Related papers: On Analysis and Generation of some Biologically Im…
We describe the emergence of a Convolution Bottleneck (CBN) structure in CNNs, where the network uses its first few layers to transform the input representation into a representation that is supported only along a few frequencies and…
Neuronal activity is found to lie on low-dimensional manifolds embedded within the high-dimensional neuron space. Variants of principal component analysis are frequently employed to assess these manifolds. These methods are, however,…
NK-Kauffman networks {\cal L}^N_K are a subset of the Boolean functions on N Boolean variables to themselves, \Lambda_N = {\xi: \IZ_2^N \to \IZ_2^N}. To each NK-Kauffman network it is possible to assign a unique Boolean function on N…
Due to the scarcity of quantitative details about biological phenomena, quantitative modeling in systems biology can be compromised, especially at the subcellular scale. One way to get around this is qualitative modeling because it requires…
We investigate how classifiers for Boolean networks (BNs) can be constructed and modified under constraints. A typical constraint is to observe only states in attractors or even more specifically steady states of BNs. Steady states of BNs…
The goal of this tutorial is to promote interest in the study of random Boolean networks (RBNs). These can be very interesting models, since one does not have to assume any functionality or particular connectivity of the networks to study…
Many discrete models of biological networks rely exclusively on Boolean variables and many tools and theorems are available for analysis of strictly Boolean models. However, multilevel variables are often required to account for threshold…
A fuzzy Boolean function is a map $f:\cube^n\to [0,1]$, where $n\in\mathbb N$. We introduce and compare three ways of saying that such a function has bounded complexity. The first is a sampling property: the value $f(x)$ can be recovered,…
We introduce combinatorial interpretability, a methodology for understanding neural computation by analyzing the combinatorial structures in the sign-based categorization of a network's weights and biases. We demonstrate its power through…
In this study, we explored the utility of a descriptive and predictive bionetwork model for phospholipase C-coupled calcium signaling pathways, built with non-kinetic experimental information. Boolean models generated from these data yield…
Boolean networks have been the object of much attention, especially since S. Kauffman proposed them in the 1960's as models for gene regulatory networks. These systems are characterized by being defined on a Boolean state space and by…
In this paper we consider the problem of controlling a limited number of target nodes of a network. Equivalently, we can see this problem as controlling the target variables of a structured system, where the state variables of the system…
The time taken for gene expression varies not least because proteins vary in length considerably. This paper uses an abstract, tuneable Boolean regulatory network model to explore gene expression time variation. In particular, it is shown…
Control Barrier Functions (CBFs) aim to ensure safety by constraining the control input at each time step so that the system state remains within a desired safe region. This paper presents a framework for CBFs in stochastic systems in the…
A Boolean network (BN) with $n$ components is a discrete dynamical system described by the successive iterations of a function $f:\{0,1\}^n\to\{0,1\}^n$. In most applications, the main parameter is the interaction graph of $f$: the digraph…
Deterministic and stochastic Boolean network models are build for the dynamics of negative feedback loops of the p53 pathways. It is shown that the main function of the negative feedback in the p53 pathways is to keep p53 at a low steady…
Boolean networks (BNs) are discrete-time systems where nodes are inter-connected (here we call such connection rule among nodes as network structure), and the dynamics of each gene node is determined by logical functions. In this paper, we…
We investigate the expressive power of neural networks from the point of view of descriptive complexity. We study neural networks that use floating-point numbers and piecewise polynomial activation functions from two perspectives: 1) the…
Many research works deal with chaotic neural networks for various fields of application. Unfortunately, up to now these networks are usually claimed to be chaotic without any mathematical proof. The purpose of this paper is to establish,…
Effective control of biological systems can often be achieved through the control of a surprisingly small number of distinct variables. We bring clarity to such results using the formalism of Boolean dynamical networks, analyzing the…