Related papers: CoHSI V: Identical multiple scale-independent syst…
Novel mathematical models of three different repressilator topologies are introduced. As designable transcription factors have been shown to bind to DNA non-cooperatively, we have chosen models containing non-cooperative elements. The…
We study the asymptotic behavior of multiscale stochastic spatial gene networks. Multiscaling takes into account the difference of abundance between molecules , and captures the dynamic of rare species at a mesoscopic level. We introduce an…
The backbone of a Boolean formula is the set of literals that must be true in every assignment that satisfies the formula. This concept is fundamental to key operations on variability models, including propagating user configuration…
This article describes lossless compression algorithms for multisets of sequences, taking advantage of the multiset's unordered structure. Multisets are a generalisation of sets where members are allowed to occur multiple times. A multiset…
A new approach to estimate the Shannon entropy of a long-range correlated sequence is proposed. The entropy is written as the sum of two terms corresponding respectively to power-law (\emph{ordered}) and exponentially (\emph{disordered})…
One of the common obstacles for learning causal models from data is that high-order conditional independence (CI) relationships between random variables are difficult to estimate. Since CI tests with conditioning sets of low order can be…
Multivariate Hawkes process provides a powerful framework for modeling temporal dependencies and event-driven interactions in complex systems. While existing methods primarily focus on uncovering causal structures among observed…
The ability to discriminate similar visual stimuli is an important index of memory function. This ability is widely thought to be supported by expanding the dimensionality of relevant neural codes, such that neural representations for…
Selection pressures on proteins are usually measured by comparing homologous nucleotide sequences (Zuckerkandl and Pauling 1965). Recently we introduced a novel method, termed `volatility', to estimate selection pressures on protein…
Distributed algorithms for solving coupled semidefinite programs (SDPs) commonly require many iterations to converge. They also put high computational demand on the computational agents. In this paper we show that in case the coupled…
Evolving genomes increase a number of their genes by gene duplications. To escape degradation in a functionless pseudogene, any gene duplicate needs to be guarded by negative (purifying) selection from otherwise inevitable fixation of…
We investigate fully self-consistent multiscale quantum-classical algorithms on current generation superconducting quantum computers, in a unified approach to tackle the correlated electronic structure of large systems in both quantum…
An Independent Parallelism Theorem is proven in the theory of adhesive HLR categories. It shows the bijective correspondence between sequential independent and parallel independent direct derivations in the Weak Double-Pushout framework,…
Networked systems that occur in various domains, such as the power grid, the brain, and opinion networks, are known to obey conservation laws. For instance, electric networks obey Kirchoff's laws, and social networks display opinion…
Harnessing the intrinsic dynamics of physical systems for information processing opens new avenues for computation embodied in matter. Using simulations of a model system, we show that assemblies of DNA tiles capable of self-organizing into…
Our main models of computation (the Turing Machine and the RAM) make fundamental assumptions about which primitive operations are realizable. The consensus is that these include logical operations like conjunction, disjunction and negation,…
Predicting protein secondary structure is a fundamental problem in protein structure prediction. Here we present a new supervised generative stochastic network (GSN) based method to predict local secondary structure with deep hierarchical…
A particle-in-cell algorithm is derived with a canonical Poisson structure in the formalism of finite element exterior calculus. The resulting method belongs to the class of gauge-compatible splitting algorithms, which exactly preserve…
Probabilistic circuits (PCs) represent a probability distribution as a computational graph. Enforcing structural properties on these graphs guarantees that several inference scenarios become tractable. Among these properties, structured…
We introduce and analyze several aspects of a new model for cell differentiation. It assumes that differentiation of progenitor cells is a continuous process. From the mathematical point of view, it is based on partial differential…