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Motivation: Several different threads of research have been proposed for modeling and mining temporal data. On the one hand, approaches such as dynamic Bayesian networks (DBNs) provide a formal probabilistic basis to model relationships…
The mutations of a complex systemic disease like cancer can be modeled as stuck-at faults in the Boolean system paradigm. For a class of multiple faults, the fault identification is exceptionally significant under the incomplete access of…
Random Boolean networks, originally invented as models of genetic regulatory networks, are simple models for a broad class of complex systems that show rich dynamical structures. From a biological perspective, the most interesting networks…
We report a scalable hybrid quantum-classical machine learning framework to build Bayesian networks (BN) that captures the conditional dependence and causal relationships of random variables. The generation of a BN consists of finding a…
Probabilistic Boolean networks (PBNs) is an important mathematical framework widely used for modelling and analysing biological systems. PBNs are suited for modelling large biological systems, which more and more often arise in systems…
This Thesis presents research at the boundary between Statistical Physics and Biology. First, we have devised a class of Boolean constraint satisfaction problems (CSP) whose solutions describe the feasible operational states of a chemical…
Continuous-time systems with switch-like behaviour occur in chemical kinetics, gene regulatory networks and neural networks. Networks with hard switching, as a limiting case of smooth sigmoidal switching, retain the richest possible range…
Gene regulatory networks can be successfully modeled as Boolean networks. A much discussed hypothesis says that such model networks reproduce empirical findings the best if they are tuned to operate at criticality, i.e. at the borderline…
Progress in cell type reprogramming has revived the interest in Waddington's concept of the epigenetic landscape. Recently researchers developed the quasi-potential theory to represent the Waddington's landscape. The Quasi-potential U(x),…
Random Boolean networks (RBNs) are models of genetic regulatory networks. It is useful to describe RBNs as self-organizing systems to study how changes in the nodes and connections affect the global network dynamics. This article reviews…
A Bayesian network is a widely used probabilistic graphical model with applications in knowledge discovery and prediction. Learning a Bayesian network (BN) from data can be cast as an optimization problem using the well-known…
The stability of Boolean networks has attracted much attention due to its wide applications in describing the dynamics of biological systems. During the past decades, much effort has been invested in unveiling how network structure and…
Background: Bayesian Networks (BNs) are probabilistic graphical models that leverage Bayes' theorem to portray dependencies and cause-and-effect relationships between variables. These networks have gained prominence in the field of health…
The information bottleneck (IB) principle has been suggested as a way to analyze deep neural networks. The learning dynamics are studied by inspecting the mutual information (MI) between the hidden layers and the input and output. Notably,…
A Boolean network (BN) is a transformation of the set of Boolean configurations of a given length. A trapspace of a BN is a subcube invariant by the BN; a principal trapspace is the smallest trapspace containing a given configuration; a…
This article is set in the field of regulation networks modeled by discrete dynamical systems. It focuses on Boolean automata networks. In such networks, there are many ways to update the states of every element. When this is done…
Latent variables may lead to spurious relationships that can be misinterpreted as causal relationships. In Bayesian Networks (BNs), this challenge is known as learning under causal insufficiency. Structure learning algorithms that assume…
This paper establishes (set) identification results in a dynamic dyadic network formation model with time-varying observed covariates, lagged local network statistics, and unobserved heterogeneity in the form of fixed effects. Our framework…
This paper proposes a new test for a change point in the mean of high-dimensional data based on the spatial sign and self-normalization. The test is easy to implement with no tuning parameters, robust to heavy-tailedness and theoretically…
Contemporary neural networks still fall short of human-level generalization, which extends far beyond our direct experiences. In this paper, we argue that the underlying cause for this shortcoming is their inability to dynamically and…