful set of techniques variously called "neural machine translation" or "neural sequence-to-sequence models". These techniques have been used in a number of tasks regarding the handling of human…

Modern deep learning methods constitute incredibly powerful tools to tackle a myriad of challenging problems. However, since deep learning methods operate as black boxes, the uncertainty associated with their predictions is often…

Graph neural networks (GNN) have shown outstanding applications in many fields where data is fundamentally represented as graphs (e.g., chemistry, biology, recommendation systems). In this vein, communication networks comprise many…

Methods of modeling cellular regulatory networks as diverse as differential equations and Boolean networks co-exist, however, without any closer correspondence to each other. With the example system of the fission yeast cell cycle control…

Countless learning tasks require dealing with sequential data. Image captioning, speech synthesis, and music generation all require that a model produce outputs that are sequences. In other domains, such as time series prediction, video…

This is a tutorial and survey paper on Boltzmann Machine (BM), Restricted Boltzmann Machine (RBM), and Deep Belief Network (DBN). We start with the required background on probabilistic graphical models, Markov random field, Gibbs sampling,…

This paper investigates the learnability of the nonlinearity property of Boolean functions using neural networks. We train encoder style deep neural networks to learn to predict the nonlinearity of Boolean functions from examples of…

Probabilistic Boolean Networks have been proposed for estimating the behaviour of dynamical systems as they combine rule-based modelling with uncertainty principles. Inferring PBNs directly from gene data is challenging however, especially…

We introduce a class of neural networks derived from probabilistic models in the form of Bayesian networks. By imposing additional assumptions about the nature of the probabilistic models represented in the networks, we derive neural…

Gene Regulatory Network (GRN) plays an important role in knowing insight of cellular life cycle. It gives information about at which different environmental conditions genes of particular interest get over expressed or under expressed.…

The Random Geometric Graph (RGG) is a random graph model for network data with an underlying spatial representation. Geometry endows RGGs with a rich dependence structure and often leads to desirable properties of real-world networks such…

This paper describes the use of neural networks to enhance simulations for subsequent training of anomaly-detection systems. Simulations can provide edge conditions for anomaly detection which may be sparse or non-existent in real-world…

Unraveling the complexities of Gene Regulatory Networks (GRNs) is crucial for understanding cellular processes and disease mechanisms. Traditional computational methods often struggle with the dynamic nature of these networks. This study…

A Relational Dependency Network (RDN) is a directed graphical model widely used for multi-relational data. These networks allow cyclic dependencies, necessary to represent relational autocorrelations. We describe an approach for learning…